Conformational Studies of (2'-5') Polynucleotides: Theoretical Computations of Energy, Base Morphology, Helical Structure, and Duplex Formation

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1986 Jul 11

PMID 2426656

Citations 6

Authors

A R Srinivasan

W K Olson

Affiliations

Soon will be listed here.

Abstract

A detailed theoretical analysis has been carried out to probe the conformational characteristics of (2'-5') polynucleotide chains. Semi-empirical energy calculations are used to estimate the preferred torsional combinations of the monomeric repeating unit. The resulting morphology of adjacent bases and the tendency to form regular single-stranded structures are determined by standard computational procedures. The torsional preferences are in agreement with available nmr measurements on model compounds. The tendencies to adopt base stacked and intercalative geometries are markedly depressed compared to those in (3'-5') chains. Very limited families of regular monomerically repeating single-stranded (2'-5') helices are found. Base stacking, however, can be enhanced (but helix formation is at the same time depressed) in mixed puckered chains. Constrained (2'-5') duplex structures have been constructed from a search of all intervening glycosyl and sugar conformations that form geometrically feasible phosphodiester linkages. Both A- and B-type base stacking are found to generate non-standard backbone torsions and mixed glycosyl/sugar combinations. The 2'- and 5'-residues are locked in totally different arrangements and are thereby prevented from generating long helical structures.

Citing Articles

Solution structure of a modified 2',5'-linked RNA hairpin involved in an equilibrium with duplex.

Plevnik M, Gdaniec Z, Plavec J Nucleic Acids Res. 2005; 33(6):1749-59.

PMID: 15788747 PMC: 1069515. DOI: 10.1093/nar/gki318.

The 2-5A system: modulation of viral and cellular processes through acceleration of RNA degradation.

Player M, Torrence P Pharmacol Ther. 1998; 78(2):55-113.

PMID: 9623881 PMC: 7157933. DOI: 10.1016/s0163-7258(97)00167-8.

Comparative spectroscopic, calorimetric, and computational studies of nucleic acid complexes with 2',5"-versus 3',5"-phosphodiester linkages.

Jin R, CHAPMAN Jr W, Srinivasan A, Olson W, Breslow R, Breslauer K Proc Natl Acad Sci U S A. 1993; 90(22):10568-72.

PMID: 8248146 PMC: 47818. DOI: 10.1073/pnas.90.22.10568.

Recognition and catalysis in nucleic acid chemistry.

Breslow R, Xu R Proc Natl Acad Sci U S A. 1993; 90(4):1201-7.

PMID: 7679492 PMC: 45840. DOI: 10.1073/pnas.90.4.1201.

Visualisation of a 2'-5' parallel stranded double helix at atomic resolution: crystal structure of cytidylyl-2',5'-adenosine.

Kirshnan R, Seshadri T, Viswamitra M Nucleic Acids Res. 1991; 19(2):379-84.

PMID: 2014174 PMC: 333605. DOI: 10.1093/nar/19.2.379.

References

Brahms J, Maurizot J, MICHELSON A . Conformational stability of dinucleotides in solution. J Mol Biol. 1967; 25(3):481-95. DOI: 10.1016/0022-2836(67)90200-8. View

Doornbos J, Charubala R, Pfleiderer W, Altona C . Conformational analysis of the trinucleoside diphosphate 3'd(A2'-5'A2'-5'A). An NMR and CD study. Nucleic Acids Res. 1983; 11(13):4569-82. PMC: 326065. DOI: 10.1093/nar/11.13.4569. View

Adler A, Grossman L, Fasman G . Circular dichroism of cytosine dinucleoside monophosphates containing arabinose, ribose, and deoxyribose. Biochemistry. 1968; 7(11):3836-41. DOI: 10.1021/bi00851a008. View

Sulston J, Lohrmann R, Orgel L, Weimann B, Miles H . Non-enzymic oligonucleotide synthesis on a polycytidylate template. J Mol Biol. 1969; 40(2):227-34. DOI: 10.1016/0022-2836(69)90471-9. View

