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DOI: vitro10.1039/C4CP05425C Subpicosecond surface dynamics in genomic DNA from in grown plant species: A SERS assessment
Cristina M. Muntean a *, Ioan Bratu a, Nicolae Leopold b , Cristian Morari a, Luiza BuimagaIarinca a and Monica A. P. Purcaru c
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a
National Institute for Research & Development of Isotopic and Molecular Technologies, 67-103 Donat Str., 400293 Cluj-Napoca, Romania Babeş-Bolyai University, Faculty of Physics, 1 Kogalniceanu Str., 400084 Cluj-Napoca, Romania b
c
Transilvania University of Brasov, 50 Iuliu Maniu Str., 500091 Brasov, Romania
*Corresponding author: Dr. Cristina M. Muntean [email protected]
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DOI: 10.1039/C4CP05425C
Abstract
In this work the surface-enhanced Raman scattering total half band widths of seven genomic DNAs from leaves of chrysanthemum (Dendranthema grandiflora Ramat.),
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common sundew (Drosera rotundifolia L.), edelweiss (Leontopodium alpinum Cass), Epilobium hirsutum L., Hypericum richeri ssp. transsilvanicum (Čelak) Ciocârlan, rose (Rosa x hybrida L.) and redwood (Sequoia sempervirens D. Don. Endl.), respectively, have been measured. We have shown that surface-enhanced Raman spectroscopy (SERS) can be used to study the fast subpicosecond dynamics of DNA in the proximity of a metallic surface. The dependencies of the total half band widths and of the global relaxation times, on DNA molecular subgroup structure and on the type of genomic DNA, are reported. In our study, the full widths at half-maximum (FWHMs) for the SERS bands of genomic DNAs from different leaf tissues, are typically in the wavenumber range from 15 to 55 cm-1. Besides, it can be observed that molecular relaxation processes studied in this work, have a global relaxation time smaller than 0.71 ps and larger than 0.19 ps. A comparison between different ranges of FT-Raman and SERS band parameters, respectively, corresponding to DNA extracted from leaf tissues is given. It is shown that the interaction between DNA and a metallic surface has the potential to lead to a shortening of the vibrational relaxation times, as compared with molecular dynamics in solution. We have found that the surface dynamics of molecular subgroups in plant DNA is, in some cases, about two times faster than the solution dynamics of nucleic acids. This can be rationalized in a qualitative manner by invoking the complex landscape of the interaction energy between the molecule and silver surface.
Keywords: Genomic DNA, plant species, leaf tissue, surface-enhanced Raman scattering, full width at half-maximum (FWHM), subpicosecond global relaxation time.
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Introduction
DOI: 10.1039/C4CP05425C
Raman spectroscopy is a powerful experimental technique giving insight knowledge about the molecular dynamic processes involved in liquids mixtures (1 and references therein). Studies of relaxation processes in liquids are valuable in providing information Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
about the intermolecular interactions in condensed matter 2. Among the techniques available for the study of molecular motions in liquids, Raman scattering has the distinct advantage, that it enables simultaneous analyses of both reorientational and vibrational processes (see for example
2,3,4,5
and references therein).
Particularly, vibrational relaxation plays a crucial role in many aspects of chemistry, physics, and biology, e.g., reaction dynamics, thermal chemistry, electron transfer, photochemistry, excimer formation and photobiological processes such as vision and photosynthesis. The dynamics and vibrational relaxation processes of biomolecules in aqueous solutions have motivated several studies (see 6,7 and references therein). The macromolecular motion in fluids is generally too slow to be observed in the Raman time window that is accessible in the frequency domain. On contrary, the motion of molecular subgroups can be fast enough 5,8,9. Although there have been many observations of DNA motion over longer times, experiments measuring motions at the level of individual bases and in the picoseconds time range have been difficult 10. Comparison of the band widths of different vibrations in different nucleotide structures presented information about the nature of relaxation processes that perturb the base vibrations. It was found that vibrational dephasing and energy relaxation by interactions with water molecules plays an important role in the vibrational dynamics
11
. The same authors
have shown, that different base vibrations are sensitive to different dynamical degrees of
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Article Online freedom in the system. They have argued that backbone dynamics, hydrogen bonding, as View well DOI: 10.1039/C4CP05425C
as solvent accessibility influences the vibrational band widths 11. Particularly, picosecond and nanosecond dynamics in the interior of DNA were observed for the first time as a dynamic Stokes shift in the fluorescence of a specially designed base-pair analogue. The interior of DNA was found to be a unique dynamical Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
environment that is distinctly different from either a simple fluid or a rigid molecular crystal 10
. These authors introduced time-resolved Stokes shifts (TRSS) as a method of directly
observing the local dynamics of DNA
10
. Also, it was shown that lesions in DNA structure
can change its dynamics on the picosecond and nanosecond timescales and that these changes can be measured by time-resolved Stokes shift spectroscopy 12. Also, vibrational relaxation after spectrally selective excitation within the NH stretching band of adenine-thymine base pairs, in DNA oligomers, was studied by subpicosecond infrared-pump/anti-Stokes Raman-probe spectroscopy 13. (Sub)picosecond dynamics of DNA subgroups, as a function of pH and metal ions, respectively, was previously studied by us
14
. Monitoring the changes in the normal Raman
full widths at half-maximum (FWHMs) and, correspondingly, in the global relaxation times of the molecular subgroups in DNA, upon varying the physical-chemical parameters, was of interest. In these cases, solution dynamics of nucleic acids was under study. Besides, the dynamics of plant genomic DNA on silver surface was previously reported by us for several cases, using surface-enhanced Raman scattering (SERS)
8,15
.
Particularly, the full widths at half-maximum (FWHMs) of the SERS bands in genomic DNAs from in vitro-grown apple leaf tissues were typically in the wavenumber range from 14 cm-1 to 52 cm-1. Also, the molecular relaxation processes studied in that work, had a global relaxation time smaller than 0.76 ps and larger than 0.20 ps 8. In this paper the SERS total half band widths of seven genomic DNAs from leaf
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Ramat.), common sundew (Drosera rotundifolia L.), edelweiss (Leontopodium alpinum Cass), Epilobium hirsutum L., Hypericum richeri ssp. transsilvanicum (Čelak) Ciocârlan, rose (Rosa x hybrida L.) and redwood (Sequoia sempervirens D. Don. Endl.), respectively], have been measured. The dependencies of the total half band widths and of the corresponding Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
global relaxation times, on DNA molecular subgroup structure and on the type of genomic plant DNA are reported. It is shown that changes in the subpicosecond dynamics of molecular subgroups in genomic DNAs from leaves, in the proximity of a silver surface, can be monitored with surface-enhanced Raman spectroscopy (SERS).
Experimental
Leaves from in vitro grown plant species represented the source material for extraction of genomic DNAs. These leaves were obtained from plants of chrysanthemum (Dendranthema grandiflora Ramat.), common sundew (Drosera rotundifolia L.), edelweiss (Leontopodium
alpinum
Cass),
Epilobium
hirsutum
L.,
Hypericum
richeri
ssp.
transsilvanicum (Čelak) Ciocârlan, rose (Rosa x hybrida L.) and redwood (Sequoia sempervirens D. Don. Endl.), respectively, as described elsewhere 16. Genomic DNA was isolated from leaves of the above mentioned species, respectively, using the GenEluteTM Plant Genomic DNA Miniprep Kit (G2N350-1KT) from SigmaAldrich, that uses 100 mg fresh leaf tissue per sample. Isolated DNA was dissolved in 10 mM Tris, 1 mM EDTA, pH 8.0 16. Analytical reagent grade chemicals were used. The silver colloidal SERS substrate was prepared by reducing Ag+ with hydroxylamine. Metallic nanoparticles with an estimated
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medium diameter of 34 nm have been obtained
17,18
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preparation, was presented elsewhere 19,16. Each sample was prepared by adding 500 μl silver colloid into a 1-ml glass cuvette. 10 μl of DNA solutions, respectively, were used for the preparation of the silver nanoparticle systems. The pH value of all measured SERS mixtures, containing colloidal nanoparticles and DNA extracts was of 6.5. Other details on the Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
preparation of DNA-nanoparticle systems are given elsewhere 16. A DeltaNu Advantage spectrometer (DeltaNu, Laramie, WY) equipped with a doubled frequency Nd:YAG laser, emitting at 532 nm and having a 45 mW laser power was used for recording the SERS spectra, at room temperature 16. The band parameters (full widths at half-maximum-FWHMs and global relaxation times) were determined for this data set. Also, for each band profile, an individual baseline was taken into account. The FWHMs were evaluated from the half maximum of the SERS bands.
