Michael W. Davidson ono W. David Wilson' Georg o Srote Un vers t y
Atlanta, Georgio 30303
II
I
Textbook Errors, 727
Strand Polarity: Antiparallel Molecular lmteractions in Nucleic Acids
Polynucleotide chains are unbranched polymers formed by 3,,5'-phosphdiester bridges between adjacent nucleotides. A single stranded polynucleotide has a free 5' terminus and a free 3' terminus on the rihose (or deoxyrihose) phosphate backbone. When two such complementary strands interact to form a double helix, the strands could he oriented such that the two free 3' terminals are adjacent to each other a t the same end of the double helix. This is defined as a parallel interaction and polynucleotide strands bonded as such are said to have the same polarity. An antiparallel (opposite polarity) interaction would possess a douhle helical structure with one free 3' terminus and one free 5' terminus a t each end of the molecule. The illustrations in many modem biochemistry textbwks depicting codon-anticodon base pairing indicate that these interactions occur with parallel polarity. There is now, however, considerable evidence that not only codon-anticodon, but all naturally occurring douhle helical nucleic acid molecular segments involve antiparallel in*o-o"+;",."
Opposite strand polarity is the type of molecular recognition found to occur during replication, transcription, codon-anticdon interactions during translation, and in synthetic polynucleotides of random sequence (1): In their proposal on the secondary structure of deoxyribonucleic acid (DNA), Watson and Crick (2,3) postulated that the two complementary strands of the douhle helix should be oriented in an antiparallel manner. Their reasoning was based on the fact that data from X-ray diffraction analysis of DNA fibers in the B form indicated a two-fold rotational axis perpendicular to the fiber axis (4). X-ray studies on DNA in both the A and C forms (5, 6) showed that these species, which differ from the B form in the degree of hydration, also possess a similar dyad axis. Komherg and -his 17) - ~ -associates ~-~ , , have conducted nearest neiehbor nucleotide frequency analysis on DNA synthesized in uitm and have nrovided strone s u.. n ~ o r t i n eevidence for opposite polarity between complementary DNA strands in the douhle helix. Extension of the nearest neighbor analysis to messenger RNA indicates that an an6parallel arrangement occurs between the messenger and its complimentary DNA template during transcription (8, 9). Evidence for opposite strand polarity in DNA douhle helices has also been provided by complementary polynucleotide sequence analysis (10). ~
~
~
~
~
-
Suggestions of material suitable for this column and guest columns suitable for puhlication directly should be sent with as many details as possible, and particularly with reference to modem textbooks, to W. H. Eherbardt, School of Chemistry, Georgia Institute of Technology, Atlanta, Georgia 30332. Since the purpose of this column is to prevent the spread and continuation of errors and not the evaluation of individual texts, the sources of e m s discussed will not be cited. In order to be presented, an error must occur in at least two independent recent standard hooks. 1 Author to whom correspondence should he addressed.
DNA 1
~'-PTPGPGPCPTPGP- 3'
DNA 2
3' -PAPCPCPGPAPCP-~'
mRNA tRNA
5'-pUpGpGpCpUpGp-
3'
ApCpC GpApC
1'
(pep
$leu
I
Transcription of messenger RNA (rnRNA) occurs utilizing DNA strand two (DNA 2) as a template. The two mRNA trinucleotide genetic codewords depicted will be recognized by two transfer RNA RRNA) molecules, one of Which carries tryptophan (shown here with the growing peptide chain esterified to the tRNA 3' terminus) and occupies the "peptidvi site" ot the ribosome adiacent to the 5' end of the messenger. The other tRNA molecule is iocaled nearer the 3' terminus of mRNA in the "amino-acyl" ribosomal binding site and has leucine, which will be the next amino acid added to the peptide.-bonded at its 3' end. Note that antioarallel interactions occur between the two ComDlementarV DNA strands, between the mRNA molecule and its template (DNA 2). and between mRNA and the anticodon sequencesot the two tRNA molecules.
