Hydration of DNA Bases: Analysis of Crystallographic Data BOHDAN SCHNEIDER,’ DAWN COHEN,’ and HELEN M. BERMAN’ Departments of ’Chemistry and ‘Computer Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903
SYNOPSIS
We present a systematic analysis of water structure around nucleic acid bases. We have examined 28 crystal structures of oligonucleotides, and have studied the patterns of water around the four bases, guanine, cytosine, adenine, and thymine. The geometries of water positions were calculated up to 4.00 A from base atoms. We have found conformationdependent differences in both the geometry and extent of hydration of the bases.
INTRODUCTION Ever since Franklin and Gosling1examined the first fibers of DNA, it has been known that relative humidity and ionic strength affect the conformation of DNA. Although there have been many experimental and theoretical studies on DNA hydration (for reviews see Refs. 2-8), the role of water in DNA conformational transitions is not as yet understood. In this paper, we examine the question of how the organization of water molecules differs around DNA molecules with different conformations. There are a t least three different classes of water molecules around DNA molecule^.^ The first layer is impermeable to ions; the second has fast exchange of water molecules and ions with bulk water, and is only partially ordered. The third layer is bulk solvent. Thermodynamic measurements, as well as statistical mechanics approaches, have been used to explain the dynamic behavior of water molecules and ions around DNA molecules.’O~l’ Nuclear magnetic resonance experiments have shown that amplitudes of backbone movement, as well as base movement, depend on relative humidity and temperat~re.”-’~ Although NMR and thermodynamic methods provide invaluable information about the dynamics of DNA molecules at different humidities and ionic strengths, they do not provide specific information about the positions of solvent molecules. Information about the positions of water mole-
Biopolymers, Vol. 32, 725-750 (1992) 0 1992 John Wiley & Sons, Inc.
CCC 0006-3525/92/070725-26$04.00
cules in the first and second hydration layers can be obtained using x-ray crystallography. Oligonucleotide crystals are well hydrated, with water contents of up to 50%. However, because DNA molecules can be quite flexible, the resolution of diffraction is sometimes limited, making it difficult to observe solvent molecules and ions. The positions of most water molecules are less constrained than those of covalently bound DNA atoms in crystal structures and can undergo continuous fluctuation. As a result, generally only about 25% of the water molecules are crystallographically ordered in nucleic acid crystals. Notwithstanding these drawbacks, highly organized water molecules have been observed in many nucleotide structure^.'^^'^ Several papers4,5,s,’9-21 discuss water bridges in representative structures, as well as the relationship between DNA polymorphism in crystals and their different water structures. In one case, an attempt is made to quantitate hydration for different DNA conformational types by comparing the number of contacts between water molecules, base atoms, and backbone atoms in representative structures of the A-, B-, and Z-conformational classes. Another studyz0attempts to relate phosphate-phosphate distances in different DNA conformations to differences in hydration, proposing that the “economy of hydration” is the driving force in the B to A transition. Although this is an intuitively appealing concept, its validity has not been substantiated in newer experimental result^.^ In analyses of the solvent-accessible surfaces of nucleic acid structures, 22,23 the differences between solvent-accessible surfaces of A- and B-DNA type helices are shown to be surprisingly small. 726
726
SCHNEIDER, COHEN, AND BERMAN
Table I The structures Included in this Study Listed by Conformational Typea Resolution NO. PDB
NDB ADDBOl ADJ022 ADH007 ADH024 ADH008
A A A A A
2 1 2
6 lBNA BDLOOl 7 1DN9 BDL007 8 2BNA BDLOO2 9 3BNA BDLB03 10 4BNA BDLB04 11 3DNB BDJ008 12 4DNB BDLB13 13 1D25 BDJB27 14 1D28 BDL028
B B B B B B B B B
2 2 2 2 2 1 2
ZDFOO2 ZDFB03 ZDFB04 ZDFBl2 ZDD015 ZDFOOl ZDFBll ZDBO2O ZDFB21
Z
2 2 2 2 2 2 2 2 2
UDPOll UDDOO6 UDB004 UDB005 UDB007
U U U U U
1 2 3 4 5
lANA 1D13 3ANA 5ANA 9DNA
15 16 17 18 19 20 21 22 23
lDCG 1DN4 1DN5 lDNF lZNA 2DCG
24 25 26 27 28
1D16
-
1D24 -
(A)
R
C51CCGG ACCGGCCGGT GGGATCCC GTACGTAC GCCCGGGC
2.0 2.0 2.5 2.25 1.8
16.5 18.0 16.6 18.4 17.1
CGCGAATTCGCG CGCATATATGCG CGCGAATTCGCG CGCGAATTCSB‘CGCG CGCGAATTCSB’CGCG CCAAGATTGG CGCGA~~~~ATTCGCG CCAGGCCTGG CGTGAATTCACG
1.9 2.2 2.7 3.0 2.3 1.3 2.0 1.6 2.7
CGCGCG
1.o
C 5 B r c CSBrcGCSBr ~ CG C5Br C5Brc~C5Brc~
1.6 1.4 1.5 1.5 0.9 1.3 0.85 1.9
Type Chain
Z Z
Z Z Z Z
Z Z
1 1
1
2
1 1 1
2 1
Sequence
CG
CGCGCSFUG CGCG CGCGCG CC~NH~ACGTG CG CGCO~M~GCG CGCGCGTTTTCGCGCG ATAT CG CG TT
2.1 1.04 0.91 0.86 1.14
W
+ ion
W Contacts
Ref.
