Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1981 Dec;78(12):7440–7444. doi: 10.1073/pnas.78.12.7440

First approximation of a stereochemical rationale for the genetic code based on the topography and physicochemical properties of "cavities" constructed from models of DNA.

L B Hendry, E D Bransome Jr, M S Hutson, L K Campbell
PMCID: PMC349283  PMID: 6950386

Abstract

To examine the question of whether or not the genetic code has a stereochemical basis, we used artificial constructs of the topography and physicochemical features of unique "cavities" formed by removal of the second codon base in B-DNA. The effects of base changes on the stereochemistry of the cavities are consistent with the pattern of the genetic code. Fits into the cavities of the side chains of the 20 L amino acids involved in protein synthesis can be demonstrated by using conventional physicochemical principles of hydrogen bonding and steric constraints. The specificity of the fits is remarkably consistent with the genetic code.

Full text

PDF
7440

Images in this article

7442Image
on p.7442
7443Image
on p.7443

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. AKINRIMISI E. O., TSO P. O. INTERACTIONS OF PURINE WITH PROTEINS AND AMINO ACIDS. Biochemistry. 1964 May;3:619–626. doi: 10.1021/bi00893a004. [DOI] [PubMed] [Google Scholar]
  2. Adawadkar P., Wilson W. D., Brey W., Gabbay E. J. Letter: Stereospecific interaction of dipeptide amides with DNA. Evidence for partial intercalation and bending of the helix. J Am Chem Soc. 1975 Apr 2;97(7):1959–1961. doi: 10.1021/ja00840a062. [DOI] [PubMed] [Google Scholar]
  3. Alff-Steinberger C. The genetic code and error transmission. Proc Natl Acad Sci U S A. 1969 Oct;64(2):584–591. doi: 10.1073/pnas.64.2.584. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Batchinsky A. G., Ratner V. A. A cybernetic approach to the origin of the genetic coding mechanism. II. Formation of the code series. Orig Life. 1976 Aug;7(3):229–233. doi: 10.1007/BF00926940. [DOI] [PubMed] [Google Scholar]
  5. Baxter C. S., Byvoet P. Intercalating agents as probes of the spatial relationship between chromatin components. Biochem Biophys Res Commun. 1975 Mar 3;63(1):286–291. doi: 10.1016/s0006-291x(75)80041-6. [DOI] [PubMed] [Google Scholar]
  6. Co T., Maki A. H. Effect of stacking interactions with poly(riboadenylic acid) on the triplet state properties of tryptophan. Biochemistry. 1978 Jan 10;17(1):182–186. doi: 10.1021/bi00594a027. [DOI] [PubMed] [Google Scholar]
  7. Coleman J. E., Armitage I. M. Tyrosyl-base-phenylalanyl intercalation in gene 5 protein-DNA complexes: proton nuclear magnetic resonance of selectively deuterated gene 5 protein. Biochemistry. 1978 Nov 14;17(23):5038–5045. doi: 10.1021/bi00616a028. [DOI] [PubMed] [Google Scholar]
  8. Crick F. H. The origin of the genetic code. J Mol Biol. 1968 Dec;38(3):367–379. doi: 10.1016/0022-2836(68)90392-6. [DOI] [PubMed] [Google Scholar]
  9. Dickerson R. E. Sequence and structure homologies in bacterial and mammalian-type cytochromes. J Mol Biol. 1971 Apr 14;57(1):1–15. doi: 10.1016/0022-2836(71)90116-1. [DOI] [PubMed] [Google Scholar]
  10. Dimicoli J. L., Hélène C. Interactions of aromatic residues of proteins with nucleic acid. II. Proton magnetic resonance studies of the binding of tyramine and tyrosine-containing peptides to poly(adenylic acid) and deoxyribonucleic acid. Biochemistry. 1974 Feb 12;13(4):724–730. doi: 10.1021/bi00701a014. [DOI] [PubMed] [Google Scholar]
