Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

Large Antiviral Polyamide-DNA Interactions

Polyamides are minor groove DNA binding agents derived from the natural product distamycin A. PA1 is a large 12 ring polyamide bioactive against the HPV16 virus in cell and tissue culture (Edwards, et al., 2011). To better understand the basis of this phenomenon, the interactions of PA1 with the regulatory sequence of the HPV16 genome (7348-122 bp) are being examined. Using an FeEDTA conjugate of PA1, 38 affinity cleavage (AC) patterns were detected for this fragment using capillary electrophoresis (CE). Quantitative DNase I footprinting analysis indicates that perfect sites bind PA1 with Kds between 0.7-2.2 nM. Due to the density of sites, Kds for single, double, triple and quadruple mismatch sites were characterized. These Kds range from 1-3 nM to 20 nM. A limited single mismatch study of one PA1 site in the context of a 120mer indicates that the position of the substitution made no difference in affinity. Using AC and EDTA conjugates, we report that unlike smaller 8-ring hairpin PAs, introduction of a chiral turn in this large polyamide has no effect on binding orientation (forward vs. reverse). Studies of isolated PA1 sites by fluorescence spectroscopy and CE are also underway.


This research has been supported by NIH (AI083803) and NanoVir, LLC under its NIH grant AI062182. We are grateful for access to the NanoVir discoveries.

T.G. Edwards, K.J. Koeller, U. Slomczynska, K. Fok, M. Helmus, J.K. Bashkin, C. Fisher, (2011). HPV episome levels are potently decreased by pyrrole-imidazole polyamides, Antiviral Res. 91, 177-186.

Elena Vasilieva
Yang Song
Kevin J. Koeller
G. Davis Harris
James K. Bashkin
Cynthia M. Dupureur

Department of Chemistry & Biochemistry
Center for Nanoscience
University of Missouri-St. Louis
One University Blvd.
St. Louis, MO

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