Products Cited in Publications Worldwide Decoding complexity in biomolecular recognition of DNA i-motifs with microarrays

Decoding complexity in biomolecular recognition of DNA i-motifs with microarrays

Yazdani, Kamyar; Seshadri, Srinath; Tillo, Desiree; Yang, Mo; Sibley, Christopher D.; Vinson, Charles; Schneekloth, John S. Jr.

DOI: PMID:

Abstract

DNA i-motifs (iMs) are non-canonical C-rich secondary structures implicated in numerous cellular processes. Though iMs exist throughout the genome, our understanding of iM recognition by proteins or small mols. is limited to a few examples. We designed a DNA microarray containing 10976 genomic iM sequences to examine the binding profiles of four iM-binding proteins, mitoxantrone and the iMab antibody. iMab microarray screens demonstrated that pH 6.5, 5% BSA buffer was optimal, and fluorescence was correlated with iM C-tract length. hnRNP K broadly recognizes diverse iM sequences, favoring 3-5 cytosine repeats flanked by thymine-rich loops of 1-3 nucleotides. Array binding mirrored public ChIP-Seq datasets, in which 35% of well-bound array iMs are enriched in hnRNP K peaks. In contrast, other reported iM-binding proteins had weaker binding or preferred G-quadruplex (G4) sequences instead. Mitoxantrone broadly binds both shorter iMs and G4s, consistent with an intercalation mechanism. These results suggest that hnRNP K may play a role in iM-mediated regulation of gene expression in vivo, whereas hnRNP A1 and ASF/SF2 are possibly more selective in their binding preferences. This powerful approach represents the most comprehensive investigation of how biomols. selectively recognize genomic iMs to date.

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Mitoxantrone

A20795165271-80-998%

Mitoxantrone

375.0/1g

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