Binding studies of a large antiviral polyamide to a natural HPV sequence

• Published in: Biochimie 2014-07, Vol.102, p.83-91
• Main Authors: He, Gaofei, Vasilieva, Elena, Harris, George Davis, Koeller, Kevin J., Bashkin, James K., Dupureur, Cynthia M.
• Format: Article
• Language: English
• Subjects: Affinity cleavage; Alanine - chemistry; Antiviral Agents - chemistry; Antiviral Agents - pharmacology; Binding constant; Binding Sites; DNA - chemistry; Footprinting; HPV; Human papillomavirus 16; Human papillomavirus 16 - chemistry; Human papillomavirus 16 - genetics; Imidazoles - chemistry; Nucleic Acid Conformation - drug effects; Nylons - chemistry; Nylons - pharmacology; Polyamide; Pyrroles - chemistry
• ISSN: 0300-9084; 1638-6183
• DOI: 10.1016/j.biochi.2014.02.011

PA1 is a large hairpin polyamide (dImPyPy-β-PyPyPy-γ-PyPy-β-PyPyPyPy-β-Ta; Py = pyrrole, Im = imidazole, β = beta alanine) that targets the sequence 5′-WWGWWWWWWW-3′ (W = A or T) and is effective in eliminating HPV16 in cell culture (Edwards, T. G., Koeller, K. J., Slomczynska, U., Fok, K., Helmus, M., Bashkin, J. K., Fisher, C., Antiviral Res. 91 (2011) 177–186). Described here are its DNA binding properties toward a natural DNA, a 523 bp portion of HPV16 (2150–2672) containing three predicted perfect match sites. Strategies for obtaining binding data on large fragments using capillary electrophoresis are also described. Using an Fe EDTA conjugate of PA1, 19 affinity cleavage (AC) patterns were detected for this fragment. In many cases, there are multiple possible binding sequences (perfect, single and double mismatch sites) consistent with the AC data. Quantitative DNase I footprinting analysis indicates that perfect and most single mismatch sites bind PA1 with Kds between 0.7 and 4 nM, indicating excellent tolerance for the latter. Double mismatch sites exhibit Kds between 12 and 62 nM. A large fraction of the accessible sequence is susceptible to PA1 binding, much larger than predicted based on the literature of polyamide-DNA recognition rules. •Perfect match sites for a 14 ring antiviral PA on the HPV 16 genome bind with low nM affinity.•Single mismatch sites are bound with affinities similar to those observed with perfect sites.•Affinities for double mismatch PA sites on the HPV 16 genome vary from low to mid nM.•Most of the DNA from the HPV sequence under study is susceptible to binding by the single 14-ring PA studied here.