Recognition of T*G mismatched base pairs in DNA by stacked imidazole-containing polyamides: surface plasmon resonance and circular dichroism studies.
An imidazole-containing polyamide trimer, f-ImImIm, where f is a formamido group, was recently found using NMR methods to recognize T*G mismatched base pairs. In order to characterize in detail the T*G recognition affinity and specificity of imidazole-containing polyamides, f-ImIm, f-ImImIm and f-PyImIm were synthesized. The kinetics and thermodynamics for the polyamides binding to Watson-Crick and mismatched (containing one or two T*G, A*G or G*G mismatched base pairs) hairpin oligonucleotides were determined by surface plasmon resonance and circular dichroism (CD) methods. f-ImImIm binds significantly more strongly to the T*G mismatch-containing oligonucleotides than to the sequences with other mismatched or with Watson-Crick base pairs. Compared with the Watson-Crick CCGG sequence, f-ImImIm associates more slowly with DNAs containing T*G mismatches in place of one or two C*G base pairs and, more importantly, the dissociation rate from the T*G oligonucleotides is very slow (small k(d)). These results clearly demonstrate the binding selectivity and enhanced affinity of side-by-side imidazole/imidazole pairings for T*G mismatches and show that the affinity and specificity increase arise from much lower k(d) values with the T*G mismatched duplexes. CD titration studies of f-ImImIm complexes with T*G mismatched sequences produce strong induced bands at approximately 330 nm with clear isodichroic points, in support of a single minor groove complex. CD DNA bands suggest that the complexes remain in the B conformation.
Lacy
Eilyn R
ER
Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.
Cox
Kari K
KK
Wilson
W David
WD
Lee
Moses
M
D020137:Base Pair Mismatch; D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D003848:Deoxyguanine Nucleotides / Q000378:metabolism; D007093:Imidazoles / Q000737:chemistry / Q000378:metabolism*; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009692:Nucleic Acid Heteroduplexes; D009757:Nylons / Q000737:chemistry* / Q000378:metabolism*; D020349:Surface Plasmon Resonance; D013816:Thermodynamics; D013942:Thymine Nucleotides / Q000378:metabolism
D003848:Deoxyguanine Nucleotides; D007093:Imidazoles; D009692:Nucleic Acid Heteroduplexes; D009757:Nylons; D013942:Thymine Nucleotides; D004247:DNA