34
27 31 12 24 19
74 41 32 37 53
30 31 32 33 34
17.8 18.7 15.1 17.3 21.6 18.5 16.9 16.0 17.0
80 43 83 44 114 69+ 3 87 41 2 85
54 18 41 18 55 57 42 49 48
95 33 85 38 116 121 93 80 99
26 35 36 17, 37 17,37 38 39 40 41
13.5 13.3 12.5 17.2 21.0 14.0 21.7 13.6 19.0
84
70 54 61 58 55 55 62 15 45
159 114 143 94 109 120 146 38 104
42 18 18 43 44 45 46 47 48
31 36 6 13 11
79 78 16 37 31
49 50 51 52 53
20.0 15.3 6.0 4.1 13.1
86 36 9 52
+1
+
+4 61 83
+1 74 + 2 83 + 1 13 + 2 58
84
60 70 42 3 7 15
+1 +1 +4
a For each structure the Brookhaven Protein Database name (PDB) and the Nucleic Acid Database (NDB) name are given. Also listed are the number of chains in the asymmetric unit (Chain), sequence of one strand (Sequence), crystallographic resolution of the structure determination (Resolution), crystallographic residual index (R), total number of refined positions of water molecules and ions in the asymmetric unit (W ion), number of water molecules interacting with the structure’s bases, counted separately for each base (W), number of contacts between the structure’s base atoms and water molecules (Contacts), and the bibliographic reference for the structure (Ref.).
+
Several theoretical studies have been done in attempts to account for nucleic acid hydration. Molecular dynamics methods have successfully ~ i m u l a t e d the ~ ~ ,structure ~~ and dynamics of the dCpG /proflavine complex l5 and the hydration around the dodecamer d ( CGCGAATTCGCG)z.269z7 The dodecamer simulationz5 showed an ordered water pattern in the minor groove corresponding to the “spine of hydration” observed in the crystal s t r ~ c t u r e . In ’ ~ another molecular dynamics study, the hydration of a B-DNA decamer structure, ( dCCAACGTTGG)z,z9 was simulated. In agreement with the experimental x-ray structure of the decarner,” the authors revealed two types of minor groove hydration and proposed that the positions of water oxygens in the minor groove depend primarily on groove width rather than base sequence.
In general, a great deal of attention has been focused on descriptions of water bridges and other networks within nucleic acid structures in the known conformational classes. No study, so far, has systematically placed all available crystal structures into a common framework where hydration could be quantitatively examined in terms of number of water-nucleic acid contacts as well as in terms of the geometry of contacts. As the number of known oligonucleotide structures is now quite large, it is timely to present a comprehensive analysis. In this paper, we analyze the hydration of bases from single crystals of oligodeoxynucleotides(DNA) whose coordinates are available as of 1991. The number of these structures was sufficient to discuss hydration of the bases in terms of a number of contacts between water molecules and base atoms, and
727
HYDRATION OF DNA BASES
Table I1 Number of Water Molecules Lying Closer Than 4.00 and Number of Their Contacts to the Base Atoms“ Base
A
G
A-DNA
B-DNA
2-DNA
U-DNA
All Types
Structures Bases Waters Contacts Contacts/atom Fraction
3 5 12 19 0.38 6.8%
9 36 76 182 0.50 64.8%
1 2 14 35 1.59 12.5%
1 2 17 45 2.25 16.0%
14 45 119 281
Structures Bases Waters Contacts Contacts/atom Fraction
5 20 47 126 0.57 11.6%
9 59 119 244 0.38 22.5%
9 46 286 639 1.26 58.8%
3 9 27 77 0.78 7.1%
26 134 479 1086
9 (7) 44 (32) 156 (109) 316 (231) 0.87 (0.90) 51.6% (45.9%)
3 9 17 29 0.40 4.7% (5.8%)
