Biophysical Society Thematic Meeting| Santa Cruz 2018

Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes

Thursday Speaker Abstracts

Mismatched Base-pairs Locally Distort DNA Structure and Can Induce Increased DNA- binding by Transcription Factor Proteins Ariel Afek , Honglue Shi, Atul Rangadurai, Hashim Al Hashimi, Raluca Gordan. Duke, Durham, NC, USA. The local structure of genomic DNA can vary drastically from the ideal B-form double helix, and one cause for structural deformations is the pairing of non-complementary bases (i.e. mis-paired bases, or mismatches). DNA mismatches are frequently formed by spontaneous base deamination, replication errors, and genetic recombination. Mismatches alter DNA structure and the functional groups available in the major/minor grooves, which can affect interactions with regulatory transcription factors (TFs). Currently, very little is known about the effects of mismatches and other DNA structural changes on TF binding. We present Saturation Mismatch Binding Assay (SaMBA), the first assay to characterize the effects of mismatches on TF-DNA binding in high-throughput. For genomic sequences of interest, SaMBA generates DNA duplexes containing all possible single-base mismatches, and quantitatively assesses the effects of the mismatches on TF-DNA interactions. We applied SaMBA to measure binding of 20 TFs (covering 14 structural families) to thousands of mismatched sequences, and mapped the impact of mismatches on these TFs. Interestingly, for all tested factors we found that DNA mismatches within TF binding sites can significantly increase TF binding levels compared to the wild-type sequences. Furthermore, for several TFs we have identified non-specific genomic regions that become strongly bound after certain mismatches are introduced. Structural analyses of mismatches that increase TF binding revealed that these mismatched are oftentimes distorting the naked DNA such that its structure becomes similar to that of bound DNA sites, thus explaining the increased binding measured in our assay. In addition to providing new insights into the role of DNA structure in protein-DNA recognition, our finding of increased TF binding to mismatched DNA is important for understanding DNA repair and the formation of mutations in the genome, directions that we currently investigating.

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