I Textbook Errors, 727 Michael W. Davidson ono W. David Wilson'

Georg o Srote Un vers t y I Strand Polarity: Antiparallel Atlanta, Georgio 30303 I Molecular lmteractions in Nucleic Acids

Polynucleotide chains are unbranched polymers formed by 3,,5'-phosphdiester bridges between adjacent nucleo- tides. A single stranded polynucleotide has a free 5' ter- minus and a free 3' terminus on the rihose (or deoxyri- hose) phosphate backbone. When two such complementa- ry 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 polynu- cleotide 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 mol- ecule. 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 co- don-anticodon, but all naturally occurring douhle helical nucleic acid molecular segments involve antiparallel in- *o-o"+;",."

Opposite strand polarity is the type of molecular recog- nition found to occur during replication, transcription, co- don-anticdon interactions during translation, and in syn- thetic 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 analy- sis of DNA fibers in the B form indicated a two-fold rota- tional axis perpendicular to the fiber axis (4). X-ray stud- ies 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 associates 17) have conducted nearest neiehbor - - ~ - ~ ~-~ ~ ~ , ,

nucleotide frequency analysis on DNA synthesized in uitm and have nrovided strone sun~ort ine evidence for ~ ~ - .. opposite polarity between complementary DNA strands in the douhle helix. Extension of the nearest neighbor analy- sis to messenger RNA indicates that an an6parallel ar- rangement occurs between the messenger and its compli- mentary DNA template during transcription (8, 9). Evi- dence 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 col- umns suitable for puhlication directly should be sent with as many details as possible, and particularly with reference to mod- em 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 5'-pUpGpGpCpUpGp- 3'

tRNA ApCpC GpApC

1 ' I (pep $leu

Transcription of messenger RNA (rnRNA) occurs utilizing DNA strand two (DNA 2) as a template. The two mRNA trinucleotide genetic code- words depicted will be recognized by two transfer RNA RRNA) mole- cules, one of Which carries tryptophan (shown here with the growing peptide chain esterified to the tRNA 3' terminus) and occupies the "pep- tidvi 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 an- tioarallel interactions occur between the two ComDlementarV DNA strands, between the mRNA molecule and its template (DNA 2). and be- tween mRNA and the anticodon sequencesot the two tRNA molecules.

From results of nucleotide sequence analysis of yeast al- any1 transfer RNA, Holley suggested that large intramo- lecular 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 pos- sess 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 co- workers have recently reported diffraction data on the so- dium 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 ex- hibit Watson and Crick base pairing.

The sequence and polarity of all sixty-four trinucleo- tides which comprise the genetic code have been deter- mined (17, 18). As each new transfer RNA species has been sequenced, i t has been found that a trinucleotide ex- ists in the proposed anticodon region which could bind in a complementary (in accordance with the wobble hypothe- sis, 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 po- larity 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 im- plications of antiparallel interactions for molecular biolo- gy 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 mole- cule into messenger RNA, and finally translation of this encoded information from messenger RNA into a peptide chain through codon-anticodon interactions at the ribo- some. No parallel interactions have been found in natu- rally occurring double helical polynucleotides. This, of course, includes codon-anticodon pairing and students' at- tention should be drawn to this fact and any ambiguities about parallel interactions clarified.

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(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. ,anda ;ed . , ~cience. Is5,435(lk9741.

(15) Rosenbq , 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 Sp-

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324 / Jownal o f Chemical Education