26 (24) 131 (113) 319 (258) 612 (503)
3 8 36 90 1.25 32.4%
17 52 149 278
C (Unmodified) Structures Bases Waters Contacts Contacts/atom Fraction
5 (5) 9 (9) 20 (18) 58 (54) 45 (36) 101 (96) 81 (68) 186 (175) 0.50 (0.47) 0.43 (0.41) 13.2% (13.5%) 30.3% (34.8%)
T
3 5 9 11 0.24 4.0%
Structures Bases Waters Contacts Contacts/atom Fraction
All bases
A from Bases
Structures Bases Waters Contacts Contacts/atom
5 50 113 237 0.50
9 35 86 150 0.48 54.0% 9 188 382 762 0.43
2 4 18 27 0.75 9.7% 9 96 474 1017 1.09
5 28 97 241 0.92 ~~
-
100.0%
-
100.0%
-
100% (100%)
-
100.0% 28 362 1066 2257 -
For each base type in A-, B-, Z-, and U-DNA conformations are listed number of analyzed structures (Structures), number of bases in these structures (Bases), number of water molecules closer than 4.00 A to any atom in these bases (Waters), number of contacts between these water molecules and the base atoms (Contacts),average number of contacts per base atom (Contacts/atom), and fraction of all contacts that fall in a particular conformation (Fraction). Since each base was analyzed separately and one water molecule can interact with several bases, the number of water molecules listed under “All Bases” is higher than the actual number of interacting water molecules. The number of contacts is larger than the number of water molecules since one water molecule can form contacts to more than one base atom. a
in terms of positions of water molecules relative to the bases. Both views reveal significant differences among different DNA conformations and different base types.
METHODS Twenty-eight structures from the Nucleic Acid Data Bank5* (NDB) containing 362 bases were used in this study (see Table I for a listing of analyzed structures, Refs. 17,18,26,30-53). A structure was included in this analysis if it met the following cri-
teria: ( a ) the structure was determined using single crystal x-ray crystallography; ( b ) the molecule is a deoxynucleotide with at least two bases in a chain; ( c ) the molecule is not complexed with other molecules other than counterions; and ( d ) the coordinates for both nucleotide and solvent are publicly available. Our approach extended that of a study” that compared hydration of mononucleotides and dinucleotides. Coordinates of base and solvent atoms of oligonucleotides were retrieved from the Nucleic Acid Data Bank.54Contacts between base atoms and solvent molecules were calculated for each base sepa-
Table 111 Quantitative Measures of Hydration by Base Atom and DNA Type (a) Guanine DNA
Twe A
B
Z
U
Contact Category
N2
“4.001 N [3.201 n (4.001 n [3.20] f [4.001 f t3.201
06
N7
19 4 0.95 0.20 11 9
11 3 0.55 0.15 23 30
22 13 1.10 0.65 13 15
26 9 1.30 0.45 11 12
14 1 0.70 0.05 7 5
“4.001 N [3.201 n [4.00] n [3.20] f [4.001 f 13.201
30 2 0.51 0.03 18 4
13 6 0.22 0.10 28 60
43 18 0.73 0.31 26 21
52 21 0.88 0.36 18 28
49 4 0.83 0.07 24 21
57 0 -
N [4.00] “3.201 n [4.00] n [3.20] f t4.001 f 13.201
116 39 2.52 0.85 69 85
23 1 0.50 0.02 49 10
87 45 1.89 0.98 52 52
139 41 3.02 0.89 59 54
121 12 2.63 0.26 60 63
150 3
N(4.001 “3.201 n [4.00] n (3.201 f [4.001
4 1 0.44 0.11 2 2
14 10 1.56 1.11 8 12
18 5 2.00 0.56 8 7
19 2 2.11 0.22 9 11
22 0
fwol
0 0 -
-
0 0
C8
N1, C2, C4 C5, C6, N9
N3
34 2 -
13 -
-
22 -
-
57 -
-
8 -
All Atoms 126 32 6.30 1.60 12 13 244 51 4.14 0.86 23 21 639 138 13.89 3.00 59 58 77 18 8.56 2.00 7 7
(b) Adenine DNA Twe
Contact Category
A
“4.001 “3.201 n [4.00] nt3.201