Results and discussions
SERS spectra of DNAs from the above mentioned species are presented in Figure 1. Relating to molecular dynamics processes, Rakov developed one of the well-known procedures of obtaining the relaxation times and the activation energy 4-5,7-8,14,20,21. In this approximation, the total half band width of the depolarized Raman lines contains two contributions 4-5,8,14,20. The total half band width can be written as: 1 / 2 0 T 0
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1 . (1) c r
The potential barrier against reorientation can be obtained as:
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DOI: 10.1039/C4CP05425C
Figure 1. SERS spectra of genomic DNAs from leaves of in vitro grown plant species of chrysanthemum, Drosera, Leontopodium, Epilobium, Hypericum, Rosa and Sequoia, respectively, as labeled in the figure. DNA-silver nanoparticle complexes were investigated. Bottom, Raman spectrum of the silver colloid and buffer (blank spectrum). [C. M. Muntean, N. Leopold, A. Halmagyi, S. Valimareanu (2013) “Surface-enhanced Raman scattering assessment of DNA from leaf tissues adsorbed on silver colloidal nanoparticles”, J. Raman Spectrosc., 44(6): 817-822. Copyright © 2013 John Wiley & Sons, Ltd. Reproduced with permission].
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U r 0 exp or , (2) kT
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where 0 is the period of the molecule oscillation around the equilibrium position, and U or is the energy barrier or the activation energy 8,7,14,20.
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The Rakov relationship can be written as: 1 / 2 0
1 U or exp . (3) c 0 kT
From the 1 / 2 0 vs
10 3 dependencies one can obtain U or as the slope of this T
linear dependence 4,8,14,20. For large molecules, in aqueous solutions, the vibrational contribution becomes important. From Raman measurements, using polarized light, it is possible to do the selection of these two contributions
7,8,14,20
. As a first approximation, one can assume, the existence of
a global relaxation time, , obtained from the total Raman half band width. This band parameter can be related with the intrinsic parameters of the analyzed system through the relationship:
v ,1R , 2 R
1
c 1v/,12R , 2 R
, (4)
where the half band width includes the vibrational ( 1v/ 2 ) and rotational ( 11/R2, 2 R ) contributions and c is the velocity of light. 11/R2, 2 R is obtained from IR (1R) and Raman (2R) bands, respectively 4-5,14,20. The development of fast and accurate curve fitting programs allows the analysis of the vibrational spectra of complicated biological molecules, containing often more than 40 vibrational bands (5,11 and references therein). In this paper we will concentrate on the vibrational band widths. Only the relatively isolated nucleic acids vibrations will be considered
5,8,14,20
. A study of the SERS vibrational
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genomic DNAs from different leaf tissues, respectively, is of interest. This work follows previous studies of us, concerning SERS band parameters of genomic DNAs extracted from leaves of different plants 8,15. For the case of aqueous solutions of DNA molecules, we can suppose that the Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
dominant relaxation mechanism is the vibrational one. The values of the global relaxation time suggest also the existence of a vibrational relaxation time, because the reorientational movement is much more slower for the DNA macromolecule in aqueous solution 5,20. The surface-enhanced Raman band parameters (full width at half-maximum, global relaxation time) of the vibrations near 610 cm-1 (deoxyribose, C3’ endo-anti), 675 cm-1 (dG), 728 cm-1 (dA), 980 cm-1 (deoxyribose), 1166 cm-1 (dC, dT, deoxyribose), 1357 cm-1 (dT, dA, dG, dC), 1503 cm-1 (dA) and 1602 cm-1 (dG, dA, dC), characterizing genomic DNAs from seven in vitro grown plant species, respectively, are presented in Table 1 (16,22-28 and references therein). The chosen bands were the most prominent vibrations in the SERS spectra, suitable for molecular dynamics analysis. In respect of this, one can select only those vibrational modes for which one can split up the maxima, until each profile can be separated from one another at least at half intensity. The FWHM is typically in the wavenumber range from 15 to 55 cm-1 for data presented in this table. The limit wavenumber values belong to DNA from Leontopodium. For some vibrations, the FWHMs could not be determined, due to the overlapping with other vibrational modes. Besides, the global relaxation times were evaluated on the basis of Eq. 4. From the SERS vibrations around 610 cm-1, 675 cm-1, 728 cm-1, 980 cm-1, 1166 cm-1, 1357 cm-1, 1503 cm-1 and 1602 cm-1 (see Table 1), it can be observed that the global relaxation times, for molecular subgroups in genomic DNA from different in vitro grown plant species, are slower than 0.19 ps and faster than 0.71 ps. The best vibrational energy transfer process was
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Leontopodium (global relaxation time 0.19 ps) and the slowest dynamics was found for the band near 613 cm-1 (deoxyribose, C3’ endo-anti), also in the case of Leontopodium DNA (global relaxation time 0.71 ps). Previously, the FT-Raman band parameters for the vibrations at 879 cm-1 Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
(deoxyribose, dA), 1047 cm-1 (CO stretching C-O-P-O-C, dG), 1089 cm-1 ( P-O symmetric stretching of PO2- ), 1124 cm-1 (dA), 1272 cm-1 (dC, dG, dT), 1276 cm-1 (dC), 1455 cm-1 (deoxyribose, dA, dC, dT), and 1482 cm-1 (dG, dA)
29
of genomic DNAs from leaf tissues
were reported by us, characterizing the solution molecular dynamics of plant nucleic acids 5. In that work, it could be observed that the molecular relaxation processes have a global relaxation time smaller than 1.36 ps and larger than 0.46 ps 5. For the cases of overlapped Raman profiles, only half of the total half band width (FWHM), in the side where the bands were not superposed, was taken into account and later on it was multiplied by two. In the followings, we will present the variation intervals of the global relaxation times, associated with each vibrational mode in Table 1. The global relaxation time characterizing the band near 612 cm-1 (deoxyribose, C3’ endo-anti) varied between 0.53-0.71 ps. The smallest global relaxation time (0.53 ps) and the largest half band width (20 cm-1), have been detected for the SERS band at 610 cm-1, in the case of DNA extracted from Sequoia. These differences in molecular relaxation processes of deoxyribose, C3’ endo-anti might be due to structural neighbourhood of this entity, in DNAs originating from different sources. The dG band profile near 675 cm-1, is characterized by global relaxation times in the subpicosecond range 0.37-0.46 ps. Similar global relaxation times of 0.48 ps have been found by us for the profile near
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species, respectively. A larger global relaxation time was found for this band in the case of DNA from Rosa (0.53 ps). Referring to the deoxyribose vibration near 980 cm-1, the vibrational energy transfer processes are characterized by global relaxation times ranging between 0.37-0.44 ps. Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
The global relaxation times of the SERS bands near 1166 cm-1 (dC, dT, deoxyribose), have the values of 0.48 ps for DNA from Sequoia and 0.27 ps, respectively in the case of DNA from Hypericum. Besides, vibrational energy transfer processes characterized by global relaxation times between 0.37-0.53 ps have been found by us for the band near 1357 cm-1 (dT, dA, dG, dC). For some cases, this band seems to be rather stable, as far as dynamical properties are concerned. On the other hand, it is to be observed that nitrogenous bases containing structural subgroups have smaller global relaxation times as compared with those of deoxyribose, C3’ endo-anti entity. Also, the band widths of the SERS vibration around 1503 cm-1 (dA), are sensitive to a dynamics active on a time scale from 0.41 ps (Rosa DNA) to 0.51 ps (Sequoia DNA). As far as the band parameters of the vibration near 1602 cm-1 (dG, dA, dC) are concerned, global relaxation time varied between 0.19-0.25 ps. The carbonyl vibration in leaf tissues DNAs studied in this work has broad band widths, ranging between 43-55 cm-1. The molecular dynamics associated with this band is the most rapid one, as compared with the relaxation processes of other structural groups, characterized in this work. We have found that the SERS bands of DNA from Sequoia and Rosa plants, respectively, are suitable for the study of dynamical behaviour of molecular subgroups in nucleic acids extracted from leaf tissues, since they display the largest number of modes with band parameters determined (see Table 1).
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View Article Online Table 1. Total half band widths (cm-1) of SERS vibrational markers and global DOI:relaxation 10.1039/C4CP05425C times of molecular subgroups, in genomic DNA from leaves of in vitro grown plant species.
