{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.dna-binding-protein","code":"thing-q2252764","url":"https://ver.cy/models/thing/q2252764/","name":"DNA-binding protein","alternateNames":["Adenovirus E2 proteins","Restriction modification methylase Eco57I, protein family","Spo11/DNA topoisomerase VI, subunit A, N-terminal domain, protein family","EcoEI R protein C-terminal domain, protein family","DNA polymerase I-like, H3TH domain, protein family","Transposase IS3/IS911family","Transposase, IS801/IS1294","Transposase, IS1","Transposase, IS116/IS110/IS902","Transposase, mutator type","Transposase IS200-like superfamily","Bacteriophage Mu, transposase family"],"kind":"thing","status":"published","version":"0.2.0-wave.2","language":"en","classifiers":{"family":"Thing Registry","category":"Physical world and living systems","entryKind":"thing","plane":"PHY","domain":["PHY.MAT"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"A protein with DNA-binding domains that confer specific or general affinity for single- or double-stranded DNA; binding may be sequence-specific, as in many transcription factors and restriction and modification enzymes, non-sequence-specific, as in histones and polymerases, or directed toward DNA damage or structure, as in many repair proteins; DNA-binding proteins use varied structural motifs and participate in gene expression, replication, repair and recombination and are classified in protein family databases.","purpose":"Let an agent explain DNA-binding proteins and their kinds, describe binding mechanisms and functions, relate them to gene regulation and disease at a general level, and support database lookups.","scope":{"in":[],"out":[],"boundaries":[]},"distinguishingFeatures":["DNA binding","Structural motifs","Regulatory roles","Family classification"],"structure":{"bundles":[{"id":"understand","name":"Understand","description":"What DNA-binding proteins are.","layers":[{"id":"kinds","name":"Kinds","description":"Kinds and motifs.","findings":[{"id":"kinds-finding","name":"Kinds","description":"Kinds.","questions":[{"text":"What kinds of DNA-binding proteins exist, and which structural motifs let them recognise DNA?","kind":"definition"},{"text":"How do specific and non-specific binding differ?","kind":"definition"}]}]},{"id":"functions","name":"Functions","description":"Functions.","findings":[{"id":"functions-finding","name":"Functions","description":"Functions.","questions":[{"text":"How do DNA-binding proteins regulate transcription, replication, repair, recombination and transposition?","kind":"definition"},{"text":"Which entry fits a specific family?","kind":"action"}]}]}]},{"id":"study","name":"Study","description":"Studying binding.","layers":[{"id":"methods","name":"Methods","description":"Experimental methods.","findings":[{"id":"methods-finding","name":"Methods","description":"Methods.","questions":[{"text":"How is DNA binding studied with techniques such as ChIP-seq, footprinting and structural biology?","kind":"provenance"},{"text":"How are binding sites predicted?","kind":"action"}]}]},{"id":"databases","name":"Databases","description":"Databases.","findings":[{"id":"databases-finding","name":"Databases","description":"Databases.","questions":[{"text":"Which databases classify DNA-binding protein families and structures?","kind":"provenance"},{"text":"How can a protein be looked up?","kind":"action"}]}]}]},{"id":"medicine","name":"Medicine","description":"Health relevance.","layers":[{"id":"disease","name":"Disease","description":"In disease.","findings":[{"id":"disease-finding","name":"Disease","description":"Disease.","questions":[{"text":"How do mutations in DNA-binding proteins relate to cancer and genetic conditions, according to research?","kind":"provenance"},{"text":"Is the user asking about their own genetic results, which needs a clinician?","kind":"boundary"}]}]},{"id":"tools","name":"Tools","description":"As tools.","findings":[{"id":"tools-finding","name":"Tools","description":"Tools.","questions":[{"text":"How are DNA-binding proteins used as tools, from restriction enzymes to engineered nucleases?","kind":"provenance"},{"text":"Which entry fits genome editing?","kind":"action"}]}]}]},{"id":"learn","name":"Learn","description":"Teaching and history.","layers":[{"id":"teach","name":"Teach","description":"Teaching.","findings":[{"id":"teach-finding","name":"Teach","description":"Teaching.","questions":[{"text":"How can