B
Z
N1, C4, C5, C6, N9
c2
N3
N6
N7
C8
3 .2 0.60 0.40 8 8
5 0 1.00 0.00 10 0
3 1 0.60 0.20 6 5
2 0 0.40 0.00 5
-
f 14.001 f [3.201
4 1 0.80 0.20 10 14
-
-
“4.001 N [3.20] n [4.00] n [3.20] f [4.001 f P.201
26 6 0.72 0.17 67 86
28 19 0.78 0.53 76 79
29 8 0.81 0.22 59 62
31 15 0.86 0.42 60 68
28 3 0.78 0.08 68
37 2
64
-
-
“4.001 “3.201 n [4.00] n [3.20] f [4.001 f i3.201
2 0 1.00 0.00 5 0
2 0 1.00 0.00 5 0
5 2 2.50 1.oo 10 15
8 1 4.00 0.50 15 5
5 1 2.50 0.50 12
11 1
19
-
-
2 0 -
3
-
-
All Atoms 19 4 3.80 0.80 7 6 182 53 5.06 1.47 65 73 35 5 17.50 2.50 13 7
Table I11 (Continued from the previous page.) (b) Adenine
U
“4.001 “3.201 n[4.00] n [3.20] f ~4.001 f 13.201
7 0 3.50 0.00 18 0
10 3 5.00 1.50 20 23
4 3 2.00 1.50 11 13
10 5 5.00 2.50 19 23
6 0 3.00
-
0.00 15 -
14 -
8 0
45 11 22.50 5.50 16 15
(c) Cytosineb DNA Type
Contact Category
02
N4
c5
Br or I
A
“4.001 “3.201 n [4.00] n [3.20] f [4.00] f l3.201
16 (15) 5 (5) 0.80 (0.83) 0.25 (0.28) 13 (15) 7 (9)
19 (17) 5 (5) 0.95 (0.94) 0.25 (0.28) 13 (13) 9 (10)
18 (16) 5 (5) 0.90 (0.89) 0.25 (0.28) 14 (13) 36 (38)
6 0 3.00
“4.001 N [3.20] n [4.00] n [3.20] f [4.00] f L3.201
15 6 0.26 0.10 12 8
53 19 0.91 0.33 36 33
(52) (19) (0.96) (0.35) (40) (38)
53 (52) 6 (5) 0.91 (0.96) 0.10 (0.09) 41 (41) 43 (38)
3 1 0.75 0.25
z
“4.001 “3.201 n [4.00] n [ 3.201 f[4.00] f[3.20]
82 (60) 58 (44) 1.86 (1.88) 1.32 (1.38) 67 (62) (80) 82
68 (51) 31 (23) 1.55 (1.60) 0.71 (0.72) 46 (40) 53 (46)
50 (50) 2 (2) 1.14 (1.56) 0.05 (0.06) 39 (40) 14 (15)
U
“4.001 “3.201 n [4.00] n [3.20]
B
f t4.001 fw o l
(13) (4) (0.24) (0.07) (13) (7)
9 2 1.00 0.22 7 3
8 1 0.89 0.11
9 3 1.00 0.33 (9) (4)
6 5
(7) (6)
6 7
N1, C2, N3 C4, C6 22 1 13 -
81 (68) 16 (16) 4.05 (3.78) 0.80 (0.89) 13 (14) 11 (13)
-
62 0 37 -
186 (175) 32 (28) 3.21 (3.24) 0.55 (0.52) 30 (35) 21 (23)
35 2 2.92 0.05 -
81 1 48 -
316 (231) 94 (70) 7.18 (7.22) 2.14 (2.19) 52 (46) 63 (58)
-
3 0 2 -
-
-
-
(6)
-
(8)
All Atoms
29 6 3.22 0.67 5 (6) 4 (6)
(d) Thymine DNA Type
Contact Category
A
B
02
04
N [4.001 “3.201 n [4.00] n [3.20] f i4.001 f 13.201
3 1 0.60 0.20
4 0 0.80
5
8 0
N[4.00] “3.201 n [4.00] n[3.20] f [4.001 f 13.201
28 17 0.80 0.49 49 57
3
-
23 8 0.66 0.23 47 36
Me 4 1 0.80 0.20 5 11
51 5 1.46 0.14 65 56
N1, C2, N3 C4, C5, C6 0 0 -
All Atoms 11 2 2.20 0.40 4 3
150 32 4.29 0.91 54 48
730
SCHNEIDER, COHEN, AND BERMAN
Table 111 (Continued from the previous page.) ~~~
~~~
~~
~
~~
~
~~
(d) Thymine
Z
U
“4.001 “3.201 n [4.00] n [3.20] f 14.001 f [3.201
4 0 1.00 0.00 7 0
8 4 2.00 1.00 16 18
“4.001 N [ 3.201 n [4.00] nt3.201 f l4.001 f [3.201
22 12 2.75 1.50 39 40
14 10 1.75 1.25
29 45
7 0 1.75 0.00 9 0
8 0 10 -
16 3 2.00 0.38 21 33
38 4 42 -
27
4 6.75 1.00 10 6 90 29 11.25 3.63 32 43
a For each base atom in each DNA type, three measures of local hydration are shown: “ d ] , the total number of contacts I d A between the base atom and water; n [ d ] ,the average number of contacts ~d A per base between the base atom and water; f [ d ] , percent of all contacts
SYNOPSIS
We present a systematic analysis of water structure around nucleic acid bases. We have examined 28 crystal structures of oligonucleotides, and have studied the patterns of water around the four bases, guanine, cytosine, adenine, and thymine. The geometries of water positions were calculated up to 4.00 A from base atoms. We have found conformationdependent differences in both the geometry and extent of hydration of the bases.
