Biopolym. Cell. 1989; 5(1):16-22.
http://dx.doi.org/10.7124/bc.000038
Structure and Function of Biopolymers
Buckle of the A-T pair in the Bh-form of poly(dA):poly(dT)
1Lipanov A. A., 1Beglov D. B., 1Alexeev D. G., 1Skuratovsky I. Ya.
  1. Institute of Molecular Genetics, Academy of Sciences of the USSR
    Moscow, USSR

Abstract

The structures of calcium and sodium salts of poly(dA): poly(dT) have been refined on the basis of X-ray diffraction in fibres using two parameter flexible sugar, and allowing for the possible A-T buckle. The bases of one chain, probably thymines, are tilted in the Na-poly(dA):poly(dT) structure at an angle of about —13°, while the tilt of the other chain bases is negligible. A number of unique features warrant a special designation, Bh, to distinguish poly(dA) : poly(dT) structure from other B-type structures. The refined structural parameters may be significant for the interpretation of data on DNA bends containing sufficiently long dAn:dTn tracts.
Full text: (PDF, in Russian)

References

[1] Arnott S, Selsing E. Structures for the polynucleotide complexes poly(dA) with poly (dT) and poly(dT) with poly(dA) with poly (dT). J Mol Biol. 1974;88(2):509-21.
[2] Arnott S, Chandrasekaran R, Hall IH, Puigjaner LC. Heteronomous DNA. Nucleic Acids Res. 1983;11(12):4141-55.
[3] Alexeev D. G., Lipanov A. A., Skuratovsky I. Ya. Structure of the calcium salt of poly(dA) : poly(dT) as revealed by the X-ray diffraction analysis in fibres. Biopolym Cell. 1986; 2(4):189-195.
[4] Alexeev DG, Lipanov AA, Skuratovskii IYa. Poly(dA).poly(dT) is a B-type double helix with a distinctively narrow minor groove. Nature. 1987 Feb 26-Mar 4;325(6107):821-3.
[5] Alexeev DG, Lipanov AA, Skuratovskii IYa. The structure of poly(dA).poly(dT) as revealed by an X-ray fibre diffraction. J Biomol Struct Dyn. 1987;4(6):989-1012.
[6] Park HS, Arnott S, Chandrasekaran R, Millane RP, Campagnari F. Structure of the alpha-form of poly[d(A)].poly[d(T)] and related polynucleotide duplexes. J Mol Biol. 1987;197(3):513-23.
[7] Chuprina VP. Regularities in formation of the spine of hydration in the DNA minor groove and its influence on the DNA structure. FEBS Lett. 1985;186(1):98-102.
[8] Chuprina VP. Anomalous structure and properties of poly (dA).poly(dT). Computer simulation of the polynucleotide structure with the spine of hydration in the minor groove. Nucleic Acids Res. 1987;15(1):293-311.
[9] Drew HR, Dickerson RE. Structure of a B-DNA dodecamer. III. Geometry of hydration. J Mol Biol. 1981;151(3):535-56.
[10] Koo HS, Wu HM, Crothers DM. DNA bending at adenine . thymine tracts. Nature. 1986 Apr 10-16;320(6062):501-6.
[11] Drew HR, Travers AA. DNA structural variations in the E. coli tyrT promoter. Cell. 1984;37(2):491-502.
[12] Peck LJ, Wang JC. Sequence dependence of the helical repeat of DNA in solution. Nature. 1981;292(5821):375-8.
[13] Rhodes D, Klug A. Sequence-dependent helical periodicity of DNA. Nature. 1981;292(5821):378-80.
[14] Lipanov AA, Chuprina VP. The structure of poly(dA):poly(dT) in a condensed state and in solution. Nucleic Acids Res. 1987;15(14):5833-44.
[15] Edmondson SP, Johnson WC Jr. Base tilt of poly[d(A)]-poly[d(T)] and poly[d(AT)]-poly[d(AT)] in solution determined by linear dichroism. Biopolymers. 1985;24(5):825-41.
[16] Bartenev VN, Kameneva NG, Lipanova AA. A statistical stereochemical model of the flexible furanose ring. Acta Cryst B. 1987;43(3):275–80.
[17] Beglov DB, Kameneva NG, Lipanov AA. Two-parametric statistical model of the flexible furanose. Abstr. 2nd All-Union Seminar on the Application of mat. methods in biology. Pushchino, 1987; 62-63.
[18] Altona C, Sundaralingam M. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J Am Chem Soc. 1972;94(23):8205-12.
[19] Dickerson R.E, Kopka ML, Pjura P. Biological macromolecules and assemblies. Eds F. Jurnac, A. McPherson. New York : Wiley, 1985. Vol. 2. 365 p.
[20] Cruse WB, Salisbury SA, Brown T, Cosstick R, Eckstein F, Kennard O. Chiral phosphorothioate analogues of B-DNA. The crystal structure of Rp-d[Gp(S)CpGp(S)CpGp(S)C]. J Mol Biol. 1986;192(4):891-905.
[21] Prive GG, Heinemann U, Chandrasegaran S, Kan LS, Kopka ML, Dickerson RE. Helix geometry, hydration, and G.A mismatch in a B-DNA decamer. Science. 1987;238(4826):498-504.
[22] Hamilton WC. Significance tests on the crystallographic R factor. Acta Cryst. 1965;18(3):502–10.
[23] Baret JF, Carbone GP, Penon P. Infrared dichroism of polynucleotides of repeated sequence. I. Poly(dA)-poly(dT) and poly[d(A-T)]-poly[d(A-T)]. Biopolymers. 1978;17(10):2319–39.
[24] Semenov MA, Bol’bukh TV. Resonant oscillations in reacting carbonyl spiral polynucleotides. Kharkiv, 1982; 27 p. (Preprint. UkSSR. Inst Radio Physics and Electronics, 190).
[25] Lipanov AA. Spatial structure of DNA complexes with alkali metal ions and water molecules: Author. dis. ... kand biol nauk. Moscow, 1986; 21 p.
[26] Skuratovskii IYa, Hasnain SS, Alexeev DG, Diakun GP, Volkova LI. EXAFS studies of the calcium salts of natural DNA and polydA:polydT. J Inorg Biochem. 1987;29(4):249-57.
[27] Bartenev VN, Golovamov EuI, Kapitonova KA, Mokulskii MA, Volkova LI, Skuratovskii IYa. Structure of the B DNA cationic shell as revealed by an X-ray diffraction study of CsDNA. Sequence-specific cationic stabilization of B form DNA. J Mol Biol. 1983;169(1):217-34.
[28] Lipanov AA, Alekseev DG, Bartenev VN, Volkova LI, Kapitonova KA, Skuratovsky IYa. Position of Cs2+ ions in the structure of DNA A-form. Biofizika. 1986; 31(2):336-8.
[29] Arnott S, Selsing E. Letter: The structure of polydeoxyguanylic acid with polydeoxycytidylic acid. J Mol Biol. 1974;88(2):551-2.
[30] Nelson HC, Finch JT, Luisi BF, Klug A. The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature. 1987 Nov 19-25;330(6145):221-6.
[31] Coll M, Frederick CA, Wang AH, Rich A. A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Proc Natl Acad Sci U S A. 1987;84(23):8385-9.