{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.guide-rna","code":"thing-q4039747","url":"https://ver.cy/models/thing/q4039747/","name":"guide RNA","alternateNames":["CRISPR-Cas system guide RNA"],"kind":"thing","status":"published","version":"0.1.0-research.1","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 guide RNA is an RNA molecule whose sequence directs a molecular complex to a complementary nucleic-acid target, including RNAs used in CRISPR targeting and mitochondrial RNA editing.","purpose":"Enable an agent to identify a guide RNA, assess its molecular condition and targeting evidence, and determine its suitability for a specified compatible biological system.","scope":{"in":["Guide RNA sequence, molecular architecture, chemical modifications and maturation state","Target recognition regions and their relationship to an identified DNA or RNA substrate","Compatibility with a specified effector and any required companion RNA","Physical preparation, concentration, integrity, purity and storage history","Evidence for guide-dependent activity, specificity and application suitability"],"out":["Effector proteins and editing complexes as independently modelled entities","DNA constructs, vectors and transcription systems that encode a guide RNA","Delivery vehicles and complete formulated products","Target organisms, cells, genomes and transcripts beyond their targeting relationships","Complete editing workflows, downstream repair pathways and resulting engineered organisms"],"boundaries":[]},"distinguishingFeatures":["A guide RNA supplies sequence-dependent recognition of a nucleic-acid substrate within a specified functional system; being a short RNA alone does not establish guide identity.","The RNA molecule is distinct from a DNA construct encoding it, even when both are informally labelled with the same guide name.","For Cas9, an engineered single-guide RNA combines guide and companion-RNA functions in one chain, whereas a dual-RNA guide uses separate crRNA and tracrRNA components.","A spacer sequence alone does not identify the complete guide: scaffold, companion requirements, termini and modifications can distinguish functionally different molecules.","The name does not uniquely imply CRISPR: RNA-editing guides require a separate mechanism classification, and antisense or RNA-interference reagents should not be merged solely because they base-pair with a target."],"structure":{"bundles":[{"id":"guide-identity-and-mechanism","name":"Guide identity and mechanism","description":"Establish which molecular entity and biological meaning the guide designation refers to.","layers":[{"id":"mechanistic-classification","name":"Mechanistic classification","description":"Distinguish guide systems before applying system-specific requirements.","findings":[{"id":"guide-role","name":"Guide role","description":"Record the process in which the RNA provides recognition or editing information. RNA-editing guidance is an evidenced use of the term: [Structural basis of the RNA-editing cascade in trypanosome mitochondria](https://www.nature.com/articles/s41586-026-10831-x).","questions":[{"text":"Which biological mechanism makes this RNA a guide, and what evidence establishes that role?","id":"guide-role-q01","kind":"definition"},{"text":"Does this record denote the RNA itself, an encoding construct, or a larger guide-containing complex?","id":"guide-role-q02","kind":"boundary"}]}]},{"id":"molecular-identity","name":"Molecular identity","description":"Resolve guide names into sequence-defined molecular variants.","findings":[{"id":"sequence-and-variant-record","name":"Sequence and variant record","description":"Identify every chain, its annotated regions, terminal chemistry and modifications independently of target-based nicknames.","questions":[{"text":"What complete sequences, chain boundaries, termini and chemical modifications define this guide variant?","id":"sequence-and-variant-record-q01","kind":"definition"},{"text":"Which accession, design version or supplier record establishes that identity, and was it independently verified?","id":"sequence-and-variant-record-q02","kind":"provenance"}]}]}]},{"id":"target-recognition","name":"Target recognition","description":"Describe the intended substrate and the sequence relationship through which the guide recognizes it.","layers":[{"id":"target-reference","name":"Target reference","description":"Anchor recognition to a defined DNA or RNA sequence.","findings":[{"id":"target-alignment","name":"Target alignment","description":"Preserve target identity, version, strand and guide-to-target pairing rather than recording only a gene name.","questions":[{"text":"Which substrate sequence, reference version, coordinates and strand define the intended target?","id":"target-alignment-q01","kind":"definition"},{"text":"How does the recognition region align to that substrate, including mismatches, gaps and relevant sample variants?","id":"target-alignment-q02","kind":"measurement"}]}]},{"id":"recognition-constraints","name":"Recognition constraints","description":"Capture requirements imposed by the particular guide-effector mechanism.","findings":[{"id":"recognition-eligibility","name":"Recognition eligibility","description":"Treat adjacent motifs, substrate accessibility and pairing requirements as system-dependent conditions; do not assume a universal PAM requirement.","questions":[{"text":"Which adjacent-sequence, pairing or substrate-state requirements apply to this exact guide-effector system?","id":"recognition-eligibility-q01","kind":"definition"},{"text":"What evidence supports target accessibility in the intended biological context?","id":"recognition-eligibility-q02","kind":"provenance"}]}]}]},{"id":"architecture-and-effector-compatibility","name":"Architecture and effector compatibility","description":"Determine whether the guide has the structural components required by its functional partners.","layers":[{"id":"guide-architecture","name":"Guide architecture","description":"Separate target-recognition regions from structural