INTRODUCTION Ever since Franklin and Gosling1examined the first fibers of DNA, it has been known that relative humidity and ionic strength affect the conformation of DNA. Although there have been many experimental and theoretical studies on DNA hydration (for reviews see Refs. 2-8), the role of water in DNA conformational transitions is not as yet understood. In this paper, we examine the question of how the organization of water molecules differs around DNA molecules with different conformations. There are a t least three different classes of water molecules around DNA molecule^.^ The first layer is impermeable to ions; the second has fast exchange of water molecules and ions with bulk water, and is only partially ordered. The third layer is bulk solvent. Thermodynamic measurements, as well as statistical mechanics approaches, have been used to explain the dynamic behavior of water molecules and ions around DNA molecules.’O~l’ Nuclear magnetic resonance experiments have shown that amplitudes of backbone movement, as well as base movement, depend on relative humidity and temperat~re.”-’~ Although NMR and thermodynamic methods provide invaluable information about the dynamics of DNA molecules at different humidities and ionic strengths, they do not provide specific information about the positions of solvent molecules. Information about the positions of water mole-
Biopolymers, Vol. 32, 725-750 (1992) 0 1992 John Wiley & Sons, Inc.
CCC 0006-3525/92/070725-26$04.00
cules in the first and second hydration layers can be obtained using x-ray crystallography. Oligonucleotide crystals are well hydrated, with water contents of up to 50%. However, because DNA molecules can be quite flexible, the resolution of diffraction is sometimes limited, making it difficult to observe solvent molecules and ions. The positions of most water molecules are less constrained than those of covalently bound DNA atoms in crystal structures and can undergo continuous fluctuation. As a result, generally only about 25% of the water molecules are crystallographically ordered in nucleic acid crystals. Notwithstanding these drawbacks, highly organized water molecules have been observed in many nucleotide structure^.'^^'^ Several papers4,5,s,’9-21 discuss water bridges in representative structures, as well as the relationship between DNA polymorphism in crystals and their different water structures. In one case, an attempt is made to quantitate hydration for different DNA conformational types by comparing the number of contacts between water molecules, base atoms, and backbone atoms in representative structures of the A-, B-, and Z-conformational classes. Another studyz0attempts to relate phosphate-phosphate distances in different DNA conformations to differences in hydration, proposing that the “economy of hydration” is the driving force in the B to A transition. Although this is an intuitively appealing concept, its validity has not been substantiated in newer experimental result^.^ In analyses of the solvent-accessible surfaces of nucleic acid structures, 22,23 the differences between solvent-accessible surfaces of A- and B-DNA type helices are shown to be surprisingly small. 726
726
SCHNEIDER, COHEN, AND BERMAN
Table I The structures Included in this Study Listed by Conformational Typea Resolution NO. PDB
NDB ADDBOl ADJ022 ADH007 ADH024 ADH008
A A A A A
2 1 2
6 lBNA BDLOOl 7 1DN9 BDL007 8 2BNA BDLOO2 9 3BNA BDLB03 10 4BNA BDLB04 11 3DNB BDJ008 12 4DNB BDLB13 13 1D25 BDJB27 14 1D28 BDL028
B B B B B B B B B
2 2 2 2 2 1 2
ZDFOO2 ZDFB03 ZDFB04 ZDFBl2 ZDD015 ZDFOOl ZDFBll ZDBO2O ZDFB21
Z
2 2 2 2 2 2 2 2 2
UDPOll UDDOO6 UDB004 UDB005 UDB007
U U U U U
1 2 3 4 5
lANA 1D13 3ANA 5ANA 9DNA
15 16 17 18 19 20 21 22 23
lDCG 1DN4 1DN5 lDNF lZNA 2DCG
24 25 26 27 28
1D16
-
1D24 -
(A)
R
C51CCGG ACCGGCCGGT GGGATCCC GTACGTAC GCCCGGGC
2.0 2.0 2.5 2.25 1.8
16.5 18.0 16.6 18.4 17.1
CGCGAATTCGCG CGCATATATGCG CGCGAATTCGCG CGCGAATTCSB‘CGCG CGCGAATTCSB’CGCG CCAAGATTGG CGCGA~~~~ATTCGCG CCAGGCCTGG CGTGAATTCACG
1.9 2.2 2.7 3.0 2.3 1.3 2.0 1.6 2.7
CGCGCG
1.o
C 5 B r c CSBrcGCSBr ~ CG C5Br C5Brc~C5Brc~
1.6 1.4 1.5 1.5 0.9 1.3 0.85 1.9
Type Chain
Z Z
Z Z Z Z
Z Z
1 1
1
2
1 1 1
2 1
Sequence
CG
CGCGCSFUG CGCG CGCGCG CC~NH~ACGTG CG CGCO~M~GCG CGCGCGTTTTCGCGCG ATAT CG CG TT
2.1 1.04 0.91 0.86 1.14
W
+ ion
W Contacts
Ref.
