Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

DNA Binding Studies of Large Antiviral Polyamides

Polyamides are minor groove DNA binding agents derived from the natural product distamycin A. PA1 is a large 12 ring polyamide discovered by NanoVir LLC;it is 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 (7662-122 bp) are being examined. Using affinity cleavage as detected by capillary electrophoresis, with PA1 attached to methyl propyl ethidium iron EDTA, 10 binding sites of PA1 were identified in this part of the HPV genome. Polyamide perfect binding sites were as predicted by recognition rules (Dervan & Edelson, 2003). Quantitative DNaseI footprinting indicates that both perfect and single mismatch sites are bound with Kds in the low nM range. Interestingly, a wide range of Kds are observed for double mismatch sites (1-60 nM) and is under examination. This work will permit us to build a map of PA binding to HPV sequences, thus informing mechanisms of in vivo behavior.


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.


    P.B. Dervan, B.S. Edelson, (2003). Recognition of the DNA minor groove by pyrrole-imidazole polyamides, Curr. Opin. Struct. Biol. 13, 284-299.

    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
Gaofei He
Kevin J. Koeller
G. Davis Harris
Cynthia M. Dupureur,
James K. Bashkin

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

Ph: (314) 516-4392
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