νmax (cm-1)
Δν1/2 (cm-1)
610 675 728 982 1166 1353 1503 1602
20* 27 22* 29 22* 27 21 48
612 675 729 981 1356 1502 1602
16 29 20* 28 28 26** 48
1165 1354 1598
39 20* 50*
611 980 1356 1602
18 24 25 43
613 1355 1604
15 28 55
612 979 1357 1602
16* 25 27 46
609 682 726 978 1360 1607
18 23 22 26 29 46
τSERS (ps) Sequoia 0.53 0.39 0.48 0.37 0.48 0.39 0.51 0.22 Rosa 0.66 0.37 0.53 0.38 0.38 0.41 0.22 Hypericum 0.27 0.53 0.21 Epilobium 0.59 0.44 0.42 0.25 Leontopodium 0.71 0.38 0.19 Drosera 0.66 0.42 0.39 0.23 Chrysanthemum 0.59 0.46 0.48 0.41 0.37 0.23
Tentative assignment 16,22-28 a Deoxyribose, C3’ endo-anti dG dA Deoxyribose dC, dT, deoxyribose dT, dA, dG, dC dA dG, dA, dC Deoxyribose, C3’ endo-anti dG dA Deoxyribose dT, dA, dG, dC dA dG, dA, dC dC, dT, deoxyribose dT, dA, dG, dC dG, dA, dC Deoxyribose, C3’ endo-anti Deoxyribose dT, dA, dG, dC dG, dA, dC Deoxyribose, C3’ endo-anti dT, dA, dG, dC dG, dA, dC Deoxyribose, C3’ endo-anti Deoxyribose dT, dA, dG, dC dG, dA, dC Deoxyribose, C3’ endo-anti dG dA Deoxyribose dT, dA, dG, dC dG, dA, dC
a
Abbreviations: dA - deoxyadenosine; dG - deoxyguanosine; dC - deoxycytidine; dT deoxythymidine. * Low frequency side of the band was read; later on the respective profile was symmetrized. ** High frequency side of the band was read; later on the respective profile was symmetrized.
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View Article Online We have obtained similarities and differences between the relaxation of DOI: times 10.1039/C4CP05425C
different molecular subgroups in DNA, originated from one plant, as well as from various plant species. The observed results can be explained correlating them, with local structure of genomic DNA, with nucleic acids base composition and with DNA sequence (molecular neighbourhood), respectively, which are distinctive for the plant from which DNA originated. Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
Besides, DNA conformation might modify molecular dynamics of nucleic acids subgroups. Particularly, in our systems, deoxyribose moiety was found to exhibit C3'-endo/anti conformation. Percentages of C3'-endo/anti conformations, with respect to other genomic DNA conformations, might contribute to changes in global relaxation times of molecular subgroups. Particularly, DNA from Leontopodium exhibited very different results from the other samples and these can be explained by the reasons above. After some authors, the strength of interaction between nucleobases and Ag nanoparticles is in the order of C > G > A > T. Due to the donation of nitrogen and oxygen lone pairs, the best aggregation occurred in the case of cytosine (16 and references therein). As an observation, the global relaxation time of dG residues (675 cm-1) is lower (0.39 ps) as compared with the global relaxation times of dA residues (728 cm-1), respectively (0.48 ps) in the case of Sequoia. For Rosa DNA, the dynamics of dG residues (675 cm-1) is faster (0.37 ps) as compared with the dynamics of dA residues (729 cm-1), (0.53 ps). This behavior might be explained by the different strength of interaction between guanine, adenine and silver nanoparticles surface, respectively. Smaller differences between the global relaxation times of dG (682 cm-1) (0.46 ps) and dA (726 cm-1) (0.48 ps) residues, respectively, are to be found in the case of chrysanthemum nucleic acids. Besides, a comparison between different ranges of the Raman band parameters, in the case of aqueous solution nucleic acids dynamics (investigated by FT-Raman spectroscopy)
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given in Table 2.
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Table 2. Comparison between different ranges of the Raman band parameters, in the case of aqueous solution dynamics (FT-Raman) and surface dynamics (SERS) of DNA extracted from different leaf tissues (5,8,15 and references therein). DNA molecules
FWHM range Δν/cm-1
Genomic DNA from in vitrogrown plant species, FTRaman study Genomic DNA from in vitrogrown apple leaf tissues, SERS study Genomic DNA from in vitrogrown plant species, SERS study
7.8 - 23.1
Global relaxation time range τ/ps 0.46 - 1.36
14-52
0.20-0.76
13-42
0.25-0.82
It is to be observed, that the surface dynamics of molecular subgroups in plant DNA is more rapid (in some cases, about two times faster) than the solution dynamics of nucleic acids. This means, that the mobility of DNA subgroups is greater even in the case of interaction with a silver surface. An explanation of this observation might be, that in solution are possible to be present molecular associations, solvent interactions, etc., leading to a slower dynamics (a slower mobility). On the surface, the clusters are broken down and DNA is interacting only with the surface, having a higher mobility 8. On the other hand, stabilizing ions or molecules present on the surface of most colloidal metal nanoparticles are likely to participate in interactions with DNA, also affecting the molecular dynamics. We can also consider the possibility of energy transfer to the metal surface, resulting in shorter relaxation times of DNA subgroups. Particularly, other aspects related with the observed global relaxation times in the proximity of a surface and in solution, are discussed in the next subsection.
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View Article Online Theoretical considerations for the dynamics of DNA bases on a metallic surface DOI: 10.1039/C4CP05425C
The interactions between a molecule and its local environment lead to the broadening of the Raman peak, mainly by vibrational relaxation. The anharmonicity of the intramolecular force constants was proposed as intrinsic mechanism to explain this effect for free Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
molecules
30
. Recently, the importance of the anharmonic coupling to phonons in the Ag
substrate was pointed out in single-molecule surface-enhanced Raman spectroscopy (SMSERS) 31. In order to get an idea of the energy involved in the process, we note that by using the Heisenberg relation can be found that the energy of kT= 0.03 eV corresponds to relaxation times of up to 22 fs. Consequently, picoseconds relaxation times are expected to be obtained for energies below 0.03 eV. This suggests that the direct investigation of the relaxation times on surfaces by means of ab-initio calculations is a complicated (or even impossible) task, for realistic systems. On the other hand, qualitative insight into the process can be obtained by investigating only selected aspects of the molecule-surface interaction. While for the molecules in solution the interactions with the environment are dominated by collisions and long range interactions, for the adsorbates the picture is significantly changed. The dynamics of the adsorbed molecules takes place on a 2D space, unlike to the 3D case occurring in solution. This is expected to be the main factor determining the changes in the dynamics upon the adsorption. In this context, we can recall the existence of new features of the molecular dynamics, such as frustrated translations or the strong suppression of the rotational degrees of freedom. The investigation of the functional dependence between the position of the DNA base and the adsorption energy on the 2D surface can provide a qualitative information on the dynamics occurring at atomic scale in a SERS experiment. While such data cannot provide a
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understanding of the general features of the molecular dynamics on the surface. As model-systems we have investigated the interactions between the DNA bases [adenine (A), thymine (T), cytosine (C), guanine (G)] and the clean silver surface, respectively. Each of the four bases was allowed to adsorb on two geometric configurations: Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
with the π ring parallel and perpendicular to the surface, respectively. For each of the resulting 8 configurations we have relaxed the initial (randomly chosen) geometric structure up to a maximum gradient of 0.02 eV/Å (see Figure 2 for a geometrical representation). Next, we have generated a number of other 16 geometric structures for each DNA base by translating the molecule parallel to the surface, according to the pattern indicated in Figure 3, in order to cover symmetrically the unit cell of the Ag(111) surface. The resulting energies for each configuration were interpolated by taking into account the 2D periodic boundary conditions on the Ag(111) surface (i.e. hexagonal symmetry) in order to produce maps of the molecule-surface interaction The technical details of our calculations are the following: all calculations were performed using the DFT as implemented in the SIESTA code basis set and the RPBE exchange-correlation functional
33
32
. We used a DZP quality
. The Ag(111) surface was
generated by using a bulk parameter of 4.08 Å and a 5X5 super-cell on the XOY plane (the surface was generated to be parallel to the Z=0 plane). The slab used in calculations consisted on four layers of Ag, resulting on 100 Ag atoms (25 for each plane). Periodic boundary conditions were imposed to the model; the size of the super-cell on OZ axis was chosen to be 30 Å, so that the interactions between the periodic replicas of the model were negligible. For the first geometric structure the positions of the top layer atoms in the Ag surface, as well as the positions of the organic atoms were allowed to relax, while the other 75 atoms were
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further translation of the molecule parallel to the surface.
Figure 2. The initial geometric structures of the DNA bases, adsorbed on (111) silver surface with the π- ring parallel / perpendicular to the surface.
Figure 3. Schematic representation of the pattern used to calculate a number of 16 geometric structures for each DNA base by translating the base parallel to the surface in order to cover symmetrically the Ag(111) unit cell.
The shape of the interaction energy as a function of the X and Y coordinates are indicated in Figures 4 and 5. Since only the differences between the interactions energy in different regions are relevant for the dynamics, we subtract from these values the constant quantities in order to make the results suitable for graphical representation. It can be clearly seen that the
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Figure 4. The energy maps for the DNA bases adsorbed on Ag (111) surface with the π- ring parallel to the surface; black points indicate the calculated energy values; all energies are expressed in eV.
fluctuations of the adsorption energy are of the same order of magnitude as the thermal energy at room temperature (kT=0.03 eV). Therefore it is natural to assume that 2D translations of the adsorbed molecules are an important component of the dynamics in all the experiments. Moreover, it is also natural to assume that such dynamics will provide specific relaxation mechanisms that are not present in the solution, leading to clearly different values for the vibrational relaxation times.