and companion-binding regions.","findings":[{"id":"chain-and-scaffold-arrangement","name":"Chain and scaffold arrangement","description":"Record single-chain or multipart architecture and scaffold identity. Cas9 guide format and folding distinctions are supported by [Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage](https://www.nature.com/articles/s41467-022-28137-7).","questions":[{"text":"Which regions provide target recognition, partner binding and any additional guide function?","id":"chain-and-scaffold-arrangement-q01","kind":"definition"},{"text":"What evidence shows that the proposed chain arrangement and scaffold form a functional guide in this system?","id":"chain-and-scaffold-arrangement-q02","kind":"provenance"}]}]},{"id":"functional-partners","name":"Functional partners","description":"Identify the effector, companion RNAs and maturation dependencies.","findings":[{"id":"assembly-readiness","name":"Assembly readiness","description":"Distinguish predicted compatibility from demonstrated partner association and activity.","questions":[{"text":"Which effector variant, companion RNA and processing steps are required for this guide to function?","id":"assembly-readiness-q01","kind":"definition"},{"text":"Is the available RNA in the required mature and associated state, and what evidence supports proceeding with its intended use?","id":"assembly-readiness-q02","kind":"action"}]}]}]},{"id":"rna-preparation-and-condition","name":"RNA preparation and condition","description":"Describe the actual material carrying a guide identity and its changing condition.","layers":[{"id":"production-and-composition","name":"Production and composition","description":"Connect synthesis or isolation history with measured preparation contents.","findings":[{"id":"preparation-quality","name":"Preparation quality","description":"Record production route, lot identity, concentration basis and assays distinguishing intended guide from truncated RNA and other relevant impurities.","questions":[{"text":"How was this preparation produced and purified, and which lot-specific records connect it to the intended molecular identity?","id":"preparation-quality-q01","kind":"provenance"},{"text":"What concentration, intact fraction and relevant impurity measurements are available, with methods and detection limits?","id":"preparation-quality-q02","kind":"measurement"}]}]},{"id":"stability-and-handling","name":"Stability and handling","description":"Track conditions that affect RNA integrity and application suitability.","findings":[{"id":"condition-dependent-usability","name":"Condition-dependent usability","description":"Associate buffer, storage duration, temperature excursions and handling history with preparation-specific stability evidence.","questions":[{"text":"What buffer, temperature, elapsed storage time and handling events characterize the material now?","id":"condition-dependent-usability-q01","kind":"measurement"},{"text":"Which guide-specific acceptance criteria determine whether this preparation can be used, needs reassessment or should be rejected?","id":"condition-dependent-usability-q02","kind":"action"}]}]}]},{"id":"functional-evidence-and-use-decisions","name":"Functional evidence and use decisions","description":"Connect guide activity and specificity evidence to a bounded intended application.","layers":[{"id":"intended-response","name":"Intended response","description":"Identify the endpoint the guide-containing system is expected to produce.","findings":[{"id":"guide-dependent-performance","name":"Guide-dependent performance","description":"Record measured responses with controls and conditions while keeping guide contribution distinct from effector, delivery and downstream biology.","questions":[{"text":"Is the intended endpoint binding, cleavage, RNA editing, DNA editing, regulation or another specified response?","id":"guide-dependent-performance-q01","kind":"definition"},{"text":"What controlled measurements support that endpoint, and in which effector, delivery and biological context were they obtained?","id":"guide-dependent-performance-q02","kind":"measurement"}]}]},{"id":"specificity-and-applicability","name":"Specificity and applicability","description":"Assess alternative target interactions and limits on transferring results to a new use.","findings":[{"id":"specificity-evidence","name":"Specificity evidence","description":"Separate computational candidates, observed non-target responses and unexamined possibilities, including assay coverage and uncertainty.","questions":[{"text":"Which unintended interactions or outcomes are predicted or observed, and what reference coverage and detection limits constrain those conclusions?","id":"specificity-evidence-q01","kind":"measurement"},{"text":"Does the available evidence meet the intended application's activity and specificity criteria, or what additional evidence is required?","id":"specificity-evidence-q02","kind":"action"}]}]}]},{"id":"evidence-and-external-alignment","name":"Evidence and external alignment","description":"What the world already says about this thing, gathered so the model can be checked against it.","layers":[{"id":"reported-evidence","name":"Reported evidence","description":"Findings from the breadth pass, kept separate from the structural claims.","findings":[{"id":"evidence-confidence-notes","name":"Check these first","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these check these first hold for the sense of guide RNA this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-kinds","name":"Kinds and varieties","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these kinds and varieties hold for the sense of guide RNA this model covers, and on what evidence?","id":"evidence-kinds-q01","kind":"provenance"}]},{"id":"evidence-identifiers","name":"Identifiers and schemes","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these identifiers and schemes hold for the sense of guide RNA this model covers, and on what evidence?","id":"evidence-identifiers-q01","kind":"provenance"}]},{"id":"evidence-real-world-use","name":"Real-world