Conformational characteristics of mixed sugar puckered deoxydinucleoside triphosphate units d-pCpGp and d-pGpCp from energy minimization studies.
The deoxydinucleoside triphosphate units d-pCpGp and d-pGpCp were subjected to a rigorous theoretical investigation with a view to describing their distinctive conformational characteristics. For each unit 216 probable three-dimensional forms defined by the backbone-base dihedral angles and sugar pucker modes were considered for conformational energy minimization process and scrutinized with reference to properties, such as base-stacking, hydrogen-bonding, internal flexibility and base sequence-phosphate influence. The P-O bond torsions and the phosphate groups were treated with special attention. The results reveal a number of preferred conformational states other than the known helical forms, such as, A-, B-, C-, Z-, and Watson-Crick conformation. Many interesting one-step (change in only one of the dihedral angles or sugar puckers) conformational transitions which involve just about a kcal/mol of energy came to light. The two base sequences CG and GC were noted to differ strikingly in many of their conformational characteristics.
Ponnuswamy
P K
PK
Department of Physics, Bharathidasan University, Tamilnadu, India.
Anukanth
A
A
D004247:DNA; D003854:Deoxyribonucleotides; D003855:Deoxyribose; D015226:Dinucleoside Phosphates; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
D003854:Deoxyribonucleotides; D015226:Dinucleoside Phosphates; D003855:Deoxyribose; D004247:DNA