From results of nucleotide sequence analysis of yeast alany1 transfer RNA, Holley suggested that large intramolecular antiparallel douhle helical regions could exist in these species (11). More than 30 transfer RNA sequences have now been delineated, and all have been found to possess similar regions of possible antiparallel douhle helix (12). Single crystal X-ray analysis of' yeast phenylalanyl transfer RNA has shown that this molecule does indeed have the expected regions of opposite polarity in double helical confoimation (i3,14). X-Ray diffraction studies on large double helical DNA or RNA molecules have been hampered by the difficulty of obtaining crystals with these compounds. Rich and coworkers have recently reported diffraction data on the sodium salts of two dinucleoside phosphates, adenosyl-3', 5'-uridine phosphate (15) and guanylyl-3',5'-cytidine phosphate (161, demonstrating that these compounds exist in right-handed antiparallel double helices which exhibit Watson and Crick base pairing. The sequence and polarity of all sixty-four trinucleotides which comprise the genetic code have been determined (17, 18). As each new transfer RNA species has been sequenced, i t has been found that a trinucleotide exists in the proposed anticodon region which could bind in a complementary (in accordance with the wobble hypothesis, cf. (19))and antiparallel manner to the codon specified for that particular amino-acyl transfer RNA molecule. Strong and direct evidence for interactions of opposite polarity between codon-anticodon sequences is provided by ribosomal affinity binding studies of isolated anticodon regions of transfer RNA with specific codon trinucleotides (20,21). Volume 52, Number 5, May 1975 / 323
In the early days of investigations into the genetic code, little was known about transfer RNA in general and the anticodon region in particular. Much has been learned about all nucleic acids in recent years, and the broad implications of antiparallel interactions for molecular biology and biochemistry can be seen best from the figure. This figure shows that opposite strand polarity is involved in all aspects of the transfer of genetic information from DNA replication, transcription of the genetic DNA molecule into messenger RNA, and finally translation of this encoded information from messenger RNA into a peptide chain through codon-anticodon interactions at the ribosome. No parallel interactions have been found in naturally occurring double helical polynucleotides. This, of course, includes codon-anticodon pairing and students' attention should be drawn to this fact and any ambiguities about parallel interactions clarified. Literature Cited Ill Mandelstam. J., and MeQudlen. K.. "Bbehemistry of Baetuial Gmldh", 2nd Ed.. John Wiley and Sons, Ine.. New York, 1973.
324 / Jownal o f Chemical Education
i l265 o g y(1970). , (61 Amotf, S.. R o m s ~ i n B i o p h ~ ~ i i i i n d M ~ I ~ u I ~ B i21. J., Kaiser, A.O., and Kornbem, A., J. B i d Chem., 236.864 (1961). (7) J-, (8) Weiss, S. B., and Nakamoto, T., Pme. Not. Acod S u . U.B.A., 47,1403 (1961). (9) Bautz, E. K. F., and Heding, L., Blorhrm. 3,1010 (19%). (10) char^^, E.. Buchoviez. J.. T u r k , H.. and S h a ~ i m ,H, S.. N o w , ZDE, 115 (1965). (11) Haliey, R. W., Apgar, J.. Everett, G. A,, Madison, J. T.. Marmine, M., M s d l . S. H., PensuiEh, J. R., and Zsmin, A,, Science, 147,1462 (19651. (12) Venksloin. T. V.. "The Primary Strveture of Transfer RNA." 1st Ed., Plenum Press, New Yor*,1973. (13) Suddath, F. L., Quigley. G.J.. McPhe~son.A., Sneden, D., Kim, J. J., Kim, S. H.,and Rich, A, Nolurp. 248.20 (19741. 1141 Kim. S. H..Suddath. F. L..Quieiev. G. J.. McPherm. A,. Sussman.. J. L... Wan=. A.H. J.. &man, N. C . , a n d a ; e d . , ~cience.Is5,435(lk9741. (15) R o s e n b q , J . M.. Seeman. N. C., Kim, J. J. P.. Suddath. F. L..Nicholas. H. B., and Rich. A..Noture, 243.150 (1973). H6) Day, R. 0 ,Seeman, N. C., Rosenharg, J. M., and Rich. A,. Pmc. Not. Aeod. Sci. USA.. 70.849 (1973). (171 8011. D., Cherayi1,J.D.. end8ock.R.M.. J Mol. Blol.. 29, 97(1967). (181 "The Genetic Code". Cold S p e w Harbor Sympoaio on avant. Biol.. Val. 31 (1966). (19) C"ek, F. H. C . , J Ma1 Biol., 19,548 1966). (20) Clark, E.F. C.,Duh, S.K., andMarcker, K.A.,Nofurr, 219,484(1968l. (21) Dube, S. K.. Rudland, P. S., Clark, B. F. C.. and Marcker, K. A,. Cold SpHorbor Symposioon Quonl. Biol., 34,161 (1969).
