JAVIER ARSUAGA |
DNA Packaging in Bacteriophages |
Our main interest is to be able to predict the DNA configuration inside the viral capsid for small bacteriophages using random knotting techniques. |
Our work is based on an interdisciplinary approach to the problem: Biological, computational, and mathematical. |
In the biological approach we are interested in analyzing the topology of DNA molecules extracted from P4 bacteriophages. |
The following advances have been done in this direction: |
During the summer of 1998, I did a two-month (July-September) lab rotation in Dr. Rocaís Molecular Biology Laboratory in Barcelona (Spain). During this period we reproduced the results obtained by Leroy F. Liu and J. Davis (Nucleic Acid Research, Volume 9, number 15, 1981) and by applying new techniques we improved these experimental results. As a result of this collaboration we obtained more detailed experimental data on the topology of the DNA extracted from viral capsids. These results will be a key factor for our future research. |
In our computational approach we implemented several algorithms as well as a computational framework for the generation of polymer conformations in confined volumes. To statistically analyze these computer-generated conformations, we incorporated routines for knot calculation. In the future, this software will allow us to generate polymer conformations subjected to spatial restrictions and generate knot distributions associated to these conformations. |
From the knot distribution we hope to infer viral DNA packing geometry in capsids. |