  11. Dimicoli J. L., Hélène C. Interactions of aromatic residues of proteins with nucleic acids. I. Proton magnetic resonance studies of the binding of tryptophan-containing peptides to poly(adenylic acid) and deoxyribonucleic acid. Biochemistry. 1974 Feb 12;13(4):714–723. doi: 10.1021/bi00701a013. [DOI] [PubMed] [Google Scholar]
  12. Dunnill P. Triplet nucleotide-amino-acid pairing; a stereochemical basis for the division between protein and non-protein amino-acids. Nature. 1966 Jun 18;210(5042):1265–1267. doi: 10.1038/2101267a0. [DOI] [PubMed] [Google Scholar]
  13. Gabbay E. J., Adawadkar P. D., Wilson W. D. Stereospecific binding of diastereomeric peptides to salmon sperm DNA. Biochemistry. 1976 Jan 13;15(1):146–151. doi: 10.1021/bi00646a022. [DOI] [PubMed] [Google Scholar]
  14. Gabbay E. J., Sanford K., Baxter C. S., Kapicak L. Specific interaction of peptides with nucleic acids. Evidence for a "selective bookmark" recognition hypothesis. Biochemistry. 1973 Oct 9;12(21):4021–4029. doi: 10.1021/bi00745a001. [DOI] [PubMed] [Google Scholar]
  15. Gabbay E. J., Sanford K., Baxter C. S. Specific interaction of peptides with nucleic acids. Biochemistry. 1972 Aug 29;11(18):3429–3435. doi: 10.1021/bi00768a016. [DOI] [PubMed] [Google Scholar]
  16. Grantham R. Amino acid difference formula to help explain protein evolution. Science. 1974 Sep 6;185(4154):862–864. doi: 10.1126/science.185.4154.862. [DOI] [PubMed] [Google Scholar]
  17. Hendry L. B., Bransome E. D., Jr, Petersheim M. Are there structural analogies between amino acids and nucleic acids? Orig Life. 1981 Sep;11(3):203–221. doi: 10.1007/BF00931386. [DOI] [PubMed] [Google Scholar]
  18. Hendry L. B., Witham F. H., Chapman O. L. Gene regulation: the involvement of stereochemical recognition in DNA-small molecule interactions. Perspect Biol Med. 1977 Autumn;21(1):120–130. doi: 10.1353/pbm.1977.0018. [DOI] [PubMed] [Google Scholar]
  19. Hendry L. B., Witham F. H. Stereochemical recognition in nucleic acid-amino acid interactions and its implications in biological coding: a model approach. Perspect Biol Med. 1979 Spring;22(3):333–345. doi: 10.1353/pbm.1979.0002. [DOI] [PubMed] [Google Scholar]
  20. Hopfield J. J. Origin of the genetic code: a testable hypothesis based on tRNA structure, sequence, and kinetic proofreading. Proc Natl Acad Sci U S A. 1978 Sep;75(9):4334–4338. doi: 10.1073/pnas.75.9.4334. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Jorré R. P., Curnow R. N. The evolution of the genetic code. Biochimie. 1975;57(10):1147–1154. doi: 10.1016/s0300-9084(76)80576-7. [DOI] [PubMed] [Google Scholar]
  22. Jungck J. R. The genetic code as a periodic table. J Mol Evol. 1978 Aug 2;11(3):211–224. doi: 10.1007/BF01734482. [DOI] [PubMed] [Google Scholar]
  23. Kline E. L., Brown C. S., Bankaitis V., Montefiori D. C., Craig K. Metabolite gene regulation of the L-arabinose operon in Escherichia coli with indoleacetic acid and other indole derivatives. Proc Natl Acad Sci U S A. 1980 Apr;77(4):1768–1772. doi: 10.1073/pnas.77.4.1768. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. LENGYEL P., SPEYER J. F., OCHOA S. Synthetic polynucleotides and the amino acid code. Proc Natl Acad Sci U S A. 1961 Dec 15;47:1936–1942. doi: 10.1073/pnas.47.12.1936. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Lacey J. C., Jr, Pruitt K. M. Origin of the genetic code. Nature. 1969 Aug 23;223(5208):799–804. doi: 10.1038/223799a0. [DOI] [PubMed] [Google Scholar]