34
27 31 12 24 19
74 41 32 37 53
30 31 32 33 34
17.8 18.7 15.1 17.3 21.6 18.5 16.9 16.0 17.0
80 43 83 44 114 69+ 3 87 41 2 85
54 18 41 18 55 57 42 49 48
95 33 85 38 116 121 93 80 99
26 35 36 17, 37 17,37 38 39 40 41
13.5 13.3 12.5 17.2 21.0 14.0 21.7 13.6 19.0
84
70 54 61 58 55 55 62 15 45
159 114 143 94 109 120 146 38 104
42 18 18 43 44 45 46 47 48
31 36 6 13 11
79 78 16 37 31
49 50 51 52 53
20.0 15.3 6.0 4.1 13.1
86 36 9 52
+1
+
+4 61 83
+1 74 + 2 83 + 1 13 + 2 58
84
60 70 42 3 7 15
+1 +1 +4
a For each structure the Brookhaven Protein Database name (PDB) and the Nucleic Acid Database (NDB) name are given. Also listed are the number of chains in the asymmetric unit (Chain), sequence of one strand (Sequence), crystallographic resolution of the structure determination (Resolution), crystallographic residual index (R), total number of refined positions of water molecules and ions in the asymmetric unit (W ion), number of water molecules interacting with the structure’s bases, counted separately for each base (W), number of contacts between the structure’s base atoms and water molecules (Contacts), and the bibliographic reference for the structure (Ref.).
+
Several theoretical studies have been done in attempts to account for nucleic acid hydration. Molecular dynamics methods have successfully ~ i m u l a t e d the ~ ~ ,structure ~~ and dynamics of the dCpG /proflavine complex l5 and the hydration around the dodecamer d ( CGCGAATTCGCG)z.269z7 The dodecamer simulationz5 showed an ordered water pattern in the minor groove corresponding to the “spine of hydration” observed in the crystal s t r ~ c t u r e . In ’ ~ another molecular dynamics study, the hydration of a B-DNA decamer structure, ( dCCAACGTTGG)z,z9 was simulated. In agreement with the experimental x-ray structure of the decarner,” the authors revealed two types of minor groove hydration and proposed that the positions of water oxygens in the minor groove depend primarily on groove width rather than base sequence.
In general, a great deal of attention has been focused on descriptions of water bridges and other networks within nucleic acid structures in the known conformational classes. No study, so far, has systematically placed all available crystal structures into a common framework where hydration could be quantitatively examined in terms of number of water-nucleic acid contacts as well as in terms of the geometry of contacts. As the number of known oligonucleotide structures is now quite large, it is timely to present a comprehensive analysis. In this paper, we analyze the hydration of bases from single crystals of oligodeoxynucleotides(DNA) whose coordinates are available as of 1991. The number of these structures was sufficient to discuss hydration of the bases in terms of a number of contacts between water molecules and base atoms, and
727
HYDRATION OF DNA BASES
Table I1 Number of Water Molecules Lying Closer Than 4.00 and Number of Their Contacts to the Base Atoms“ Base
A
G
A-DNA
B-DNA
2-DNA
U-DNA
All Types
Structures Bases Waters Contacts Contacts/atom Fraction
3 5 12 19 0.38 6.8%
9 36 76 182 0.50 64.8%
1 2 14 35 1.59 12.5%
1 2 17 45 2.25 16.0%
14 45 119 281
Structures Bases Waters Contacts Contacts/atom Fraction
5 20 47 126 0.57 11.6%
9 59 119 244 0.38 22.5%
