Qualitative analysis of sequence specific binding of flavones to DNA using restriction endonuclease activity assays

Authors

  • Elizabeth Duran,

    1. Department of Chemistry and Biochemistry, Florida International University, Miami, FL
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  • Victoria P. Ramsauer,

    1. Department of Pharmaceutical Sciences, Bill Gatton College of Pharmacy, East Tennessee State University, Johnson City, TN 37614
    2. Department of Internal Medicine, James Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614
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  • Maria Ballester,

    1. Division of Math Science and Technology, Farquhar College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, 33314
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  • Ruben D. Torrenegra,

    1. Departamentos de Quimica y Quimica Farmaceutica, Universidad de Ciencias Aplicadas y Ambientales, Bogota, Colombia
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  • Oscar E. Rodriguez,

    1. Departamentos de Quimica y Quimica Farmaceutica, Universidad de Ciencias Aplicadas y Ambientales, Bogota, Colombia
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  • Stephen A. Winkle

    Corresponding author
    • Department of Chemistry and Biochemistry, Florida International University, Miami, FL
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  • This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Correspondence to: Stephen Winkle; e-mail: winkles@fiu.edu

Abstract

Flavones, found in nature as secondary plant metabolites, have shown efficacy as anti-cancer agents. We have examined the binding of two flavones, 5,7-dihydroxy-3,6,8-trimethoxy-2-phenyl-4H-chromen-4-one (5,7-dihydroxy-3,6,8-trimethoxy flavone; FlavA) and 3,5-dihydroxy-6,7,8-trimethoxy-2-phenyl-4H-chromen-4-one (3,5-dihydroxy-6,7,8-trimethoxy flavone; FlavB), to phiX174 RF DNA using restriction enzyme activity assays employing the restriction enzymes Alw44, AvaII, BssHII, DraI, MluI, NarI, NciI, NruI, PstI, and XhoI. These enzymes possess differing target and flanking sequences allowing for observation of sequence specificity analysis. Using restriction enzymes that cleave once with a mixture of supercoiled and relaxed DNA substrates provides for observation of topological effects on binding. FlavA and FlavB show differing sequence specificities in their respective binding to phiX. For example, with relaxed DNA, FlavA shows inhibition of cleavage with DraI (reaction site 5′TTTAAA) but not BssHII (5′GCGCGC) while FlavB shows the opposite results. Evidence for tolological specificity is also observed, Molecular modeling and conformational analysis of the flavones suggests that the phenyl ring of FlavB is coplanar with the flavonoid ring while the phenyl ring of FlavA is at an angle relative to the flavonoid ring. This may account for aspects of the observed sequence and topological specificities in the effects on restriction enzyme activity. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 530–537, 2013.

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