DNA-protein interactions be taught with structures and examples?","kind":"action"},{"text":"Which misconceptions arise?","kind":"provenance"}]}]},{"id":"history","name":"History","description":"History.","findings":[{"id":"history-finding","name":"History","description":"History.","questions":[{"text":"How were DNA-binding proteins discovered, from repressors to zinc fingers?","kind":"provenance"},{"text":"Which references are standard?","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Explain how DNA-binding proteins work and their families from scientific sources.","Distinguish sequence-specific from non-specific binding in explanations."],"mustNot":["Interpret a person's own mutation in a DNA-binding protein as medical advice.","Use outdated family classifications without saying so.","Overstate the predictive power of binding site predictions.","Assist genetic engineering outside lawful and approved laboratory settings."],"requiresHuman":["Using results about DNA-binding proteins in diagnosis or treatment."]},"ethics":{"considerations":["Mutations in these proteins cause diseases whose carriers need careful counselling.","Tools built from them, such as gene editors, carry large ethical stakes."],"affectedParties":["Patients and carriers","Research participants","Researchers"]},"owners":{"steward":"Nobody owns the class; protein databases curate the records.","roles":[],"masterSystems":["Protein sequence and structure databases"]},"relations":[{"target":"Q106952127","type":"parent","note":"registry parent class"},{"target":"Q8054","type":"parent","note":"registry parent class"},{"target":"nucleic acid binding protein","type":"related","note":"category"},{"target":"protein","type":"related","note":"category"},{"target":"gene expression","type":"related","note":"regulation"},{"target":"deoxyribonucleic acid","type":"related","note":"binding target"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.dna-binding-protein","Wikidata: Q2252764 (https://www.wikidata.org/wiki/Q2252764)"]},"properties":{"applicability":"required","items":["Molecular mass:  kDa - Molecular mass varies among proteins and is determined from sequence composition or measured by mass spectrometry.","Hydrodynamic radius:  nm - Hydrodynamic radius is measured in solution and depends on protein shape, assembly state and experimental conditions.","DNA-binding dissociation constant:  mol/L - The dissociation constant is measured using equilibrium binding assays with a specified DNA substrate and solution conditions."]},"recognition":{"applicability":"required","items":["Binds DNA specifically or non-specifically","Structural binding motifs","RNA-binding proteins bind RNA instead","Not visible; molecular structures resolved by crystallography."]},"capabilities":{"applicability":"required","items":["explain kinds and mechanisms","describe functions","relate to regulation and disease","support database lookups"]},"hazards":{"applicability":"required","items":["Confusing specific and non-specific binding","Outdated family classifications","Agents giving medical advice on mutations"]},"interfaces":{"applicability":"required","items":["Protein family databases such as Pfam and InterPro","Structural data standards","Research ethics for genetic studies"]},"context":{"applicability":"required","items":["Proteins that interact with DNA.","transcription factors","histones and chromatin proteins","polymerases and helicases","restriction and modification enzymes","repair, recombination and transposase proteins"]}},"sources":[{"title":"Wikidata item Q2252764: DNA-binding protein","url":"https://www.wikidata.org/wiki/Q2252764","note":"identity and sense of the item"},{"title":"Wikipedia: DNA-binding protein","url":"https://en.wikipedia.org/wiki/DNA-binding_protein","note":"general description of the item"}],"openQuestions":["Should transcription factors be a separate entry?","How should databases be linked?","How should structures be linked?"],"resources":{"spec":"/models/things/publications/thing-q2252764/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q2252764/spec.json"],"providers":["Claude"],"researchStatus":"unreviewed","generatedAt":"2026-09-11T23:44:46Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"filled","interaction.identity":"filled","interaction.properties":"filled","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-07T12:16:31+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass"},"score":1.0}}