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Figure 5. The energy maps for the DNA bases adsorbed on (111) silver surface with the πring perpendicular to the surface; black points indicate the calculated energy values; all energies are expressed in eV.
Also, we note the dynamics on the surface is expected to be different for each of the four DNA bases, as well as for different orientations with respect to the surface (i.e. parallel or perpendicular). Precisely, the dynamics will take place along the yellow regions in the Figures 4 and 5 (i.e. minimum of the molecule-surface interaction energy). The most remarkable feature of our theoretical analysis is that, similar energetic landscapes can occur for the DNA bases paired in a nucleic acid chain, respectively. Indeed, for the A and T the
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representation, while for the C and G is suggested a dynamics along vertical lines.
Conclusions
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This work presents a surface-enhanced Raman spectroscopic study based on the vibrational total half band widths of molecular subgroups in seven genomic DNAs extracted from in vitro grown plant species of chrysanthemum (Dendranthema grandiflora Ramat.), common sundew (Drosera rotundifolia L.), edelweiss (Leontopodium alpinum Cass), Epilobium hirsutum L., Hypericum richeri ssp. transsilvanicum (Čelak) Ciocârlan, rose (Rosa x hybrida L.) and redwood (Sequoia sempervirens D. Don. Endl.), respectively. Besides, the corresponding global relaxation times have been derived. We have shown that surface-enhanced Raman scattering can be used to study the fast subpicosecond dynamics of DNA from plant tissues, in the proximity of a metallic surface. SERS band parameters were obtained for the vibrational modes near 610 cm-1 (deoxyribose, C3’ endo-anti), 675 cm-1 (dG), 728 cm-1 (dA), 980 cm-1 (deoxyribose), 1166 cm-1 (dC, dT, deoxyribose), 1357 cm-1 (dT, dA, dG, dC), 1503 cm-1 (dA) and 1602 cm-1 (dG, dA, dC), respectively (16,19-25 and references therein). Study of vibrational total half band widths of genomic DNA from leaf tissues, revealed a sensitivity of FWHM to the source of nucleic acid. Moreover, this proved to be dependent on the vibration under study. The SERS total half band widths of genomic DNA vibrations revealed a dynamic picture on a subpicosecond time scale 8. In our study, the full widths at half-maximum (FWHMs) of the SERS bands in genomic DNAs from different leaf tissues, are typically in the wavenumber range from 15 to 55 cm-1. Besides, the total half band widths in the SERS spectra are sensitive to a dynamics active on time scales from 0.19 ps to 0.71 ps. The carbonyl vibration in leaf tissues DNAs
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global relaxation times between 0.19-0.25 ps. A comparison between different ranges of Raman band parameters of plant genomic DNA, in the case of aqueous solution dynamics (investigated by FT-Raman spectroscopy) and surface dynamics (investigated by SERS) has also been given 5,8. Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
We have found experimentally, that the surface dynamics of molecular subgroups in plant DNA is, in some cases, about two times faster than the solution dynamics of nucleic acids. Reduced dimensionality and the suppression of the rotational degrees of freedom are mainly responsible for this. Our theoretical studies indicate that the translation of DNA bases on surface is expected to be an important component of the dynamics at room temperature; it is natural to assume that this will lead to relaxation mechanisms completely different to those present in solution. A second feature of our theoretical analysis is that, similar energetic landscapes can occur for the DNA bases paired in a nucleic acid chain, respectively. Indeed, for the A and T the dynamics on the surface is expected to take place along lines placed at 60 degrees in our representation, while for the C and G is suggested a dynamics along vertical lines.
Acknowledgements
The authors wish to thank to Dr. Adela Halmagyi and to Dr. Sergiu Valimareanu from the Institute of Biological Research, Cluj-Napoca, Romania, for isolating the genomic DNAs from different leaf tissues. Thanks are also due to the reviewers of this manuscript and to Dr. Nicoleta Tosa from National Institute for Research & Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania, for useful comments. This work was supported by a grant of the Ministry of National Education, National Authority for Scientific Research
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CNCS – UEFISCDI, Romania, project number PN-II-ID-PCE-2012-4-0115.
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References 1. T.G. Devi and G. Upadhayay, Spectrochim. Acta A-M, 2012, 91, 106.
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2. T. Iliescu, I. Bratu, R. Grecu, T. Veres and D. Maniu, J. Raman Spectrosc., 1994, 25, 403. 3. T. Iliescu, S. Aştilean, I. Bratu, R. Grecu and D. Maniu, J. Chem. Soc. Faraday T., 1996, 92, 175. 4. C.M. Muntean and I. Bratu, Spectrosc - Int. J., 2008, 22, 475. 5. C.M. Muntean and I. Bratu, Spectrosc - Int. J., 2009, 23, 281. 6. A. Hernanz, I. Bratu and R. Navarro, J. Phys. Chem. B, 2004, 108, 2438. 7. C.M. Muntean, I. Bratu, K. Nalpantidis and M.A.P. Purcaru, Spectrosc - Int. J., 2009, 23, 141. 8. C.M. Muntean, I. Bratu, N. Leopold and M.A.P. Purcaru, Spectrosc - Int. J., 2011, 26, 59. 9. C. Otto, P.A. Terpstra, G.M.J. Segers-Nolten and J. Greve, in J.C. Merlin et al. (eds.), Spectroscopy of Biological Molecules, 1995, Kluwer Academic Publishers, Dordrecht, 313. 10. E.B. Brauns, M.L. Madaras, R.S. Coleman, C.J. Murphy and M.A. Berg, J. Am. Chem. Soc., 1999, 121, 11644. 11. P.A. Terpstra, C. Otto and J. Greve, Biopolymers, 1997, 41, 751. 12. M.M. Somoza, D. Andreatta, C.J. Murphy, R.S. Coleman and M.A. Berg, Nucleic Acids Res., 2004, 32, 2494. 13. V. Kozich, Ł. Szyc, E.T.J. Nibbering, W. Werncke and T. Elsaesser, Chem. Phys. Lett., 2009, 473, 171. 14. C.M. Muntean and I. Bratu, Spectrosc - Int. J., 2007, 21, 193. 15. C.M. Muntean, I. Bratu and N. Leopold, Spectrosc – Int. J., 2011, 26, 245. 16. C.M. Muntean, N. Leopold, A. Halmagyi and S. Valimareanu, J. Raman Spectrosc., 2013, 44, 817. 17. C.M. Muntean, N. Leopold, A. Halmagyi and S. Valimareanu, J. Raman Spectrosc., 2011, 42, 1925. 18. N. Leopold and B. Lendl, J. Phys. Chem. B, 2003, 107, 5723.
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View Article Online 19. C.M. Muntean, N. Leopold, A. Halmagyi and S. Valimareanu, J. RamanDOI: Spectrosc., 10.1039/C4CP05425C 2011, 42, 844.
20. C.M. Muntean and I. Bratu, Spectrosc - Int. J., 2008, 22, 345. 21. A.V. Rakov, Opt. Spektrosk. +, 1959, 7, 202. 22. L. Sun, Y. Song, L. Wang, C. Guo, Y. Sun, Z. Liu and Z. Li, J. Phys. Chem. C, 2008, 112, 1415.
Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
23. C.-Y. Wu, W.-Y. Lo, C.-R. Chiu and T.-S. Yang, J. Raman Spectrosc., 2006, 37, 799. 24. L. Qiu, P. Liu, L. Zhao, M. Wen, H. Yang and S. Fan, Vib. Spectrosc., 2014, 72, 134. 25. W. Ke, D. Zhou, J. Wu and K. Ji, Appl. Spectrosc., 2005, 59, 418. 26. L. Sun, Y. Sun, F. Xu, Y. Zhang, T. Yang, C. Guo, Z. Liu and Z. Li, Nanotechnology, 2009, 20, 125502. 27. C.V. Pagba, S.M. Lane and S. Wachsmann-Hogiu, J. Raman Spectrosc., 2010, 41, 241. 28. R. Treffer, X. Lin, E. Bailo, T. Deckert-Gaudig and V. Deckert, Beilstein J. Nanotechnol., 2011, 2, 628. 29. C.M. Muntean, A. Halmagyi, M.D. Puia and I. Pavel, Spectrosc – Int. J., 2009, 23, 59. 30. A. L. Harris, L. Rothberg, L. H. Dubois, N. J. Levinos and L. Dhar, Phys. Rev. Lett., 1990, 64, 2086. 31. C. Artur, E. C. Le Ru and P. G. Etchegoin, J. Phys. Chem. Lett., 2011, 2, 3002. 32. J. M. Soler, E. Artacho, J. D. Gale, A. García, J. Junquera, P. Ordejón, and D. Sánchez-Portal, J. Phys.: Condens. Matter., 2002, 14, 2745. 33. B. Hammer, L. B. Hansen, and J. K. Nørskov, Phys. Rev. B, 1999, 59, 7413.