9 46 286 639 1.26 58.8%
3 9 27 77 0.78 7.1%
26 134 479 1086
9 (7) 44 (32) 156 (109) 316 (231) 0.87 (0.90) 51.6% (45.9%)
3 9 17 29 0.40 4.7% (5.8%)
26 (24) 131 (113) 319 (258) 612 (503)
3 8 36 90 1.25 32.4%
17 52 149 278
C (Unmodified) Structures Bases Waters Contacts Contacts/atom Fraction
5 (5) 9 (9) 20 (18) 58 (54) 45 (36) 101 (96) 81 (68) 186 (175) 0.50 (0.47) 0.43 (0.41) 13.2% (13.5%) 30.3% (34.8%)
T
3 5 9 11 0.24 4.0%
Structures Bases Waters Contacts Contacts/atom Fraction
All bases
A from Bases
Structures Bases Waters Contacts Contacts/atom
5 50 113 237 0.50
9 35 86 150 0.48 54.0% 9 188 382 762 0.43
2 4 18 27 0.75 9.7% 9 96 474 1017 1.09
5 28 97 241 0.92 ~~
-
100.0%
-
100.0%
-
100% (100%)
-
100.0% 28 362 1066 2257 -
For each base type in A-, B-, Z-, and U-DNA conformations are listed number of analyzed structures (Structures), number of bases in these structures (Bases), number of water molecules closer than 4.00 A to any atom in these bases (Waters), number of contacts between these water molecules and the base atoms (Contacts),average number of contacts per base atom (Contacts/atom), and fraction of all contacts that fall in a particular conformation (Fraction). Since each base was analyzed separately and one water molecule can interact with several bases, the number of water molecules listed under “All Bases” is higher than the actual number of interacting water molecules. The number of contacts is larger than the number of water molecules since one water molecule can form contacts to more than one base atom. a
in terms of positions of water molecules relative to the bases. Both views reveal significant differences among different DNA conformations and different base types.
METHODS Twenty-eight structures from the Nucleic Acid Data Bank5* (NDB) containing 362 bases were used in this study (see Table I for a listing of analyzed structures, Refs. 17,18,26,30-53). A structure was included in this analysis if it met the following cri-
teria: ( a ) the structure was determined using single crystal x-ray crystallography; ( b ) the molecule is a deoxynucleotide with at least two bases in a chain; ( c ) the molecule is not complexed with other molecules other than counterions; and ( d ) the coordinates for both nucleotide and solvent are publicly available. Our approach extended that of a study” that compared hydration of mononucleotides and dinucleotides. Coordinates of base and solvent atoms of oligonucleotides were retrieved from the Nucleic Acid Data Bank.54Contacts between base atoms and solvent molecules were calculated for each base sepa-
Table 111 Quantitative Measures of Hydration by Base Atom and DNA Type (a) Guanine DNA
Twe A
B
Z
U
Contact Category
N2
“4.001 N [3.201 n (4.001 n [3.20] f [4.001 f t3.201
06
N7
19 4 0.95 0.20 11 9
11 3 0.55 0.15 23 30
22 13 1.10 0.65 13 15
26 9 1.30 0.45 11 12
14 1 0.70 0.05 7 5
“4.001 N [3.201 n [4.00] n [3.20] f [4.001 f 13.201
30 2 0.51 0.03 18 4
13 6 0.22 0.10 28 60
43 18 0.73 0.31 26 21
52 21 0.88 0.36 18 28
49 4 0.83 0.07 24 21
57 0 -
N [4.00] “3.201 n [4.00] n [3.20] f t4.001 f 13.201
116 39 2.52 0.85 69 85
23 1 0.50 0.02 49 10
87 45 1.89 0.98 52 52
139 41 3.02 0.89 59 54
121 12 2.63 0.26 60 63
150 3
N(4.001 “3.201 n [4.00] n (3.201 f [4.001
4 1 0.44 0.11 2 2
14 10 1.56 1.11 8 12
