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

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 molecules is limited to a few examples. We designed a DNA microarray containing 10976...

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Published in:Nucleic acids research Vol. 51; no. 22; pp. 12020 - 12030
Main Authors: Yazdani, Kamyar, Seshadri, Srinath, Tillo, Desiree, Yang, Mo, Sibley, Christopher D, Vinson, Charles, Schneekloth, John S
Format: Journal Article
Language:English
Published: England Oxford University Press 11.12.2023
Subjects:
Chemical Biology and Nucleic Acid Chemistry
DNA - chemistry
G-Quadruplexes
Heterogeneous-Nuclear Ribonucleoprotein K
Humans
Mitoxantrone
Nucleotide Motifs
Oligonucleotide Array Sequence Analysis
ISSN:0305-1048, 1362-4962, 1362-4962
Online Access:Get full text
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Summary: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 molecules 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 biomolecules selectively recognize genomic iMs to date. Graphical Abstract Graphical Abstract
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The authors wish it to be known that, in their opinion, the first three authors should be regarded as Joint First Authors.
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkad981