Article

Systematic DNA nicking reveals the structural logic of protein recognition

2025-07-04

Abstract excerpt

Transcription factors (TFs) bind to specific genomic sites to regulate gene expression 1,2 . These interactions almost universally require DNA deformation and the accumulation of local mechanical strain within the double helix. As a result, TF-DNA recognition is determined not only by the linear base sequence but also by the spatial alignment of bases and phosphates, as well as their ability to adopt and retain s...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 9e3aa8bb-4370-5768-b572-879cb91fa0ea
DOI: 10.1101/2025.06.30.662289

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Systematic DNA nicking reveals the structural logic of protein recognitionDOI 10.1101/2025.06.30.662289Read

DNA Mechanical Strain Steers Transcription Factor RecognitionSemantic proximity Read

Protein-mediated stabilization and nicking of the non-template DNA strand dramatically affect R-loop formation <i>in vitro</i>Semantic proximity Read

NickSeq for genome-wide strand-specific identification of DNA single-strand break sites with single nucleotide resolutionSemantic proximity Read

Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA.Semantic proximity Read

DNA mismatches reveal conformational penalties in protein-DNA recognition.Semantic proximity Read

Characterization of nick binding and sealing by LIG1 Huntington’s disease-asssociated K845N variant at biochemical, structural, and single-molecule levelsSemantic proximity Read

Assessing base-resolution DNA mechanics on the genome scaleSemantic proximity Read

Novel DNA endonuclease activity of human ERK1 proteinSemantic proximity Read

A Dynamic Search Mechanism Enables APE1 to Identify AP-Sites in DNASemantic proximity Read

Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule levelSemantic proximity Read

Unusual DNA conformations.Semantic proximity Read

AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop.Semantic proximity Read