This Article Full Text Full Text (PDF) All Versions of this Article: biophysj.105.080564v1 91/3/904    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Caesar, C. E. B. Articles by Nordén, B. Search for Related Content PubMed PubMed Citation Articles by Caesar, C. E. B. Articles by Nordén, B.

A Polarized-Light Spectroscopy Study of Interactions of a Hairpin Polyamide with DNA

Christina E. B. Caesar ^*, Richard Johnsson , Ulf Ellervik , Keith R. Fox , Per Lincoln ^* and Bengt Nordén ^*

^* Department of Chemistry and Bioscience, Chalmers University of Technology, S-41296 Gothenburg, Sweden; Department of Bioorganic Chemistry, Lund University, S-221 00 Lund, Sweden; and Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Southampton SO16 7PX, United Kingdom

Correspondence: Address reprint requests to Bengt Nordén, Tel.: 46-31-7723041; E-mail: norden{at}chalmers.se.

We here study the interactions of a polyamide with large DNA, and compare to those of minor groove binder distamycin (DST), including high ligand/DNA binding ratios. Specific as well as nonspecific binding is probed using polarized-light spectroscopy combined with singular value decomposition analysis. Circular and linear dichroism data confirm binding geometries consistent with minor groove binding for both of the ligands. Interestingly, at high and intermediate ligand/DNA ratios the polyamide exhibits no significant sequence discrimination between mixed-sequence (calf thymus) and AT DNA as compared to DST. Each ligand is concluded to exhibit two different binding modes depending upon ligand/DNA ratio and nucleo-base sequence. At high binding ratios, distinct differences between the ligands are observed: circular dichroism spectra exciton effects provide evidence of bimolecular interactions of the polyamide when bound to AT-DNA, whereas no effects are seen with DST or mixed-sequence DNA. Also linear dichroism indicates that a change in binding geometry occurs at high polyamide/AT ratios, and that the effect occurs only with polyamide in contrast to DST. Since the effect is insignificant with DST, or with calf thymus DNA, it is concluded that it relates to the sizes of the ligands and the minor grooves, becoming critical in the limit of crowding.