-.
Atlanta, Georgio 30303
II
I
Textbook Errors, 727
Strand Polarity: Antiparallel Molecular lmteractions in Nucleic Acids
Polynucleotide chains are unbranched polymers formed by 3,,5'-phosphdiester bridges between adjacent nucleotides. A single stranded polynucleotide has a free 5' terminus and a free 3' terminus on the rihose (or deoxyrihose) phosphate backbone. When two such complementary strands interact to form a double helix, the strands could he oriented such that the two free 3' terminals are adjacent to each other a t the same end of the double helix. This is defined as a parallel interaction and polynucleotide strands bonded as such are said to have the same polarity. An antiparallel (opposite polarity) interaction would possess a douhle helical structure with one free 3' terminus and one free 5' terminus a t each end of the molecule. The illustrations in many modem biochemistry textbwks depicting codon-anticodon base pairing indicate that these interactions occur with parallel polarity. There is now, however, considerable evidence that not only codon-anticodon, but all naturally occurring douhle helical nucleic acid molecular segments involve antiparallel in*o-o"+;",."
Opposite strand polarity is the type of molecular recognition found to occur during replication, transcription, codon-anticdon interactions during translation, and in synthetic polynucleotides of random sequence (1): In their proposal on the secondary structure of deoxyribonucleic acid (DNA), Watson and Crick (2,3) postulated that the two complementary strands of the douhle helix should be oriented in an antiparallel manner. Their reasoning was based on the fact that data from X-ray diffraction analysis of DNA fibers in the B form indicated a two-fold rotational axis perpendicular to the fiber axis (4). X-ray studies on DNA in both the A and C forms (5, 6) showed that these species, which differ from the B form in the degree of hydration, also possess a similar dyad axis. Komherg and -his 17) - ~ -associates ~-~ , , have conducted nearest neiehbor nucleotide frequency analysis on DNA synthesized in uitm and have nrovided strone s u.. n ~ o r t i n eevidence for opposite polarity between complementary DNA strands in the douhle helix. Extension of the nearest neighbor analysis to messenger RNA indicates that an an6parallel arrangement occurs between the messenger and its complimentary DNA template during transcription (8, 9). Evidence for opposite strand polarity in DNA douhle helices has also been provided by complementary polynucleotide sequence analysis (10). ~
~
~
~
~
-
Suggestions of material suitable for this column and guest columns suitable for puhlication directly should be sent with as many details as possible, and particularly with reference to modem textbooks, to W. H. Eherbardt, School of Chemistry, Georgia Institute of Technology, Atlanta, Georgia 30332. Since the purpose of this column is to prevent the spread and continuation of errors and not the evaluation of individual texts, the sources of e m s discussed will not be cited. In order to be presented, an error must occur in at least two independent recent standard hooks. 1 Author to whom correspondence should he addressed.
DNA 1
~'-PTPGPGPCPTPGP- 3'
DNA 2
3' -PAPCPCPGPAPCP-~'
mRNA tRNA
5'-pUpGpGpCpUpGp-
3'
ApCpC GpApC
1'
(pep
$leu
I
Transcription of messenger RNA (rnRNA) occurs utilizing DNA strand two (DNA 2) as a template. The two mRNA trinucleotide genetic codewords depicted will be recognized by two transfer RNA RRNA) molecules, one of Which carries tryptophan (shown here with the growing peptide chain esterified to the tRNA 3' terminus) and occupies the "peptidvi site" ot the ribosome adiacent to the 5' end of the messenger. The other tRNA molecule is iocaled nearer the 3' terminus of mRNA in the "amino-acyl" ribosomal binding site and has leucine, which will be the next amino acid added to the peptide.-bonded at its 3' end. Note that antioarallel interactions occur between the two ComDlementarV DNA strands, between the mRNA molecule and its template (DNA 2). and between mRNA and the anticodon sequencesot the two tRNA molecules.
