Biennial Report 2005-2007 - Saha Institute of Nuclear Physics

210 Biennial Report 2005-07provide an insight into their role in the structural and functional context of RNA.Shayantani Mukherjee, Manju Bansal†, Dhananjay BhattacharyyaBP6.1.3.2 Non-Canonical Base Pairs and Higher Order Structures in Nucleic Acids:Crystal Structure Database AnalysisNon-canonical base pairs, mostly present in the RNA, often play a prominent role towards maintainingtheir structural diversity. Higher order structures like base triples are also important in definingand stabilizing the tertiary folded structure of RNA. We have developed a new program BPFINDto analyze different types of canonical and non-canonical base pairs and base triples involving atleast two direct hydrogen bonds formed between polar atoms of the bases or sugar O2 only. Weconsidered 104 possible types of base pairs, out of which examples of 87 base pair types are foundto occur in the available RNA crystal structures. Analysis indicates that approximately 32.7% basepairs in the functional RNA structures are non-canonical, which include different types of GA andGU Wobble base pairs apart from a wide range of base pair possibilities. We further noticed thatmore than 10.4% of these base pairs are involved in triplet formation, most of which play importantrole in maintaining long-range tertiary contacts in the three-dimensional folded structure ofRNA. Apart from detection, the program also gives a quantitative estimate of the conformationaldeformation of detected base pairs in comparison to an ideal planar base pair. This helps us togain insight into the extent of their structural variations and thus assists in understanding theirspecific role towards structural and functional diversity.Jhuma Das, Shayantani Mukherjee, Abhijit Mitra†, Dhananjay BhattacharyyaBP6.1.3.3 Understanding Base Sequence Dependent DNA Flexibility from Stacking EnergyCalculated by Density Functional TheoryStacking energy of 10 possible DNA base-pair steps (bp step) were calculated using density functionaltheory (DFT) within the ultrasoft pseudo-potential plane wave method using projector augmentedwave method and local density approximation for the exchange-correlation functional asimplemented in the Vienna ab initio Simulation Package (VASP). We study the twist angle dependencyof stacking energy, as it was difficult to explain such variations using classical theory. Wefound that even in an anhydrous medium, the twist angle for different bp steps, at stacking energyminimum, matches extremely well with the values of twist angle obtained from crystal structuredata. From the twist angle dependent stacking energy profile, we have also generated twist angledistributions for all the bp steps and calculated variance of the distribution. Our calculatedvariances show trends similar to the experimental results for which sufficient numbers of crystalstructure data are available. The d(TA).d(TA) doublet step shows maximum variance among the10 possible bp steps, indicating its maximum flexibility. This may be the reason for unusual deformationobserved at the TATA-box while binding to TBP protein.Sudipta Samanta†, Kabir Mukul, Jaydeb Chakrabarti†, Dhananjay BhattacharyyaBP