Brugia Malayi - Clark Science Center - Smith College

Developing a Method for DNA Sequence-based Rigidity Analysis
Emily Flynn
This summer, I extended KINARI-Web to perform rigidity analysis on nucleic acids and protein-nucleic acid complexes with
known structures. KINARI-Web 1 is a freely available server for protein rigidity analysis developed by Professor Streinu’s research
group (Linkage Lab) at Smith College. Many structures in the Protein Data Bank (PDB), including viruses and ribosomes,
were crystallized with both proteins and nucleic acids present. Previously, KINARI could only analyze the protein portion
of the structure, but with the extension I developed, it can now identify the rigid and flexible regions in the entire complex.
KINARI works by inputting a PDB file and then processes the file to identify of covalent and non-covalent interactions within
the macromolecule. A mechanical model is created using these interactions, and rigidity analysis is run using the pebble game
algorithm. The results of rigidity analysis can then be viewed in a JMol based visualizer. In order to extend KINARI to analyze
DNA and RNA, functionality was added to identify the structures present in a PDB file, and place covalent bonds accordingly.
The procedures for identifying non-covalent interactions, specifically hydrogen bonds and hydrophobic interactions, were also
adapted to recognize nucleic acids.
In addition, I began developing a method to analyze the rigidity of DNA molecules from sequence alone. There are a huge
number of DNA sequences available (>135 million in GenBank), but relatively few DNA structures (