Towards Sequence-Based DNA Flexibility Analysis

Emily Flynn, Smith College
Filip Jagodzinski, Central Washington University
Ileana Streinu, Smith College

Peer reviewed accepted manuscript.


In this poster, we present an extension to our freely available KINARI-Web server to identify rigid and flexible regions of nucleic acids and protein-nucleic acid complexes contained in the Protein Data Bank (PDB). The goal is to explore the effect of DNA and RNA on the rigidity and stability of these structures. We also propose an approach for determining DNA rigidity based solely on sequence. Currently, only the rigidity of DNA molecules whose structures have been deposited in the PDB (approx. <4,000 files) can be analyzed. Once fine-tuned and validated, this new coordinate-free method for investigating DNA flexibility could be applied to the more than 135 million sequences in GenBank, and to nanostructure design.