Proton Magnetic Resonance Studies of 2'-,3'-, and 5'-deoxyadenosine Conformations in Solution

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1977 Apr 1

PMID 301272

Citations 5

Authors

E Westhof

H Plach

I Cuno

H D Ludemann

Affiliations

Soon will be listed here.

Abstract

Proton magnetic resonance studies of 2'-deoxyadenosine (2'-dA), 3'-deoxyadenosine (3'-dA), 5'-deoxyadenosine (5'-dA) and 8-bromo-5'-deoxyadenosine (8-Br-5'-dA) have been carried out in the temperature range between -60 degrees and +40 degrees C for ND3 solutios, +40 degrees and +100 degrees C for D2O solutions, and finally +10 degrees and +60 degrees C for pyridine solutions. The analysis is based on the two-state S in equilibrium N model of the ribose moiety proposed by Altona and Sundaralingam. In all solvents, 2'-dA favours slightly the S state of the ribose and the g+ conformer of the exocyclic CH2OH group. However, 3'-dA prefers strongly the N state of the ribose and the g+ conformation. Both the S and N states of the ribose are equally favoured by 5'-DA and 8-Br-5'-dA. Evidence for the existence of an intramolecular hydrogen bond between 0(5') and N3 in purine (beta)-nucleosides is presented. It is also concluded that cordycepin (3'-dA) exists in solution mainly in the anti conformation of the base relative to the ribose.

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13C NMR relaxation and conformational flexibility of the deoxyribose ring.

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References

Donohue J, Trueblood K . Base pairing in DNA. J Mol Biol. 1960; 2:363-71. DOI: 10.1016/s0022-2836(60)80047-2. View

Ludemann H, Roder O, Westhof E, Goldammer E, Muller A . Conformation of the common purine (beta) ribosides in solution: further evidence for a correlation between N-S state of the ribose moiety and syn-anti equilibrium. Biophys Struct Mech. 1975; 1(2):121-37. DOI: 10.1007/BF00539774. View

Hruska F, Wood D, Singh H . Effect of temperature and protonation upon the conformation of 2'-o-methyladenosine. Correlation of conformational parameters in purine nucleosides. Biochim Biophys Acta. 1977; 474(1):129-40. DOI: 10.1016/0005-2787(77)90220-9. View

Hruska F, Wood D, Mynott R, Sarma R . H NMR study of the conformation of the ribose phosphate moiety of 6-azauridine-5'-monophosphate--a nucleotide with an unusual conformation. FEBS Lett. 1973; 31(1):153-5. DOI: 10.1016/0014-5793(73)80094-8. View

Remin M, SHUGAR D . Conformational analysis of cytidine, 1-beta-D-(arabinofuranosyl)cytosine and their O'-methyl derivatives by proton magnetic resonance spectroscopy. J Am Chem Soc. 1973; 95(24):8146-56. DOI: 10.1021/ja00805a031. View

Altona C, Sundaralingam M . Conformational analysis of the sugar ring in nucleosides and nucleotides. Improved method for the interpretation of proton magnetic resonance coupling constants. J Am Chem Soc. 1973; 95(7):2333-44. DOI: 10.1021/ja00788a038. View

Sarma R, Lee C, Evans F, Yathindra N, Sundaralingam M . Probing the interrelation between the glycosyl torsion, sugar pucker, and the backbone conformation in C(8) substituted adenine nucleotides by 1H and 1H-(31P) fast Fourier transform nuclear magnetic resonance methods and conformational energy.... J Am Chem Soc. 1974; 96(23):7337-48. DOI: 10.1021/ja00830a028. View

Davies D, Danyluk S . Nuclear magnetic resonance studies of 5'-ribo- and deoxyribonucleotide structures in solution. Biochemistry. 1974; 13(21):4417-34. DOI: 10.1021/bi00718a027. View

Ludemann H, Westhof E, Roder O . A dynamic correlation between ribose conformation and glycosyl torsion angle of dissolved xanthosine studies by continuous-wave-mode and pulsed nuclear-magnetic-resonance methods. Eur J Biochem. 1974; 49(1):143-50. DOI: 10.1111/j.1432-1033.1974.tb03819.x. View

10.

Davies D, Danyluk S . Nuclear magnetic resonance studies of 2'- and 3'-ribonucleotide structures in solution. Biochemistry. 1975; 14(3):543-54. DOI: 10.1021/bi00674a013. View

11.

Son T, GUSCHLBAUER W . Necleoside conformations. 19. Temperature and pH effects on the conformation of guanosine phosphates. Nucleic Acids Res. 1975; 2(6):873-86. PMC: 343474. DOI: 10.1093/nar/2.6.873. View

12.

Evans F, Sarma R . Comparative study of the structure and conformation in aqueous solution of the antileukemic agent 6-thiopurine ribonucleoside 5'-phosphate to that of common purine 5'-nucleotides. J Am Chem Soc. 1975; 97(11):3215-8. DOI: 10.1021/ja00844a049. View

13.

Westhof E, Roder O, Croneiss I, Ludemann H . Ribose conformations in the common purine(beta)ribosides, in some antibiotic nucleosides, and in some isopropylidene derivatives: a comparison. Z Naturforsch C Biosci. 1975; 30(2):131-40. DOI: 10.1515/znc-1975-3-401. View

14.

Prusiner P, Yathindra N, Sundaralingam M . Effect of ribose O(2')-methylation on the conformation of nucleosides and nucleotides. Biochim Biophys Acta. 1974; 366(2):115-23. DOI: 10.1016/0005-2787(74)90325-6. View

15.

BERTHOD H, PULLMAN B . Molecular orbital calculations on the conformation of nucleic acids and their constituents. I. Conformational energies of beta-nucleosides with C(3')-and C(2')-endo sugars. Biochim Biophys Acta. 1971; 232(4):595-606. DOI: 10.1016/0005-2787(71)90750-7. View

16.

Ludemann H, Westhof E, Cuno I . Ribose conformations of 8-azapurine nucleosides in solution. Z Naturforsch C Biosci. 1976; 31(3-4):135-40. DOI: 10.1515/znc-1976-3-407. View

17.

Sundaralingam M, Arora S . Crystal structure of the aminoglycosyl antibiotic puromycin dihydrochloride pentahydrate. Models for the terminal 3'-aminoacyladenosine moieties of transfer RNA's and protein-nucleic acid interactions. J Mol Biol. 1972; 71(1):49-70. DOI: 10.1016/0022-2836(72)90400-7. View

18.

Fox J, WATANABE K, Bloch A . Nucleoside antibiotics. Prog Nucleic Acid Res Mol Biol. 1966; 5:251-313. DOI: 10.1016/s0079-6603(08)60236-6. View

19.

HASCHEMEYER A, Rich A . Nucleoside conformations: an analysis of steric barriers to rotation about the glycosidic bond. J Mol Biol. 1967; 27(2):369-84. DOI: 10.1016/0022-2836(67)90026-5. View