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DOI: vitro10.1039/C4CP05425C Subpicosecond surface dynamics in genomic DNA from in grown plant species: A SERS assessment
Cristina M. Muntean a *, Ioan Bratu a, Nicolae Leopold b , Cristian Morari a, Luiza BuimagaIarinca a and Monica A. P. Purcaru c
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a
National Institute for Research & Development of Isotopic and Molecular Technologies, 67-103 Donat Str., 400293 Cluj-Napoca, Romania Babeş-Bolyai University, Faculty of Physics, 1 Kogalniceanu Str., 400084 Cluj-Napoca, Romania b
c
Transilvania University of Brasov, 50 Iuliu Maniu Str., 500091 Brasov, Romania
*Corresponding author: Dr. Cristina M. Muntean [email protected]
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Abstract
In this work the surface-enhanced Raman scattering total half band widths of seven genomic DNAs from leaves of chrysanthemum (Dendranthema grandiflora Ramat.),
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common sundew (Drosera rotundifolia L.), edelweiss (Leontopodium alpinum Cass), Epilobium hirsutum L., Hypericum richeri ssp. transsilvanicum (Čelak) Ciocârlan, rose (Rosa x hybrida L.) and redwood (Sequoia sempervirens D. Don. Endl.), respectively, have been measured. We have shown that surface-enhanced Raman spectroscopy (SERS) can be used to study the fast subpicosecond dynamics of DNA in the proximity of a metallic surface. The dependencies of the total half band widths and of the global relaxation times, on DNA molecular subgroup structure and on the type of genomic DNA, are reported. In our study, the full widths at half-maximum (FWHMs) for the SERS bands of genomic DNAs from different leaf tissues, are typically in the wavenumber range from 15 to 55 cm-1. Besides, it can be observed that molecular relaxation processes studied in this work, have a global relaxation time smaller than 0.71 ps and larger than 0.19 ps. A comparison between different ranges of FT-Raman and SERS band parameters, respectively, corresponding to DNA extracted from leaf tissues is given. It is shown that the interaction between DNA and a metallic surface has the potential to lead to a shortening of the vibrational relaxation times, as compared with molecular dynamics in solution. We have found that the surface dynamics of molecular subgroups in plant DNA is, in some cases, about two times faster than the solution dynamics of nucleic acids. This can be rationalized in a qualitative manner by invoking the complex landscape of the interaction energy between the molecule and silver surface.
Keywords: Genomic DNA, plant species, leaf tissue, surface-enhanced Raman scattering, full width at half-maximum (FWHM), subpicosecond global relaxation time.
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Introduction
DOI: 10.1039/C4CP05425C
Raman spectroscopy is a powerful experimental technique giving insight knowledge about the molecular dynamic processes involved in liquids mixtures (1 and references therein). Studies of relaxation processes in liquids are valuable in providing information Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
about the intermolecular interactions in condensed matter 2. Among the techniques available for the study of molecular motions in liquids, Raman scattering has the distinct advantage, that it enables simultaneous analyses of both reorientational and vibrational processes (see for example
2,3,4,5
and references therein).
Particularly, vibrational relaxation plays a crucial role in many aspects of chemistry, physics, and biology, e.g., reaction dynamics, thermal chemistry, electron transfer, photochemistry, excimer formation and photobiological processes such as vision and photosynthesis. The dynamics and vibrational relaxation processes of biomolecules in aqueous solutions have motivated several studies (see 6,7 and references therein). The macromolecular motion in fluids is generally too slow to be observed in the Raman time window that is accessible in the frequency domain. On contrary, the motion of molecular subgroups can be fast enough 5,8,9. Although there have been many observations of DNA motion over longer times, experiments measuring motions at the level of individual bases and in the picoseconds time range have been difficult 10. Comparison of the band widths of different vibrations in different nucleotide structures presented information about the nature of relaxation processes that perturb the base vibrations. It was found that vibrational dephasing and energy relaxation by interactions with water molecules plays an important role in the vibrational dynamics
11
. The same authors
have shown, that different base vibrations are sensitive to different dynamical degrees of
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as solvent accessibility influences the vibrational band widths 11. Particularly, picosecond and nanosecond dynamics in the interior of DNA were observed for the first time as a dynamic Stokes shift in the fluorescence of a specially designed base-pair analogue. The interior of DNA was found to be a unique dynamical Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
environment that is distinctly different from either a simple fluid or a rigid molecular crystal 10
. These authors introduced time-resolved Stokes shifts (TRSS) as a method of directly
observing the local dynamics of DNA
10
. Also, it was shown that lesions in DNA structure
can change its dynamics on the picosecond and nanosecond timescales and that these changes can be measured by time-resolved Stokes shift spectroscopy 12. Also, vibrational relaxation after spectrally selective excitation within the NH stretching band of adenine-thymine base pairs, in DNA oligomers, was studied by subpicosecond infrared-pump/anti-Stokes Raman-probe spectroscopy 13. (Sub)picosecond dynamics of DNA subgroups, as a function of pH and metal ions, respectively, was previously studied by us
14
. Monitoring the changes in the normal Raman
full widths at half-maximum (FWHMs) and, correspondingly, in the global relaxation times of the molecular subgroups in DNA, upon varying the physical-chemical parameters, was of interest. In these cases, solution dynamics of nucleic acids was under study. Besides, the dynamics of plant genomic DNA on silver surface was previously reported by us for several cases, using surface-enhanced Raman scattering (SERS)
8,15
.
Particularly, the full widths at half-maximum (FWHMs) of the SERS bands in genomic DNAs from in vitro-grown apple leaf tissues were typically in the wavenumber range from 14 cm-1 to 52 cm-1. Also, the molecular relaxation processes studied in that work, had a global relaxation time smaller than 0.76 ps and larger than 0.20 ps 8. In this paper the SERS total half band widths of seven genomic DNAs from leaf
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Ramat.), common sundew (Drosera rotundifolia L.), edelweiss (Leontopodium alpinum Cass), Epilobium hirsutum L., Hypericum richeri ssp. transsilvanicum (Čelak) Ciocârlan, rose (Rosa x hybrida L.) and redwood (Sequoia sempervirens D. Don. Endl.), respectively], have been measured. The dependencies of the total half band widths and of the corresponding Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
global relaxation times, on DNA molecular subgroup structure and on the type of genomic plant DNA are reported. It is shown that changes in the subpicosecond dynamics of molecular subgroups in genomic DNAs from leaves, in the proximity of a silver surface, can be monitored with surface-enhanced Raman spectroscopy (SERS).
Experimental
Leaves from in vitro grown plant species represented the source material for extraction of genomic DNAs. These leaves were obtained from plants of chrysanthemum (Dendranthema grandiflora Ramat.), common sundew (Drosera rotundifolia L.), edelweiss (Leontopodium
alpinum
Cass),
Epilobium
hirsutum
L.,
Hypericum
richeri
ssp.
transsilvanicum (Čelak) Ciocârlan, rose (Rosa x hybrida L.) and redwood (Sequoia sempervirens D. Don. Endl.), respectively, as described elsewhere 16. Genomic DNA was isolated from leaves of the above mentioned species, respectively, using the GenEluteTM Plant Genomic DNA Miniprep Kit (G2N350-1KT) from SigmaAldrich, that uses 100 mg fresh leaf tissue per sample. Isolated DNA was dissolved in 10 mM Tris, 1 mM EDTA, pH 8.0 16. Analytical reagent grade chemicals were used. The silver colloidal SERS substrate was prepared by reducing Ag+ with hydroxylamine. Metallic nanoparticles with an estimated
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medium diameter of 34 nm have been obtained
17,18
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preparation, was presented elsewhere 19,16. Each sample was prepared by adding 500 μl silver colloid into a 1-ml glass cuvette. 10 μl of DNA solutions, respectively, were used for the preparation of the silver nanoparticle systems. The pH value of all measured SERS mixtures, containing colloidal nanoparticles and DNA extracts was of 6.5. Other details on the Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
preparation of DNA-nanoparticle systems are given elsewhere 16. A DeltaNu Advantage spectrometer (DeltaNu, Laramie, WY) equipped with a doubled frequency Nd:YAG laser, emitting at 532 nm and having a 45 mW laser power was used for recording the SERS spectra, at room temperature 16. The band parameters (full widths at half-maximum-FWHMs and global relaxation times) were determined for this data set. Also, for each band profile, an individual baseline was taken into account. The FWHMs were evaluated from the half maximum of the SERS bands.
Results and discussions
SERS spectra of DNAs from the above mentioned species are presented in Figure 1. Relating to molecular dynamics processes, Rakov developed one of the well-known procedures of obtaining the relaxation times and the activation energy 4-5,7-8,14,20,21. In this approximation, the total half band width of the depolarized Raman lines contains two contributions 4-5,8,14,20. The total half band width can be written as: 1 / 2 0 T 0
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1 . (1) c r
The potential barrier against reorientation can be obtained as:
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Figure 1. SERS spectra of genomic DNAs from leaves of in vitro grown plant species of chrysanthemum, Drosera, Leontopodium, Epilobium, Hypericum, Rosa and Sequoia, respectively, as labeled in the figure. DNA-silver nanoparticle complexes were investigated. Bottom, Raman spectrum of the silver colloid and buffer (blank spectrum). [C. M. Muntean, N. Leopold, A. Halmagyi, S. Valimareanu (2013) “Surface-enhanced Raman scattering assessment of DNA from leaf tissues adsorbed on silver colloidal nanoparticles”, J. Raman Spectrosc., 44(6): 817-822. Copyright © 2013 John Wiley & Sons, Ltd. Reproduced with permission].
