Dataset Information

Recognition of abasic sites and single base bulges in DNA by a metalloinsertor.

ABSTRACT: Abasic sites and single base bulges are thermodynamically destabilizing DNA defects that can lead to cancerous transformations if left unrepaired by the cell. Here we discuss the binding properties with abasic sites and single base bulges of Rh(bpy)(2)(chrysi)(3+), a complex previously shown to bind thermodynamically destabilized mismatch sites via metalloinsertion. Photocleavage experiments show that Rh(bpy)(2)(chrysi)(3+) selectively binds abasic sites with affinities of 1-4 x 10(6) M(-1); specific binding is independent of unpaired base identity but is somewhat contingent on sequence context. Single base bulges are also selectively bound and cleaved, but in this case, the association constants are significantly lower ( approximately 10(5) M(-1)), and the binding is dependent on both unpaired base identity and bulge sequence context. A wide variety of evidence, including strand scission asymmetry, binding enantiospecificity, and MALDI-TOF cleavage fragment analysis, suggests that Rh(bpy)(2)(chrysi)(3+) binds abasic sites, like mismatches, through insertion of the bulky chrysi ligand into the base pair stack from the minor groove side and ejection of the unpaired base. At single base bulge sites, a similar, though not identical, metalloinsertion mode is suggested. The recognition of abasic sites and single base bulges with bulky metalloinsertors holds promise for diagnostic and therapeutic applications.

SUBMITTER: Zeglis BM

PROVIDER: S-EPMC2747346 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Recognition of abasic sites and single base bulges in DNA by a metalloinsertor.

Zeglis Brian M BM Boland Jennifer A JA Barton Jacqueline K JK

Biochemistry 20090201 5

Abasic sites and single base bulges are thermodynamically destabilizing DNA defects that can lead to cancerous transformations if left unrepaired by the cell. Here we discuss the binding properties with abasic sites and single base bulges of Rh(bpy)(2)(chrysi)(3+), a complex previously shown to bind thermodynamically destabilized mismatch sites via metalloinsertion. Photocleavage experiments show that Rh(bpy)(2)(chrysi)(3+) selectively binds abasic sites with affinities of 1-4 x 10(6) M(-1); spe ...[more]

PMID: 19146409

Similar Datasets

Project description:BACKGROUND: The high binding specificity of short 10 to 30 mer oligonucleotide probes enables single base mismatch (MM) discrimination and thus provides the basis for genotyping and resequencing microarray applications. Recent experiments indicate that the underlying principles governing DNA microarray hybridization - and in particular MM discrimination - are not completely understood. Microarrays usually address complex mixtures of DNA targets. In order to reduce the level of complexity and to study the problem of surface-based hybridization with point defects in more detail, we performed array based hybridization experiments in well controlled and simple situations. RESULTS: We performed microarray hybridization experiments with short 16 to 40 mer target and probe lengths (in situations without competitive hybridization) in order to systematically investigate the impact of point-mutations - varying defect type and position - on the oligonucleotide duplex binding affinity. The influence of single base bulges and single base MMs depends predominantly on position - it is largest in the middle of the strand. The position-dependent influence of base bulges is very similar to that of single base MMs, however certain bulges give rise to an unexpectedly high binding affinity. Besides the defect (MM or bulge) type, which is the second contribution in importance to hybridization affinity, there is also a sequence dependence, which extends beyond the defect next-neighbor and which is difficult to quantify. Direct comparison between binding affinities of DNA/DNA and RNA/DNA duplexes shows, that RNA/DNA purine-purine MMs are more discriminating than corresponding DNA/DNA MMs. In DNA/DNA MM discrimination the affected base pair (C.G vs. A.T) is the pertinent parameter. We attribute these differences to the different structures of the duplexes (A vs. B form). CONCLUSION: We have shown that DNA microarrays can resolve even subtle changes in hybridization affinity for simple target mixtures. We have further shown that the impact of point defects on oligonucleotide stability can be broken down to a hierarchy of effects. In order to explain our observations we propose DNA molecular dynamics - in form of zipping of the oligonucleotide duplex - to play an important role.

Dataset Information

Recognition of abasic sites and single base bulges in DNA by a metalloinsertor.

Publications

Recognition of abasic sites and single base bulges in DNA by a metalloinsertor.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets