Polymorphism of hydrogen bonding in the short double helixes of oligonucleotides: Semiempirical quantum chemical study

Abstract

ABSTRACT:The origin of heterogeneity of nucleotide steps geometry in short double helixes is studied theoretically. By using the semiempirical MNDO/PM3 technique, the stability of "propeller-like" and "step-like" forms of base H-pairing is examined in the structure of oligonucleotide duplexes of different types. The influence of end effects on the process of nucleotides packing, as well as the dependence of duplex curvature on the nature of bonded oligonucleotides, are examined. It is concluded that the structural polymorphism of base pairs most likely determines the unique packing of complementary pairs and their flexibility in DNA structure. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem 88: 579 -587, 2002

Study of horizontal sonic gas jets in gas–solid fluidized beds

“…For the structure of isolated hydrogen‐bonded base pairs 11–17, nucleosides, and nucleotides 18, it is a natural further downturn of the energy of lowest normal modes and the appearance of intermolecular character of some modes 4, 18. Note that the process of H‐bonding of the bases, as shown in our previous reports 19, 20, is accompanied by an ambiguity of the spatial form of their complementary pairing. It is caused by the bistability of a pyramidal structure of exocyclic amino groups involved in base H‐bonding.…”

“…Earlier in our publications 19, 20, and in the work of other investigators 11, 21 the applicability of semi‐empirical PM3 approach 22 to electronic structure calculations of H‐bonded nucleobases and small nucleotide duplexes was demonstrated. In the present work, the same quantum chemical technique was used to analysis of the spectrum of normal modes in short double helices of DNA molecules.…”

“…Taking into account the heterogeneity of geometrical parameters of nucleotide steps in double helices of oligonucleotides 20, it is natural to expect the “mixed” character of vibrations of all low‐frequency modes, both intermolecular and intramolecular. For the simplest duplex d(ApA) · d(TpT), 16 of 20 low modes presented in Table IV appear to be intermolecular.…”

Local piezoresponse and polarization switching in nucleobase thymine microcrystals

“…In the OZ direction, the polarization P z % 0 reflecting centrosymmetric structure, which forms a coplanar configuration in the XOY plane. [60][61][62][63] The switching polarization, DP z , is much lower in this case (see Table II for details) and does not correspond to the experimental situation.…”

Distribution of mononucleotide repeats in bacterial chromosomes: A/T-tracts dominate on G/C-tracts

“…В основе этого явления, например, может лежать исходно пониженный структурный полиморфизм водородного связывания уотсон-криковских АТ-пар по сравнению с GC-парами. Как показано в работах [Комаров, 1998;Kabanov, Komarov, 2002;Komarov, Polozov, Konoplev, 1992] GC-пары, в отличие от АТ-пар, характеризуются 4-х кратным вырождением водородного связывания оснований. Для них реализуются две структуры «пропеллероподобного» типа (правый и левый пропеллер) и две симметричные структуры «ступенькообразного» типа на одних и тех же водородных связях, в то время как АТ-пары оснований образуют только две «пропеллероподобные» структуры комплементарного H-спаривания, а «ступенькообразные» структуры у них отсутствуют.…”