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U r 0 exp or , (2) kT
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where 0 is the period of the molecule oscillation around the equilibrium position, and U or is the energy barrier or the activation energy 8,7,14,20.
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The Rakov relationship can be written as: 1 / 2 0
1 U or exp . (3) c 0 kT
From the 1 / 2 0 vs
10 3 dependencies one can obtain U or as the slope of this T
linear dependence 4,8,14,20. For large molecules, in aqueous solutions, the vibrational contribution becomes important. From Raman measurements, using polarized light, it is possible to do the selection of these two contributions
7,8,14,20
. As a first approximation, one can assume, the existence of
a global relaxation time, , obtained from the total Raman half band width. This band parameter can be related with the intrinsic parameters of the analyzed system through the relationship:
v ,1R , 2 R
1
c 1v/,12R , 2 R
, (4)
where the half band width includes the vibrational ( 1v/ 2 ) and rotational ( 11/R2, 2 R ) contributions and c is the velocity of light. 11/R2, 2 R is obtained from IR (1R) and Raman (2R) bands, respectively 4-5,14,20. The development of fast and accurate curve fitting programs allows the analysis of the vibrational spectra of complicated biological molecules, containing often more than 40 vibrational bands (5,11 and references therein). In this paper we will concentrate on the vibrational band widths. Only the relatively isolated nucleic acids vibrations will be considered
5,8,14,20
. A study of the SERS vibrational
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genomic DNAs from different leaf tissues, respectively, is of interest. This work follows previous studies of us, concerning SERS band parameters of genomic DNAs extracted from leaves of different plants 8,15. For the case of aqueous solutions of DNA molecules, we can suppose that the Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
dominant relaxation mechanism is the vibrational one. The values of the global relaxation time suggest also the existence of a vibrational relaxation time, because the reorientational movement is much more slower for the DNA macromolecule in aqueous solution 5,20. The surface-enhanced Raman band parameters (full width at half-maximum, global relaxation time) of the vibrations near 610 cm-1 (deoxyribose, C3’ endo-anti), 675 cm-1 (dG), 728 cm-1 (dA), 980 cm-1 (deoxyribose), 1166 cm-1 (dC, dT, deoxyribose), 1357 cm-1 (dT, dA, dG, dC), 1503 cm-1 (dA) and 1602 cm-1 (dG, dA, dC), characterizing genomic DNAs from seven in vitro grown plant species, respectively, are presented in Table 1 (16,22-28 and references therein). The chosen bands were the most prominent vibrations in the SERS spectra, suitable for molecular dynamics analysis. In respect of this, one can select only those vibrational modes for which one can split up the maxima, until each profile can be separated from one another at least at half intensity. The FWHM is typically in the wavenumber range from 15 to 55 cm-1 for data presented in this table. The limit wavenumber values belong to DNA from Leontopodium. For some vibrations, the FWHMs could not be determined, due to the overlapping with other vibrational modes. Besides, the global relaxation times were evaluated on the basis of Eq. 4. From the SERS vibrations around 610 cm-1, 675 cm-1, 728 cm-1, 980 cm-1, 1166 cm-1, 1357 cm-1, 1503 cm-1 and 1602 cm-1 (see Table 1), it can be observed that the global relaxation times, for molecular subgroups in genomic DNA from different in vitro grown plant species, are slower than 0.19 ps and faster than 0.71 ps. The best vibrational energy transfer process was
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Leontopodium (global relaxation time 0.19 ps) and the slowest dynamics was found for the band near 613 cm-1 (deoxyribose, C3’ endo-anti), also in the case of Leontopodium DNA (global relaxation time 0.71 ps). Previously, the FT-Raman band parameters for the vibrations at 879 cm-1 Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
(deoxyribose, dA), 1047 cm-1 (CO stretching C-O-P-O-C, dG), 1089 cm-1 ( P-O symmetric stretching of PO2- ), 1124 cm-1 (dA), 1272 cm-1 (dC, dG, dT), 1276 cm-1 (dC), 1455 cm-1 (deoxyribose, dA, dC, dT), and 1482 cm-1 (dG, dA)
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of genomic DNAs from leaf tissues
were reported by us, characterizing the solution molecular dynamics of plant nucleic acids 5. In that work, it could be observed that the molecular relaxation processes have a global relaxation time smaller than 1.36 ps and larger than 0.46 ps 5. For the cases of overlapped Raman profiles, only half of the total half band width (FWHM), in the side where the bands were not superposed, was taken into account and later on it was multiplied by two. In the followings, we will present the variation intervals of the global relaxation times, associated with each vibrational mode in Table 1. The global relaxation time characterizing the band near 612 cm-1 (deoxyribose, C3’ endo-anti) varied between 0.53-0.71 ps. The smallest global relaxation time (0.53 ps) and the largest half band width (20 cm-1), have been detected for the SERS band at 610 cm-1, in the case of DNA extracted from Sequoia. These differences in molecular relaxation processes of deoxyribose, C3’ endo-anti might be due to structural neighbourhood of this entity, in DNAs originating from different sources. The dG band profile near 675 cm-1, is characterized by global relaxation times in the subpicosecond range 0.37-0.46 ps. Similar global relaxation times of 0.48 ps have been found by us for the profile near
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species, respectively. A larger global relaxation time was found for this band in the case of DNA from Rosa (0.53 ps). Referring to the deoxyribose vibration near 980 cm-1, the vibrational energy transfer processes are characterized by global relaxation times ranging between 0.37-0.44 ps. Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
The global relaxation times of the SERS bands near 1166 cm-1 (dC, dT, deoxyribose), have the values of 0.48 ps for DNA from Sequoia and 0.27 ps, respectively in the case of DNA from Hypericum. Besides, vibrational energy transfer processes characterized by global relaxation times between 0.37-0.53 ps have been found by us for the band near 1357 cm-1 (dT, dA, dG, dC). For some cases, this band seems to be rather stable, as far as dynamical properties are concerned. On the other hand, it is to be observed that nitrogenous bases containing structural subgroups have smaller global relaxation times as compared with those of deoxyribose, C3’ endo-anti entity. Also, the band widths of the SERS vibration around 1503 cm-1 (dA), are sensitive to a dynamics active on a time scale from 0.41 ps (Rosa DNA) to 0.51 ps (Sequoia DNA). As far as the band parameters of the vibration near 1602 cm-1 (dG, dA, dC) are concerned, global relaxation time varied between 0.19-0.25 ps. The carbonyl vibration in leaf tissues DNAs studied in this work has broad band widths, ranging between 43-55 cm-1. The molecular dynamics associated with this band is the most rapid one, as compared with the relaxation processes of other structural groups, characterized in this work. We have found that the SERS bands of DNA from Sequoia and Rosa plants, respectively, are suitable for the study of dynamical behaviour of molecular subgroups in nucleic acids extracted from leaf tissues, since they display the largest number of modes with band parameters determined (see Table 1).
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View Article Online Table 1. Total half band widths (cm-1) of SERS vibrational markers and global DOI:relaxation 10.1039/C4CP05425C times of molecular subgroups, in genomic DNA from leaves of in vitro grown plant species.
νmax (cm-1)
Δν1/2 (cm-1)
610 675 728 982 1166 1353 1503 1602
20* 27 22* 29 22* 27 21 48
612 675 729 981 1356 1502 1602
16 29 20* 28 28 26** 48
1165 1354 1598
39 20* 50*
611 980 1356 1602
18 24 25 43
613 1355 1604
15 28 55
612 979 1357 1602
16* 25 27 46
609 682 726 978 1360 1607
18 23 22 26 29 46
τSERS (ps) Sequoia 0.53 0.39 0.48 0.37 0.48 0.39 0.51 0.22 Rosa 0.66 0.37 0.53 0.38 0.38 0.41 0.22 Hypericum 0.27 0.53 0.21 Epilobium 0.59 0.44 0.42 0.25 Leontopodium 0.71 0.38 0.19 Drosera 0.66 0.42 0.39 0.23 Chrysanthemum 0.59 0.46 0.48 0.41 0.37 0.23
Tentative assignment 16,22-28 a Deoxyribose, C3’ endo-anti dG dA Deoxyribose dC, dT, deoxyribose dT, dA, dG, dC dA dG, dA, dC Deoxyribose, C3’ endo-anti dG dA Deoxyribose dT, dA, dG, dC dA dG, dA, dC dC, dT, deoxyribose dT, dA, dG, dC dG, dA, dC Deoxyribose, C3’ endo-anti Deoxyribose dT, dA, dG, dC dG, dA, dC Deoxyribose, C3’ endo-anti dT, dA, dG, dC dG, dA, dC Deoxyribose, C3’ endo-anti Deoxyribose dT, dA, dG, dC dG, dA, dC Deoxyribose, C3’ endo-anti dG dA Deoxyribose dT, dA, dG, dC dG, dA, dC
a
Abbreviations: dA - deoxyadenosine; dG - deoxyguanosine; dC - deoxycytidine; dT deoxythymidine. * Low frequency side of the band was read; later on the respective profile was symmetrized. ** High frequency side of the band was read; later on the respective profile was symmetrized.
