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Calculation and analysis of low frequency normal modes for DNA
Author(s) -
Duong Tap Ha,
Zakrzewska Krystyna
Publication year - 1997
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(19970430)18:6<796::aid-jcc5>3.0.co;2-n
Subject(s) - dihedral angle , normal mode , bending , valence (chemistry) , amplitude , physics , helix (gastropod) , vibration , crystallography , flexibility (engineering) , molecular physics , chemistry , mathematics , optics , quantum mechanics , thermodynamics , molecule , hydrogen bond , ecology , statistics , biology , snail
Normal mode calculations for two alternating sequence dodecamers in A, B, and Z conformations have been performed in dihedral angle space extended to endocyclic valence angles to account for sugar ring flexibility. Normal modes are analyzed in terms of helicoidal and backbone parameter variations with special attention being paid to global deformations of the double helix such as bending, twisting, or stretching. Results show that the allomorphic form of DNA has the largest influence on the flexibility of the sugar‐phosphate backbone. Amplitudes of these vibrations follow the order: B > Z > A. In contrast, the amplitudes of helicoidal parameter variations are much more dependent on the base sequence. Global deformations of the double helix occur with characteristic times in the range of 1 to 10 ps and can be of mixed character, the strongest bending mode being at the same the time strongest stretching mode. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 796–811, 1997