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On the stability of single‐ and double‐stranded DNA helices: The application of the PPT‐MCF method on large fragments of DNA
Author(s) -
Otto P.
Publication year - 1986
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.560300207
Subject(s) - stacking , base pair , dna , chemistry , crystallography , helix (gastropod) , base (topology) , sequence (biology) , hydrogen bond , stereochemistry , chemical physics , molecular physics , molecule , mathematics , biology , ecology , mathematical analysis , biochemistry , organic chemistry , snail
The pseudo‐polarization tensor mutually consistent field ( PPT ‐ MCF ) method recently introduced [1] has been applied to study the stacking interactions between the nucleotide bases in large periodic B‐DNA fragments. The effects on the global and local binding properties caused by replacing one base in the periodic sequence by another base are investigated. The increase in the stability for comparable fragments owing to this base substitution is further enforced in the case of periodic alternating helices. The most important results are that the stacking interaction between two bases is slowly converging with the interbase distance and that the average contribution per base to the binding energy is repulsive. Furthermore, the energetical properties of double helix models in B‐ and Z‐DNA configurations, respectively, consisting of up to five base pairs have been compared. It turns out that the G C G C sequence in Z‐DNA is significantly more stable than either in periodic or periodic alternating B‐DNA. In these cases the average energy contribution of a single Watson–Crick‐type base pair is predicted also to be positive. From the calculations it follows that the double helix is not stabilized owing to the hydrogen bonding between the bases belonging to both strands, in contradiction to most other investigations.