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View Article Online We have obtained similarities and differences between the relaxation of DOI: times 10.1039/C4CP05425C
different molecular subgroups in DNA, originated from one plant, as well as from various plant species. The observed results can be explained correlating them, with local structure of genomic DNA, with nucleic acids base composition and with DNA sequence (molecular neighbourhood), respectively, which are distinctive for the plant from which DNA originated. Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
Besides, DNA conformation might modify molecular dynamics of nucleic acids subgroups. Particularly, in our systems, deoxyribose moiety was found to exhibit C3'-endo/anti conformation. Percentages of C3'-endo/anti conformations, with respect to other genomic DNA conformations, might contribute to changes in global relaxation times of molecular subgroups. Particularly, DNA from Leontopodium exhibited very different results from the other samples and these can be explained by the reasons above. After some authors, the strength of interaction between nucleobases and Ag nanoparticles is in the order of C > G > A > T. Due to the donation of nitrogen and oxygen lone pairs, the best aggregation occurred in the case of cytosine (16 and references therein). As an observation, the global relaxation time of dG residues (675 cm-1) is lower (0.39 ps) as compared with the global relaxation times of dA residues (728 cm-1), respectively (0.48 ps) in the case of Sequoia. For Rosa DNA, the dynamics of dG residues (675 cm-1) is faster (0.37 ps) as compared with the dynamics of dA residues (729 cm-1), (0.53 ps). This behavior might be explained by the different strength of interaction between guanine, adenine and silver nanoparticles surface, respectively. Smaller differences between the global relaxation times of dG (682 cm-1) (0.46 ps) and dA (726 cm-1) (0.48 ps) residues, respectively, are to be found in the case of chrysanthemum nucleic acids. Besides, a comparison between different ranges of the Raman band parameters, in the case of aqueous solution nucleic acids dynamics (investigated by FT-Raman spectroscopy)
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View Article Online and of the dynamics of DNA in the proximity of a metallic surface (investigated DOI: by SERS) is 10.1039/C4CP05425C
given in Table 2.
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Table 2. Comparison between different ranges of the Raman band parameters, in the case of aqueous solution dynamics (FT-Raman) and surface dynamics (SERS) of DNA extracted from different leaf tissues (5,8,15 and references therein). DNA molecules
FWHM range Δν/cm-1
Genomic DNA from in vitrogrown plant species, FTRaman study Genomic DNA from in vitrogrown apple leaf tissues, SERS study Genomic DNA from in vitrogrown plant species, SERS study
7.8 - 23.1
Global relaxation time range τ/ps 0.46 - 1.36
14-52
0.20-0.76
13-42
0.25-0.82
It is to be observed, that the surface dynamics of molecular subgroups in plant DNA is more rapid (in some cases, about two times faster) than the solution dynamics of nucleic acids. This means, that the mobility of DNA subgroups is greater even in the case of interaction with a silver surface. An explanation of this observation might be, that in solution are possible to be present molecular associations, solvent interactions, etc., leading to a slower dynamics (a slower mobility). On the surface, the clusters are broken down and DNA is interacting only with the surface, having a higher mobility 8. On the other hand, stabilizing ions or molecules present on the surface of most colloidal metal nanoparticles are likely to participate in interactions with DNA, also affecting the molecular dynamics. We can also consider the possibility of energy transfer to the metal surface, resulting in shorter relaxation times of DNA subgroups. Particularly, other aspects related with the observed global relaxation times in the proximity of a surface and in solution, are discussed in the next subsection.
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The interactions between a molecule and its local environment lead to the broadening of the Raman peak, mainly by vibrational relaxation. The anharmonicity of the intramolecular force constants was proposed as intrinsic mechanism to explain this effect for free Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
molecules
30
. Recently, the importance of the anharmonic coupling to phonons in the Ag
substrate was pointed out in single-molecule surface-enhanced Raman spectroscopy (SMSERS) 31. In order to get an idea of the energy involved in the process, we note that by using the Heisenberg relation can be found that the energy of kT= 0.03 eV corresponds to relaxation times of up to 22 fs. Consequently, picoseconds relaxation times are expected to be obtained for energies below 0.03 eV. This suggests that the direct investigation of the relaxation times on surfaces by means of ab-initio calculations is a complicated (or even impossible) task, for realistic systems. On the other hand, qualitative insight into the process can be obtained by investigating only selected aspects of the molecule-surface interaction. While for the molecules in solution the interactions with the environment are dominated by collisions and long range interactions, for the adsorbates the picture is significantly changed. The dynamics of the adsorbed molecules takes place on a 2D space, unlike to the 3D case occurring in solution. This is expected to be the main factor determining the changes in the dynamics upon the adsorption. In this context, we can recall the existence of new features of the molecular dynamics, such as frustrated translations or the strong suppression of the rotational degrees of freedom. The investigation of the functional dependence between the position of the DNA base and the adsorption energy on the 2D surface can provide a qualitative information on the dynamics occurring at atomic scale in a SERS experiment. While such data cannot provide a
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View Article Online realistic model dynamics for DNA adsorbed on the surface, it can provide realistic DOI: 10.1039/C4CP05425C
understanding of the general features of the molecular dynamics on the surface. As model-systems we have investigated the interactions between the DNA bases [adenine (A), thymine (T), cytosine (C), guanine (G)] and the clean silver surface, respectively. Each of the four bases was allowed to adsorb on two geometric configurations: Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
with the π ring parallel and perpendicular to the surface, respectively. For each of the resulting 8 configurations we have relaxed the initial (randomly chosen) geometric structure up to a maximum gradient of 0.02 eV/Å (see Figure 2 for a geometrical representation). Next, we have generated a number of other 16 geometric structures for each DNA base by translating the molecule parallel to the surface, according to the pattern indicated in Figure 3, in order to cover symmetrically the unit cell of the Ag(111) surface. The resulting energies for each configuration were interpolated by taking into account the 2D periodic boundary conditions on the Ag(111) surface (i.e. hexagonal symmetry) in order to produce maps of the molecule-surface interaction The technical details of our calculations are the following: all calculations were performed using the DFT as implemented in the SIESTA code basis set and the RPBE exchange-correlation functional
33
32
. We used a DZP quality
. The Ag(111) surface was
generated by using a bulk parameter of 4.08 Å and a 5X5 super-cell on the XOY plane (the surface was generated to be parallel to the Z=0 plane). The slab used in calculations consisted on four layers of Ag, resulting on 100 Ag atoms (25 for each plane). Periodic boundary conditions were imposed to the model; the size of the super-cell on OZ axis was chosen to be 30 Å, so that the interactions between the periodic replicas of the model were negligible. For the first geometric structure the positions of the top layer atoms in the Ag surface, as well as the positions of the organic atoms were allowed to relax, while the other 75 atoms were
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further translation of the molecule parallel to the surface.
Figure 2. The initial geometric structures of the DNA bases, adsorbed on (111) silver surface with the π- ring parallel / perpendicular to the surface.
Figure 3. Schematic representation of the pattern used to calculate a number of 16 geometric structures for each DNA base by translating the base parallel to the surface in order to cover symmetrically the Ag(111) unit cell.
The shape of the interaction energy as a function of the X and Y coordinates are indicated in Figures 4 and 5. Since only the differences between the interactions energy in different regions are relevant for the dynamics, we subtract from these values the constant quantities in order to make the results suitable for graphical representation. It can be clearly seen that the
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DOI: 10.1039/C4CP05425C
Figure 4. The energy maps for the DNA bases adsorbed on Ag (111) surface with the π- ring parallel to the surface; black points indicate the calculated energy values; all energies are expressed in eV.
fluctuations of the adsorption energy are of the same order of magnitude as the thermal energy at room temperature (kT=0.03 eV). Therefore it is natural to assume that 2D translations of the adsorbed molecules are an important component of the dynamics in all the experiments. Moreover, it is also natural to assume that such dynamics will provide specific relaxation mechanisms that are not present in the solution, leading to clearly different values for the vibrational relaxation times.
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DOI: 10.1039/C4CP05425C
Figure 5. The energy maps for the DNA bases adsorbed on (111) silver surface with the πring perpendicular to the surface; black points indicate the calculated energy values; all energies are expressed in eV.
