Force field parameters and NMR spectroscopy of modified nucleic acids

Modified Nucleic Acids play an important role in the functioning and stability of nucleic acids. In RNA, there are 107 naturally occurring modified nucleic acids. These modified nucleosides are present in many different kinds of RNA such as tRNA, rRNA, and snoRNA. The modified nucleosides in RNA play an important role in the stability and functioning of RNA. In addition, carcinogens covalently bind to DNA leading to a modified nucleoside. There is a dire need to understand the role of these modified nucleosides in the stability and functioning of RNA and DNA. To better understand the role of these modified nucleosides in the functioning and stability of nucleic acids, one has to either carry out structural studies or molecular dynamics simulations. To carry out MD simulations, however, there is a need to develop force field parameters for these modified nucleosides. Towards this goal we have developed parameters for all the known naturally occurring 107 modified nucleosides in RNA.;The ribosome is the molecular machine of protein synthesis. The bacterial ribosome is made of two subunits, which interact with each other by forming intersubunit bridges. The major component of these bridges is the ribosomal RNA. We have studies two such RNA loops which participate in the formation of intact ribosome. One of these RNA hairpin loops, called the 1920 loop, contain 3 highly conserved pseudouridines, which allowed us to test the force field parameters we have developed. We have also solved the solution structures of highly functional mutants of 690 loop to investigate key functional groups that are critical for ribosome function. The 690QM structure resembles the wild-type in over all shape and places key H-bond acceptor of residue 697 in proximity to G783, which is essential for 690 loop interaction with the 790 loop. The 691A mutant may require the entire central domain of 16S and the presence of proteins for proper folding.;The epigenetic marker, methylation of cytosine, plays an important role in effecting the mutagenecity of carcinogens. To test the effect of cytosine methylation on the mutagenecity of BPDE adducts, studies were carried out on DNA oligomers with BPDE adducted DNA with and without cytosine methylation. The current studies indicate that the presence of a methylated cytosine 5' of a BPDE adducted G in DNA causes conformational changes that may lead to the increased mutagenecity of the carcinogens.