18 5 2.00 0.56 8 7
19 2 2.11 0.22 9 11
22 0
fwol
0 0 -
-
0 0
C8
N1, C2, C4 C5, C6, N9
N3
34 2 -
13 -
-
22 -
-
57 -
-
8 -
All Atoms 126 32 6.30 1.60 12 13 244 51 4.14 0.86 23 21 639 138 13.89 3.00 59 58 77 18 8.56 2.00 7 7
(b) Adenine DNA Twe
Contact Category
A
“4.001 “3.201 n [4.00] nt3.201
B
Z
N1, C4, C5, C6, N9
c2
N3
N6
N7
C8
3 .2 0.60 0.40 8 8
5 0 1.00 0.00 10 0
3 1 0.60 0.20 6 5
2 0 0.40 0.00 5
-
f 14.001 f [3.201
4 1 0.80 0.20 10 14
-
-
“4.001 N [3.20] n [4.00] n [3.20] f [4.001 f P.201
26 6 0.72 0.17 67 86
28 19 0.78 0.53 76 79
29 8 0.81 0.22 59 62
31 15 0.86 0.42 60 68
28 3 0.78 0.08 68
37 2
64
-
-
“4.001 “3.201 n [4.00] n [3.20] f [4.001 f i3.201
2 0 1.00 0.00 5 0
2 0 1.00 0.00 5 0
5 2 2.50 1.oo 10 15
8 1 4.00 0.50 15 5
5 1 2.50 0.50 12
11 1
19
-
-
2 0 -
3
-
-
All Atoms 19 4 3.80 0.80 7 6 182 53 5.06 1.47 65 73 35 5 17.50 2.50 13 7
Table I11 (Continued from the previous page.) (b) Adenine
U
“4.001 “3.201 n[4.00] n [3.20] f ~4.001 f 13.201
7 0 3.50 0.00 18 0
10 3 5.00 1.50 20 23
4 3 2.00 1.50 11 13
10 5 5.00 2.50 19 23
6 0 3.00
-
0.00 15 -
14 -
8 0
45 11 22.50 5.50 16 15
(c) Cytosineb DNA Type
Contact Category
02
N4
c5
Br or I
A
“4.001 “3.201 n [4.00] n [3.20] f [4.00] f l3.201
16 (15) 5 (5) 0.80 (0.83) 0.25 (0.28) 13 (15) 7 (9)
19 (17) 5 (5) 0.95 (0.94) 0.25 (0.28) 13 (13) 9 (10)
18 (16) 5 (5) 0.90 (0.89) 0.25 (0.28) 14 (13) 36 (38)
6 0 3.00
“4.001 N [3.20] n [4.00] n [3.20] f [4.00] f L3.201
15 6 0.26 0.10 12 8
53 19 0.91 0.33 36 33
(52) (19) (0.96) (0.35) (40) (38)
53 (52) 6 (5) 0.91 (0.96) 0.10 (0.09) 41 (41) 43 (38)
3 1 0.75 0.25
z
“4.001 “3.201 n [4.00] n [ 3.201 f[4.00] f[3.20]
82 (60) 58 (44) 1.86 (1.88) 1.32 (1.38) 67 (62) (80) 82
68 (51) 31 (23) 1.55 (1.60) 0.71 (0.72) 46 (40) 53 (46)
50 (50) 2 (2) 1.14 (1.56) 0.05 (0.06) 39 (40) 14 (15)
U
“4.001 “3.201 n [4.00] n [3.20]
B
f t4.001 fw o l
(13) (4) (0.24) (0.07) (13) (7)
9 2 1.00 0.22 7 3
8 1 0.89 0.11
9 3 1.00 0.33 (9) (4)
6 5
(7) (6)
6 7
N1, C2, N3 C4, C6 22 1 13 -
81 (68) 16 (16) 4.05 (3.78) 0.80 (0.89) 13 (14) 11 (13)
-
62 0 37 -
186 (175) 32 (28) 3.21 (3.24) 0.55 (0.52) 30 (35) 21 (23)
35 2 2.92 0.05 -
81 1 48 -
316 (231) 94 (70) 7.18 (7.22) 2.14 (2.19) 52 (46) 63 (58)
-
3 0 2 -
-
-
-
(6)
-
(8)
All Atoms
29 6 3.22 0.67 5 (6) 4 (6)
(d) Thymine DNA Type
Contact Category
A
B
02
04
N [4.001 “3.201 n [4.00] n [3.20] f i4.001 f 13.201
3 1 0.60 0.20
4 0 0.80
5
8 0
N[4.00] “3.201 n [4.00] n[3.20] f [4.001 f 13.201
28 17 0.80 0.49 49 57
3
-
23 8 0.66 0.23 47 36
Me 4 1 0.80 0.20 5 11
51 5 1.46 0.14 65 56
N1, C2, N3 C4, C5, C6 0 0 -
All Atoms 11 2 2.20 0.40 4 3
150 32 4.29 0.91 54 48
730
SCHNEIDER, COHEN, AND BERMAN
Table 111 (Continued from the previous page.) ~~~
~~~
~~
~
~~
~
~~
(d) Thymine
Z
U
“4.001 “3.201 n [4.00] n [3.20] f 14.001 f [3.201
4 0 1.00 0.00 7 0
8 4 2.00 1.00 16 18
“4.001 N [ 3.201 n [4.00] nt3.201 f l4.001 f [3.201
22 12 2.75 1.50 39 40
14 10 1.75 1.25
29 45
7 0 1.75 0.00 9 0
8 0 10 -
16 3 2.00 0.38 21 33
38 4 42 -
27
4 6.75 1.00 10 6 90 29 11.25 3.63 32 43
a For each base atom in each DNA type, three measures of local hydration are shown: “ d ] , the total number of contacts I d A between the base atom and water; n [ d ] ,the average number of contacts ~d A per base between the base atom and water; f [ d ] , percent of all contacts