  26. Lacey J. C., Weber A. L., White W. E., Jr A model for the coevolution of the genetic code and the process of protein synthesis: Review and assessment. Orig Life. 1975 Jan-Apr;6(1-2):273–283. doi: 10.1007/BF01372416. [DOI] [PubMed] [Google Scholar]
  27. Martin N. C., Pham H. D., Underbrink-Lyon K., Miller D. l., Donelson J. E. Yeast mitochondrial tRNATrp can recognize the nonsense codon UGA. Nature. 1980 Jun 19;285(5766):579–581. doi: 10.1038/285579a0. [DOI] [PubMed] [Google Scholar]
  28. Melcher G. Stereospecificity of the genetic code. J Mol Evol. 1974;3(2):121–140. doi: 10.1007/BF01796558. [DOI] [PubMed] [Google Scholar]
  29. NIRENBERG M. W., MATTHAEI J. H. The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. Proc Natl Acad Sci U S A. 1961 Oct 15;47:1588–1602. doi: 10.1073/pnas.47.10.1588. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Nagyvary J., Fendler J. H. Origin of the genetic code: a physical-chemical model of primitive codon assignments. Orig Life. 1974 Jul-Oct;5(3):357–362. [PubMed] [Google Scholar]
  31. Nakashima T., Fox S. W. Selective condensation of aminoacyl adenylates by nucleoproteinoid microparticles (prebiotic-lysine-model system-genetic code). Proc Natl Acad Sci U S A. 1972 Jan;69(1):106–108. doi: 10.1073/pnas.69.1.106. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Nelsestuen G. L. Amino acid-directed nucleic acid synthesis. A possible mechanism in the origin of life. J Mol Evol. 1978 Jun 20;11(2):109–120. doi: 10.1007/BF01733887. [DOI] [PubMed] [Google Scholar]
  33. Pelc S. R., Welton M. G. Stereochemical relationship between coding triplets and amino-acids. Nature. 1966 Feb 26;209(5026):868–870. doi: 10.1038/209868a0. [DOI] [PubMed] [Google Scholar]
  34. Ralph R. K. A suggestion on the origin of the genetic code. Biochem Biophys Res Commun. 1968 Oct 24;33(2):213–218. doi: 10.1016/0006-291x(68)90770-5. [DOI] [PubMed] [Google Scholar]
  35. Ratner V. A., Batchinsky A. G. A cybernetic approach to the origin of the genetic coding mechanism. I. Methodological principles. Orig Life. 1976 Aug;7(3):225–228. doi: 10.1007/BF00926939. [DOI] [PubMed] [Google Scholar]
  36. Rendell M. S. A computer investigation into the origin of the code. J Am Chem Soc. 1972 Jun 14;94(12):4337–4341. doi: 10.1021/ja00767a051. [DOI] [PubMed] [Google Scholar]
  37. Rendell M. S., Harlos J. P., Rein R. Specificity in the genetic code. The role of nucleotide base-amino acid interaction. Biopolymers. 1971 Nov;10(11):2083–2094. doi: 10.1002/bip.360101106. [DOI] [PubMed] [Google Scholar]
  38. Salemme F. R., Miller M. D., Jordan S. R. Structural convergence during protein evolution. Proc Natl Acad Sci U S A. 1977 Jul;74(7):2820–2824. doi: 10.1073/pnas.74.7.2820. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Saxinger C., Ponnamperuma C. Experimental investigation on the origin of the genetic code. J Mol Evol. 1971;1(1):63–73. doi: 10.1007/BF01659394. [DOI] [PubMed] [Google Scholar]