Also, we note the dynamics on the surface is expected to be different for each of the four DNA bases, as well as for different orientations with respect to the surface (i.e. parallel or perpendicular). Precisely, the dynamics will take place along the yellow regions in the Figures 4 and 5 (i.e. minimum of the molecule-surface interaction energy). The most remarkable feature of our theoretical analysis is that, similar energetic landscapes can occur for the DNA bases paired in a nucleic acid chain, respectively. Indeed, for the A and T the
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Article Online dynamics on the surface is expected to take place along lines placed at 60 degrees inView our DOI: 10.1039/C4CP05425C
representation, while for the C and G is suggested a dynamics along vertical lines.
Conclusions
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This work presents a surface-enhanced Raman spectroscopic study based on the vibrational total half band widths of molecular subgroups in seven genomic DNAs extracted from in vitro grown plant species of chrysanthemum (Dendranthema grandiflora Ramat.), common sundew (Drosera rotundifolia L.), edelweiss (Leontopodium alpinum Cass), Epilobium hirsutum L., Hypericum richeri ssp. transsilvanicum (Čelak) Ciocârlan, rose (Rosa x hybrida L.) and redwood (Sequoia sempervirens D. Don. Endl.), respectively. Besides, the corresponding global relaxation times have been derived. We have shown that surface-enhanced Raman scattering can be used to study the fast subpicosecond dynamics of DNA from plant tissues, in the proximity of a metallic surface. SERS band parameters were obtained for the vibrational modes near 610 cm-1 (deoxyribose, C3’ endo-anti), 675 cm-1 (dG), 728 cm-1 (dA), 980 cm-1 (deoxyribose), 1166 cm-1 (dC, dT, deoxyribose), 1357 cm-1 (dT, dA, dG, dC), 1503 cm-1 (dA) and 1602 cm-1 (dG, dA, dC), respectively (16,19-25 and references therein). Study of vibrational total half band widths of genomic DNA from leaf tissues, revealed a sensitivity of FWHM to the source of nucleic acid. Moreover, this proved to be dependent on the vibration under study. The SERS total half band widths of genomic DNA vibrations revealed a dynamic picture on a subpicosecond time scale 8. In our study, the full widths at half-maximum (FWHMs) of the SERS bands in genomic DNAs from different leaf tissues, are typically in the wavenumber range from 15 to 55 cm-1. Besides, the total half band widths in the SERS spectra are sensitive to a dynamics active on time scales from 0.19 ps to 0.71 ps. The carbonyl vibration in leaf tissues DNAs
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global relaxation times between 0.19-0.25 ps. A comparison between different ranges of Raman band parameters of plant genomic DNA, in the case of aqueous solution dynamics (investigated by FT-Raman spectroscopy) and surface dynamics (investigated by SERS) has also been given 5,8. Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
We have found experimentally, that the surface dynamics of molecular subgroups in plant DNA is, in some cases, about two times faster than the solution dynamics of nucleic acids. Reduced dimensionality and the suppression of the rotational degrees of freedom are mainly responsible for this. Our theoretical studies indicate that the translation of DNA bases on surface is expected to be an important component of the dynamics at room temperature; it is natural to assume that this will lead to relaxation mechanisms completely different to those present in solution. A second feature of our theoretical analysis is that, similar energetic landscapes can occur for the DNA bases paired in a nucleic acid chain, respectively. Indeed, for the A and T the dynamics on the surface is expected to take place along lines placed at 60 degrees in our representation, while for the C and G is suggested a dynamics along vertical lines.
Acknowledgements
The authors wish to thank to Dr. Adela Halmagyi and to Dr. Sergiu Valimareanu from the Institute of Biological Research, Cluj-Napoca, Romania, for isolating the genomic DNAs from different leaf tissues. Thanks are also due to the reviewers of this manuscript and to Dr. Nicoleta Tosa from National Institute for Research & Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania, for useful comments. This work was supported by a grant of the Ministry of National Education, National Authority for Scientific Research
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CNCS – UEFISCDI, Romania, project number PN-II-ID-PCE-2012-4-0115.
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DOI: 10.1039/C4CP05425C
References 1. T.G. Devi and G. Upadhayay, Spectrochim. Acta A-M, 2012, 91, 106.
Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
2. T. Iliescu, I. Bratu, R. Grecu, T. Veres and D. Maniu, J. Raman Spectrosc., 1994, 25, 403. 3. T. Iliescu, S. Aştilean, I. Bratu, R. Grecu and D. Maniu, J. Chem. Soc. Faraday T., 1996, 92, 175. 4. C.M. Muntean and I. Bratu, Spectrosc - Int. J., 2008, 22, 475. 5. C.M. Muntean and I. Bratu, Spectrosc - Int. J., 2009, 23, 281. 6. A. Hernanz, I. Bratu and R. Navarro, J. Phys. Chem. B, 2004, 108, 2438. 7. C.M. Muntean, I. Bratu, K. Nalpantidis and M.A.P. Purcaru, Spectrosc - Int. J., 2009, 23, 141. 8. C.M. Muntean, I. Bratu, N. Leopold and M.A.P. Purcaru, Spectrosc - Int. J., 2011, 26, 59. 9. C. Otto, P.A. Terpstra, G.M.J. Segers-Nolten and J. Greve, in J.C. Merlin et al. (eds.), Spectroscopy of Biological Molecules, 1995, Kluwer Academic Publishers, Dordrecht, 313. 10. E.B. Brauns, M.L. Madaras, R.S. Coleman, C.J. Murphy and M.A. Berg, J. Am. Chem. Soc., 1999, 121, 11644. 11. P.A. Terpstra, C. Otto and J. Greve, Biopolymers, 1997, 41, 751. 12. M.M. Somoza, D. Andreatta, C.J. Murphy, R.S. Coleman and M.A. Berg, Nucleic Acids Res., 2004, 32, 2494. 13. V. Kozich, Ł. Szyc, E.T.J. Nibbering, W. Werncke and T. Elsaesser, Chem. Phys. Lett., 2009, 473, 171. 14. C.M. Muntean and I. Bratu, Spectrosc - Int. J., 2007, 21, 193. 15. C.M. Muntean, I. Bratu and N. Leopold, Spectrosc – Int. J., 2011, 26, 245. 16. C.M. Muntean, N. Leopold, A. Halmagyi and S. Valimareanu, J. Raman Spectrosc., 2013, 44, 817. 17. C.M. Muntean, N. Leopold, A. Halmagyi and S. Valimareanu, J. Raman Spectrosc., 2011, 42, 1925. 18. N. Leopold and B. Lendl, J. Phys. Chem. B, 2003, 107, 5723.
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View Article Online 19. C.M. Muntean, N. Leopold, A. Halmagyi and S. Valimareanu, J. RamanDOI: Spectrosc., 10.1039/C4CP05425C 2011, 42, 844.
20. C.M. Muntean and I. Bratu, Spectrosc - Int. J., 2008, 22, 345. 21. A.V. Rakov, Opt. Spektrosk. +, 1959, 7, 202. 22. L. Sun, Y. Song, L. Wang, C. Guo, Y. Sun, Z. Liu and Z. Li, J. Phys. Chem. C, 2008, 112, 1415.
Published on 06 February 2015. Downloaded by University of Sussex on 08/02/2015 07:22:13.
23. C.-Y. Wu, W.-Y. Lo, C.-R. Chiu and T.-S. Yang, J. Raman Spectrosc., 2006, 37, 799. 24. L. Qiu, P. Liu, L. Zhao, M. Wen, H. Yang and S. Fan, Vib. Spectrosc., 2014, 72, 134. 25. W. Ke, D. Zhou, J. Wu and K. Ji, Appl. Spectrosc., 2005, 59, 418. 26. L. Sun, Y. Sun, F. Xu, Y. Zhang, T. Yang, C. Guo, Z. Liu and Z. Li, Nanotechnology, 2009, 20, 125502. 27. C.V. Pagba, S.M. Lane and S. Wachsmann-Hogiu, J. Raman Spectrosc., 2010, 41, 241. 28. R. Treffer, X. Lin, E. Bailo, T. Deckert-Gaudig and V. Deckert, Beilstein J. Nanotechnol., 2011, 2, 628. 29. C.M. Muntean, A. Halmagyi, M.D. Puia and I. Pavel, Spectrosc – Int. J., 2009, 23, 59. 30. A. L. Harris, L. Rothberg, L. H. Dubois, N. J. Levinos and L. Dhar, Phys. Rev. Lett., 1990, 64, 2086. 31. C. Artur, E. C. Le Ru and P. G. Etchegoin, J. Phys. Chem. Lett., 2011, 2, 3002. 32. J. M. Soler, E. Artacho, J. D. Gale, A. García, J. Junquera, P. Ordejón, and D. Sánchez-Portal, J. Phys.: Condens. Matter., 2002, 14, 2745. 33. B. Hammer, L. B. Hansen, and J. K. Nørskov, Phys. Rev. B, 1999, 59, 7413.
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