Systematic search for structural motifs of peptide binding to double-stranded DNA.

Kolchina N, Khavinson V, Linkova N, Yakimov A, Baitin D, Afanasyeva A, Petukhov M. Nucleic Acids Res. 2019.

Organ: general-aging · Type: in-vitro · Peptides: Vilon

An open-access 2019 NAR docking and MD survey of all 400 dipeptides against dsDNA tetranucleotides, with an EMSA check that KE (Vilon) and DR shift a labelled duplex — most dipeptides did not bind.

Editorial summary of a 2019 original article in Nucleic Acids Research (open access: doi:10.1093/nar/gkz850). Companion computational survey to earlier peptide–DNA modelling, plus a small gel-shift check. Public pages cite PubMed; the DOI is the OA record. Read the paper: PMID 31598715.

Methods

The authors docked all 400 standard dipeptides, free and N-/C-terminally blocked, into the central tetranucleotide of classical B-form dsDNA (136 unique 4-bp spatial structures) with ICM-Dock, then ran AMBER MD on selected complexes. They also ran electrophoretic mobility-shift assays on a 34-bp FAM-labelled duplex with KE, DR, AE, and ED. Docking grids, MD length, and peptide concentrations belong in the primary text.

Findings

Most dipeptides were unable to bind dsDNA. The authors identified 57 selective low-energy complexes. KE (Vilon) was the highest-affinity selective charged dipeptide in their table, docking to TCGA. EMSA ranked DR then KE above AE and ED on that duplex. Blocked termini increased selectivity; the authors suggest affinity and selectivity can rise with peptide length.

This is a docking/MD paper with a limited gel-shift check. It is not evidence of gene regulation in cells or in people. Follow the PMID and the OA DOI.