Conformational Characteristics of Mixed Sugar Puckered Deoxydinucleoside Triphosphate Units d-pCpGp and d-pGpCp from Energy Minimization Studies |
| |
Authors: | P K Ponnuswamy A Anukanth |
| |
Institution: | 1. Department of Physics , Bharathidasan University , Tiruchirpalli , 620 024 , Tamilnadu , India;2. School of Biological Sciences Madurai Kamaraj University , Madurai , 625 021 , Tamilnadu , India |
| |
Abstract: | Abstract 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. |
| |
Keywords: | |
|
|