WARSHAW M, Cantor C . Oligonucleotide interactions. IV. Conformational differences between deoxy- and ribodinucleoside phosphates. Biopolymers. 1970; 9(9):1079-103. DOI: 10.1002/bip.1970.360090910. View

Kondo N, Holmes H, Stempel L, Tso O . Influence of the phosphodiester linkage (3'-5', 2'-5', and 5'-5') on the conformation of dinucleoside monophosphate. Biochemistry. 1970; 9(18):3479-98. DOI: 10.1021/bi00820a002. View

Olson W, FLORY P . Spatial configuration of polynucleotide chains. II. Conformational energies and the average dimensions of polyribonucleotides. Biopolymers. 1972; 11(1):25-56. DOI: 10.1002/bip.1972.360110103. View

Sawai H . NMR, CD and UV studies of 2'-5' and 3'-5' linked oligoadenylates. Nucleic Acids Symp Ser. 1983; (12):189-92. View

Hirao I, Ishido Y, Miura K . Difference of the 2',5'-oligoadenylate and the 3',5'-oligoadenylate in the formation of base pairings. Nucleic Acids Symp Ser. 1983; (12):193-6. View

10.

Taylor E, Olson W . Theoretical studies of nucleic acid interactions. I. Estimates of conformational mobility in intercalated chains. Biopolymers. 1983; 22(12):2667-702. DOI: 10.1002/bip.360221213. View

11.

Anukanth A, Ponnuswamy P . 2'5'-linked polynucleotides do form a double-stranded helical structure: a result from the energy minimization study of A2'p5'A. Biopolymers. 1986; 25(4):729-52. DOI: 10.1002/bip.360250414. View

12.

Taylor E, Miller K . Interactions of molecules with nucleic acids. XI. Generalization of techniques to generate nucleic acid structures with applications to intercalation sites and kinked structures. Biopolymers. 1984; 23(12):2853-78. DOI: 10.1002/bip.360231211. View

13.

Olson W, FLORY P . Spatial configurations of polynucleotide chains. I. Steric interactions in polyribonucleotides: a virtual bond model. Biopolymers. 1972; 11(1):1-23. DOI: 10.1002/bip.1972.360110102. View

14.

Olson W . Syn-anti effects on the spatial configuration of polynucleotide chains. Biopolymers. 1973; 12(8):1787-814. DOI: 10.1002/bip.1973.360120808. View

15.

Perahia D, PULLMAN B, Saran A . Molecular orbital calculations on the conformation of nucleic acids and their constituents. XI. The backbone structure of (3'-5') and (2'-5')-linked diribose monophosphates with different sugar puckers. Biochim Biophys Acta. 1974; 353(1):16-27. DOI: 10.1016/0005-2787(74)90093-8. View

16.

USHER D, McHale A . Nonenzymic joining of oligoadenylates on a polyuridylic acid template. Science. 1976; 192(4234):53-4. DOI: 10.1126/science.1257755. View

17.

Olson W . The spatial configuration of ordered polynucleotide chains. I. Helix formation and base stacking. Biopolymers. 1976; 15(5):859-78. DOI: 10.1002/bip.1976.360150505. View

18.

Sawai H . Catalysis of internucleotide bond formation by divalent metal ions. J Am Chem Soc. 1976; 98(22):7037-9. DOI: 10.1021/ja00438a050. View

19.

Wodak S . The structure of cytidilyl(2',5')adenosine when bound to pancreatic ribonuclease S. J Mol Biol. 1977; 116(4):855-75. DOI: 10.1016/0022-2836(77)90275-3. View

20.

Kerr I, Brown R . pppA2'p5'A2'p5'A: an inhibitor of protein synthesis synthesized with an enzyme fraction from interferon-treated cells. Proc Natl Acad Sci U S A. 1978; 75(1):256-60. PMC: 411225. DOI: 10.1073/pnas.75.1.256. View