From results of nucleotide sequence analysis of yeast alany1 transfer RNA, Holley suggested that large intramolecular antiparallel douhle helical regions could exist in these species (11). More than 30 transfer RNA sequences have now been delineated, and all have been found to possess similar regions of possible antiparallel douhle helix (12). Single crystal X-ray analysis of' yeast phenylalanyl transfer RNA has shown that this molecule does indeed have the expected regions of opposite polarity in double helical confoimation (i3,14). X-Ray diffraction studies on large double helical DNA or RNA molecules have been hampered by the difficulty of obtaining crystals with these compounds. Rich and coworkers have recently reported diffraction data on the sodium salts of two dinucleoside phosphates, adenosyl-3', 5'-uridine phosphate (15) and guanylyl-3',5'-cytidine phosphate (161, demonstrating that these compounds exist in right-handed antiparallel double helices which exhibit Watson and Crick base pairing. The sequence and polarity of all sixty-four trinucleotides which comprise the genetic code have been determined (17, 18). As each new transfer RNA species has been sequenced, i t has been found that a trinucleotide exists in the proposed anticodon region which could bind in a complementary (in accordance with the wobble hypothesis, cf. (19))and antiparallel manner to the codon specified for that particular amino-acyl transfer RNA molecule. Strong and direct evidence for interactions of opposite polarity between codon-anticodon sequences is provided by ribosomal affinity binding studies of isolated anticodon regions of transfer RNA with specific codon trinucleotides (20,21). Volume 52, Number 5, May 1975 / 323
In the early days of investigations into the genetic code, little was known about transfer RNA in general and the anticodon region in particular. Much has been learned about all nucleic acids in recent years, and the broad implications of antiparallel interactions for molecular biology and biochemistry can be seen best from the figure. This figure shows that opposite strand polarity is involved in all aspects of the transfer of genetic information from DNA replication, transcription of the genetic DNA molecule into messenger RNA, and finally translation of this encoded information from messenger RNA into a peptide chain through codon-anticodon interactions at the ribosome. No parallel interactions have been found in naturally occurring double helical polynucleotides. This, of course, includes codon-anticodon pairing and students' attention should be drawn to this fact and any ambiguities about parallel interactions clarified. Literature Cited Ill Mandelstam. J., and MeQudlen. K.. "Bbehemistry of Baetuial Gmldh", 2nd Ed.. John Wiley and Sons, Ine.. New York, 1973.
324 / Jownal o f Chemical Education
i l265 o g y(1970). , (61 Amotf, S.. R o m s ~ i n B i o p h ~ ~ i i i i n d M ~ I ~ u I ~ B i21. J., Kaiser, A.O., and Kornbem, A., J. B i d Chem., 236.864 (1961). (7) J-, (8) Weiss, S. B., and Nakamoto, T., Pme. Not. Acod S u . U.B.A., 47,1403 (1961). (9) Bautz, E. K. F., and Heding, L., Blorhrm. 3,1010 (19%). (10) char^^, E.. Buchoviez. J.. T u r k , H.. and S h a ~ i m ,H, S.. N o w , ZDE, 115 (1965). (11) Haliey, R. W., Apgar, J.. Everett, G. A,, Madison, J. T.. Marmine, M., M s d l . S. H., PensuiEh, J. R., and Zsmin, A,, Science, 147,1462 (19651. (12) Venksloin. T. V.. "The Primary Strveture of Transfer RNA." 1st Ed., Plenum Press, New Yor*,1973. (13) Suddath, F. L., Quigley. G.J.. McPhe~son.A., Sneden, D., Kim, J. J., Kim, S. H.,and Rich, A, Nolurp. 248.20 (19741. 1141 Kim. S. H..Suddath. F. L..Quieiev. G. J.. McPherm. A,. Sussman.. J. L... Wan=. A.H. J.. &man, N. C . , a n d a ; e d . , ~cience.Is5,435(lk9741. (15) R o s e n b q , J . M.. Seeman. N. C., Kim, J. J. P.. Suddath. F. L..Nicholas. H. B., and Rich. A..Noture, 243.150 (1973). H6) Day, R. 0 ,Seeman, N. C., Rosenharg, J. M., and Rich. A,. Pmc. Not. Aeod. Sci. USA.. 70.849 (1973). (171 8011. D., Cherayi1,J.D.. end8ock.R.M.. J Mol. Blol.. 29, 97(1967). (181 "The Genetic Code". Cold S p e w Harbor Sympoaio on avant. Biol.. Val. 31 (1966). (19) C"ek, F. H. C . , J Ma1 Biol., 19,548 1966). (20) Clark, E.F. C.,Duh, S.K., andMarcker, K.A.,Nofurr, 219,484(1968l. (21) Dube, S. K.. Rudland, P. S., Clark, B. F. C.. and Marcker, K. A,. Cold SpHorbor Symposioon Quonl. Biol., 34,161 (1969).
-.
