ArticleNucleic acids research2019
New insights into protein-DNA binding specificity from hydrogen bond based comparative study.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 71 citations in OpenAlex.
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- An information theory approach to quantifying the sequence-dependent response of nucleic acid motors with applications to nanopore DNA sequencing.Nature communications · 2026Article
- Anti-gene oligonucleotides targeting Friedreich's ataxia expanded GAA⋅TTC repeats increase Frataxin expression.Molecular therapy. Nucleic acids · 2025Article
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- DNAproDB: an updated database for the automated and interactive analysis of protein-DNA complexes.Nucleic acids research · 2025Article
- Molecular insights into the fine-tuning of pH-dependent ArsR-mediated regulation of the SabA adhesin in Helicobacter pylori.Nucleic acids research · 2024Article
- Quantitative and systematic NMR measurements of sequence-dependent A-T Hoogsteen dynamics uncovers unique conformational specificity in the DNA double helix.bioRxiv : the preprint server for biology · 2024Article
- Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation.Nucleic acids research · 2024Article
- GMean-a semi-supervised GRU and K-mean model for predicting the TF binding site.Scientific reports · 2024Article
- Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding.Biophysical journal · 2024Article
- Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Secondary metabolites in topical infectious diseases and nanomedicine applications.Nanomedicine (London, England) · 2024Review
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- Mass Spectrometry for Assessing Protein-Nucleic Acid Interactions.Analytical chemistry · 2023Review
- Missense MED12 variants in 22 males with intellectual disability: From nonspecific symptoms to complete syndromes.American journal of medical genetics. Part A · 2023Article
- Effect of phosphorylation of protamine-like cationic peptide on the binding affinity to DNA.Biophysical journal · 2022Article
- Conformational Change of Transcription Factors from Search to Specific Binding: AThe journal of physical chemistry. B · 2022Article
- Alignment of major-groove hydrogen bond arrays uncovers shared information between different DNA sequences that bind the same protein.NAR genomics and bioinformatics · 2022Article
- Single-Stranded DNA Binding Proteins and Their Identification Using Machine Learning-Based Approaches.Biomolecules · 2022Review
- Interrogating the substrate specificity landscape of UvrC reveals novel insights into its non-canonical function.Biophysical journal · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Knowledge of protein-DNA binding specificity has important implications in understanding DNA metabolism, transcriptional regulation and developing therapeutic drugs. Previous studies demonstrated hydrogen bonds between amino acid side chains and DNA bases play major roles in specific protein-DNA interactions. In this paper, we investigated the roles of individual DNA strands and protein secondary structure types in specific protein-DNA recognition based on side chain-base hydrogen bonds. By comparing the contribution of each DNA strand to the overall binding specificity between DNA-binding proteins with different degrees of binding specificity, we found that highly specific DNA-binding proteins show balanced hydrogen bonding with each of the two DNA strands while multi-specific DNA binding proteins are generally biased towards one strand. Protein-base pair hydrogen bonds, in which both bases of a base pair are involved in forming hydrogen bonds with amino acid side chains, are more prevalent in the highly specific protein-DNA complexes than those in the multi-specific group. Amino acids involved in side chain-base hydrogen bonds favor strand and coil secondary structure types in highly specific DNA-binding proteins while multi-specific DNA-binding proteins prefer helices.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.