A Polarized-Light Spectroscopy Study of Interactions of a Hairpin Polyamide with DNA
Christina E.B. Caesar 1, Richard Johnsson 2, Ulf Ellervik 2, Keith R. Fox 3, Per Lincoln 4 and Bengt Norden 4*
1 Chemistry and Bioscience, Chalmers University of Technology
2 Department of Bioorganic Chemistry, Lund University
3 Devioson of Biochemistry and Molecular Biology, University of Southampton
4 Department of Chemistry and Bioscience, Chalmers University of Technology
* To whom correspondence should be addressed. E-mail: norden{at}chembio.chalmers.se.
Submitted on January 2, 2006
Revised on February 6, 2006
Accepted on 25 April 2006
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Abstract |
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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: in CD spectra exciton effects evidence bimolecular interactions of the polyamide when bound to AT-DNA whereas no effects are seen with DST or mixed-sequence DNA. Also LD 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 to relate to the sizes of the ligands and the minor grooves, becoming critical in the limit of crowding.
Key Words:
DNA minor groove binding ligands, Distamycin A, SVD analysis of DNA interactions, circular dichroism, linear dichroism