  40. Schwarz G., Gilligan T. J., 3rd Dual-mode cooperative binding of adenosine 5'-triphosphate to poly(L-lysine). Biochemistry. 1977 Jun 28;16(13):2835–2840. doi: 10.1021/bi00632a005. [DOI] [PubMed] [Google Scholar]
  41. Thomas B. R. The origin of the genetic code. Biochem Biophys Res Commun. 1970 Sep 30;40(6):1289–1296. doi: 10.1016/0006-291x(70)90006-9. [DOI] [PubMed] [Google Scholar]
  42. Thomas P. D., Podder S. K. Specificity in protein--nucleic acid interaction: solubility study on amino acid--nucleoside interaction. FEBS Lett. 1978 Dec 1;96(1):90–94. doi: 10.1016/0014-5793(78)81069-2. [DOI] [PubMed] [Google Scholar]
  43. Toulmé F., Hélène C., Fuchs R. P., Daune M. Binding of a tryptophan-containing peptide (lysyltryptophyllysine) to deoxyribonucleic acid modified by 2-(N-acetoxyacetylamino)fluorene. Biochemistry. 1980 Mar 4;19(5):870–875. doi: 10.1021/bi00546a007. [DOI] [PubMed] [Google Scholar]
  44. Volkenstein M. V. The genetic coding of protein structure. Biochim Biophys Acta. 1966 May 19;119(2):421–424. doi: 10.1016/0005-2787(66)90204-8. [DOI] [PubMed] [Google Scholar]
  45. WOESE C. R. A nucleotide triplet code for amino acids. Biochem Biophys Res Commun. 1961 Jun 2;5:88–93. doi: 10.1016/0006-291x(61)90017-1. [DOI] [PubMed] [Google Scholar]
  46. Weber A. L., Lacey J. C., Jr Genetic code correlations: amino acids and their anticodon nucleotides. J Mol Evol. 1978 Aug 2;11(3):199–210. doi: 10.1007/BF01734481. [DOI] [PubMed] [Google Scholar]
  47. Wetzel R. Aminoacyl-tRNA synthetase families and their significance to the origin of the genetic code. Orig Life. 1978 Sep;9(1):39–50. doi: 10.1007/BF00929712. [DOI] [PubMed] [Google Scholar]
  48. Witham F. H., Hendry L. B., Chapman O. L. Chirality and stereochemical recognition in DNA-phytohormone interactions: a model approach. Orig Life. 1978 Sep;9(1):7–15. doi: 10.1007/BF00929709. [DOI] [PubMed] [Google Scholar]
  49. Woese C. R. Evolution of the genetic code. Naturwissenschaften. 1973 Oct;60(10):447–459. doi: 10.1007/BF00592854. [DOI] [PubMed] [Google Scholar]
  50. Woese C. R. On the evolution of the genetic code. Proc Natl Acad Sci U S A. 1965 Dec;54(6):1546–1552. doi: 10.1073/pnas.54.6.1546. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Woese C. R. Order in the genetic code. Proc Natl Acad Sci U S A. 1965 Jul;54(1):71–75. doi: 10.1073/pnas.54.1.71. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Woese C. R. The fundamental nature of the genetic code: prebiotic interactions between polynucleotides and polyamino acids or their derivatives. Proc Natl Acad Sci U S A. 1968 Jan;59(1):110–117. doi: 10.1073/pnas.59.1.110. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Wolfenden R. V., Cullis P. M., Southgate C. C. Water, protein folding, and the genetic code. Science. 1979 Nov 2;206(4418):575–577. doi: 10.1126/science.493962. [DOI] [PubMed] [Google Scholar]
  54. Wong J. T. A co-evolution theory of the genetic code. Proc Natl Acad Sci U S A. 1975 May;72(5):1909–1912. doi: 10.1073/pnas.72.5.1909. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Wong J. T. The evolution of a universal genetic code. Proc Natl Acad Sci U S A. 1976 Jul;73(7):2336–2340. doi: 10.1073/pnas.73.7.2336. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Zhdanov Iu A. Ob odnoi korreliatsii v geneticheskom kode. Dokl Akad Nauk SSSR. 1974 Jul 11;217(2):456–457. [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES