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. 1978 Jun;5(6):1955–1970. doi: 10.1093/nar/5.6.1955

Base pairing structure in the poly d(G-T) double helix: wobble base pairs.

T A Early, J Olmsted 3rd, D R Kearns, A G Lezius
PMCID: PMC342137  PMID: 673842

Abstract

High resolution nuclear magnetic resonance (NMR) and ethidium bromide binding studies are used to demonstrate that poly d(G-T) forms an ordered double helical structure at low temperatures (below 24 degrees C in 0.3 M NaCl) in which G and T are hydrogen bonded together in a wobble base pair hydrogen bonding scheme as proposed earlier by Lezius and Domin. Alternative hydrogen bonding schemes involving the tautomeric form of either T or G, such as have been proposed to account for mutation rates in DNA synthesis, are eliminated.

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1955

Selected References

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  1. Aktipis S., Kindelis A. Optical properties of the deoxyribonucleic acid-ethidium bromide complex. Effect of salt. Biochemistry. 1973 Mar 13;12(6):1213–1221. doi: 10.1021/bi00730a031. [DOI] [PubMed] [Google Scholar]
  2. Bittman R. Studies of the binding of ethidium bromide to transfer ribonucleic acid: absorption, fluorescence, ultracentrifugation and kinetic investigations. J Mol Biol. 1969 Dec 14;46(2):251–268. doi: 10.1016/0022-2836(69)90420-3. [DOI] [PubMed] [Google Scholar]
  3. Chan S. I., Lee G. C., Schmidt C. F., Kreishman G. P. Guanine-uracil base-pairing. Biochem Biophys Res Commun. 1972 Feb 25;46(4):1536–1543. doi: 10.1016/0006-291x(72)90782-6. [DOI] [PubMed] [Google Scholar]
  4. Crick F. H. Codon--anticodon pairing: the wobble hypothesis. J Mol Biol. 1966 Aug;19(2):548–555. doi: 10.1016/s0022-2836(66)80022-0. [DOI] [PubMed] [Google Scholar]
  5. Doerfler W., Hogness D. S. Separation of the strands of poly d-TG: AC in alkaline CsCl. J Mol Biol. 1965 Nov;14(1):237–240. doi: 10.1016/s0022-2836(65)80243-1. [DOI] [PubMed] [Google Scholar]
  6. Early T. A., Kearns D. R., Burd J. F., Larson J. E., Wells R. D. High resolution proton nuclear magnetic resonance investigation of the structural and dynamic properties of d(C15A15)-d(T15G15). Biochemistry. 1977 Feb 8;16(3):541–551. doi: 10.1021/bi00622a031. [DOI] [PubMed] [Google Scholar]
  7. Gray D. M., Ratliff R. L. Circular dichroism evidence for G-U and G-T base pairing in poly[r(G-U)] and poly[d(G-T)]. Biopolymers. 1977 Jun;16(6):1331–1342. doi: 10.1002/bip.1977.360160613. [DOI] [PubMed] [Google Scholar]
  8. Gray D. M., Tinoco I., Jr, Chamberlin M. J. The circular dichroism of synthetic ribonucleic acids and the influence of uracil on conformation. Biopolymers. 1972;11(6):1235–1258. doi: 10.1002/bip.1972.360110609. [DOI] [PubMed] [Google Scholar]
  9. Kearns D. R. High-resolution nuclear magnetic resonance investigations of the structure of tRNA in solution. Prog Nucleic Acid Res Mol Biol. 1976;18:91–149. doi: 10.1016/s0079-6603(08)60587-5. [DOI] [PubMed] [Google Scholar]
  10. Krugh T. R., Young M. A. Nuclear magnetic resonance studies of hydrogen bonded complexes of oligonucleotides in aqueous solution. I. pdG-dC and pdG-dT. Biochem Biophys Res Commun. 1975 Feb 17;62(4):1025–1031. doi: 10.1016/0006-291x(75)90425-8. [DOI] [PubMed] [Google Scholar]
  11. Ladner J. E., Jack A., Robertus J. D., Brown R. S., Rhodes D., Clark B. F., Klug A. Atomic co-ordinates for yeast phenylalanine tRNA. Nucleic Acids Res. 1975 Sep;2(9):1629–1637. doi: 10.1093/nar/2.9.1629. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Lakowicz J. R., Weber G. Quenching of fluorescence by oxygen. A probe for structural fluctuations in macromolecules. Biochemistry. 1973 Oct 9;12(21):4161–4170. doi: 10.1021/bi00745a020. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Le Pecq J. B., Paoletti C. Interaction du bromhydrate d'éthidium (BET) avec les polyribonucléotides. Applications à l'étude des réactions d'hybridation. C R Acad Sci Hebd Seances Acad Sci D. 1965 Jun 28;260(26):7033–7036. [PubMed] [Google Scholar]
  14. LePecq J. B., Paoletti C. A fluorescent complex between ethidium bromide and nucleic acids. Physical-chemical characterization. J Mol Biol. 1967 Jul 14;27(1):87–106. doi: 10.1016/0022-2836(67)90353-1. [DOI] [PubMed] [Google Scholar]
  15. Lezius A. G., Domin E. A wobbly double helix. Nat New Biol. 1973 Aug 8;244(136):169–170. doi: 10.1038/newbio244169a0. [DOI] [PubMed] [Google Scholar]
  16. Lomant A. J., Fresco J. R. Structural and energetic consequences of noncomplementary base oppositions in nucleic acid helices. Prog Nucleic Acid Res Mol Biol. 1975;15(0):185–218. doi: 10.1016/s0079-6603(08)60120-8. [DOI] [PubMed] [Google Scholar]
  17. Olmsted J., 3rd, Kearns D. R. Mechanism of ethidium bromide fluorescence enhancement on binding to nucleic acids. Biochemistry. 1977 Aug 9;16(16):3647–3654. doi: 10.1021/bi00635a022. [DOI] [PubMed] [Google Scholar]
  18. Patel D. J., Canuel L. Nuclear magnetic resonance studies of the helix-coil transition of poly (dA-dT) in aqueous solution. Proc Natl Acad Sci U S A. 1976 Mar;73(3):674–678. doi: 10.1073/pnas.73.3.674. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Patel D. J. Proton and phosphorus NMR studies of d-CpG(pCpG)n duplexes in solution. Helix-coil transition and complex formation with actinomycin-D. Biopolymers. 1976 Mar;15(3):533–558. doi: 10.1002/bip.1976.360150310. [DOI] [PubMed] [Google Scholar]
  20. Pohl F. M., Jovin T. M., Baehr W., Holbrook J. J. Ethidium bromide as a cooperative effector of a DNA structure. Proc Natl Acad Sci U S A. 1972 Dec;69(12):3805–3809. doi: 10.1073/pnas.69.12.3805. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Quigley G. J., Seeman N. C., Wang A. H., Suddath F. L., Rich A. Yeast phenylalanine transfer RNA: atomic coordinates and torsion angles. Nucleic Acids Res. 1975 Dec;2(12):2329–2341. doi: 10.1093/nar/2.12.2329. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Robillard G. T., Hilbers C. W., Reid B. R., Gangloff J., Dirheimer G., Shulman R. G. A study of secondary and tertiary solution structure of yeast tRNA(Asp) by nuclear magnetic resonance. Assignment of G.U ring NH and hydrogen-bonded base pair proton resonances. Biochemistry. 1976 May 4;15(9):1883–1888. doi: 10.1021/bi00654a014. [DOI] [PubMed] [Google Scholar]
  23. Stannard B. S., Felsenfeld G. The conformation of polyriboadenylic acid at low temperature and neutral pH. A single-stranded rodlike structure. Biopolymers. 1975 Feb;14(2):299–307. doi: 10.1002/bip.1975.360140205. [DOI] [PubMed] [Google Scholar]
  24. Sussman J. L., Kim S. H. Idealized atomic coordinates of yeast phenylalanine transfer RNA. Biochem Biophys Res Commun. 1976 Jan 12;68(1):89–96. doi: 10.1016/0006-291x(76)90014-0. [DOI] [PubMed] [Google Scholar]
  25. Thrierr J. C., Deubel V., Leng M. Interaction between polyribouridylic acid and spermine. Biochimie. 1972;54(9):1115–1119. doi: 10.1016/s0300-9084(72)80015-4. [DOI] [PubMed] [Google Scholar]
  26. Topal M. D., Fresco J. R. Base pairing and fidelity in codon-anticodon interaction. Nature. 1976 Sep 23;263(5575):289–293. doi: 10.1038/263289a0. [DOI] [PubMed] [Google Scholar]
  27. Yguerabide J. Nanosecond fluorescence spectroscopy of macromolecules. Methods Enzymol. 1972;26:498–578. doi: 10.1016/s0076-6879(72)26026-8. [DOI] [PubMed] [Google Scholar]

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