use","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these real-world use hold for the sense of guide RNA this model covers, and on what evidence?","id":"evidence-real-world-use-q01","kind":"provenance"}]},{"id":"evidence-measurements","name":"Typical measurements","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these typical measurements hold for the sense of guide RNA this model covers, and on what evidence?","id":"evidence-measurements-q01","kind":"provenance"}]},{"id":"evidence-failure-modes-and-hazards","name":"Failure modes and hazards","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these failure modes and hazards hold for the sense of guide RNA this model covers, and on what evidence?","id":"evidence-failure-modes-and-hazards-q01","kind":"provenance"}]},{"id":"evidence-neighbours","name":"Neighbouring kinds and how to tell them apart","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these neighbouring kinds and how to tell them apart hold for the sense of guide RNA this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Explain how guide RNAs direct molecular complexes through sequence complementarity.","Distinguish guide RNAs involved in CRISPR targeting from those involved in mitochondrial RNA editing."],"mustNot":["Claim that sequence complementarity guarantees exclusive targeting or a particular biological outcome.","Treat every guide RNA as a component of a genome editing system.","Assist in using guide RNAs to cause harmful genetic changes or other biological harm."],"requiresHuman":["The responsible investigator and relevant ethics authority must decide whether a proposed guide RNA application is acceptable."]},"ethics":{"considerations":["Overstated targeting precision can obscure unintended effects and weaken informed consent.","Applications with potentially heritable consequences raise responsibilities toward people who cannot consent."],"affectedParties":["Research participants or patients affected by guide RNA applications.","Future generations or ecosystems affected by persistent biological changes."]},"owners":{"steward":"The custodian responsible for the guide RNA record and its intended application.","roles":[],"masterSystems":["Public nucleotide sequence archives where the guide RNA sequence has been deposited."]},"relations":[{"target":"Q11053","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.guide-rna","Wikidata: Q4039747 (https://www.wikidata.org/wiki/Q4039747)"]},"properties":{"applicability":"required","items":["Guide mechanism: CRISPR-associated targeting; RNA-editing guidance; other evidenced mechanism; unresolved","Complete molecular sequence: 5′-to-3′ sequence for every RNA chain, with annotated regions and explicit ambiguity","Chain and recognition-region length: nucleotides per chain and per annotated recognition region","Chemical constitution: Position-specific base, sugar and backbone modifications; terminal chemistry","Target relationship: Reference accession and version, substrate type, sequence, coordinates, strand and alignment","Effector and companion compatibility: Named effector variant, scaffold version and required companion RNA, with evidence status","Maturation and association state: Precursor or mature; free, companion-paired, effector-bound or unknown","Preparation concentration: mol/L or mass/volume, with molecular-weight basis, method and uncertainty","Intact guide fraction: Percentage, with assay, denominator and measurement date","Context-specific functional response: Endpoint-specific units or percentage, with controls, biological context and uncertainty"]},"recognition":{"applicability":"required","items":["A documented molecular diagram identifies the guide RNA strand and its complementary nucleic acid target.","Annotations identifying the associated molecular complex distinguish the guide RNA's biological context.","Neither a sample's visible appearance nor an unannotated RNA shape establishes guide RNA identity."]},"capabilities":{"applicability":"required","items":["Resolve whether two guide records describe the same molecule, a sequence variant or different preparations.","Check whether guide architecture and companion requirements match a named effector.","Map an annotated recognition region to a versioned target and flag ambiguous or incompatible matches.","Compare predicted specificity with experimentally observed target and non-target responses.","Assess preparation suitability against explicit integrity, purity and storage requirements.","Select, defer or reject a guide for a stated application while preserving the supporting evidence and unresolved conditions."]},"hazards":{"applicability":"required","items":["Unintended targeting can alter or regulate nucleic acids beyond the intended target.","Degradation, contamination or incorrect sequence identity can cause failed experiments and misleading conclusions.","Incompatible guide RNA and molecular complex combinations can produce ineffective or unexpected activity.","Biological delivery can provoke unwanted cellular responses that depend on the material and receiving system."]},"interfaces":{"applicability":"required","items":["The Abbreviations and Symbols for Nucleic Acids, Polynucleotides, and Their Constituents recommendations issued jointly by the International Union of Pure and Applied Chemistry and the International Union of Biochemistry apply to guide RNA sequence notation."]},"context":{"applicability":"required","items":["Guide RNAs occur in biological systems where sequence complementarity helps direct molecular complexes to nucleic acid targets.","Research uses designed guide RNAs to direct compatible CRISPR complexes for targeting, editing or regulation.","Some mitochondrial RNA editing systems use guide RNAs to specify changes to RNA transcripts."]}},"sources":[{"title":"Wikidata item Q4039747: guide RNA","url":"https://www.wikidata.org/wiki/Q4039747","note":"identity and sense of the item"},{"title":"Wikipedia: Guide RNA","url":"https://en.wikipedia.org/wiki/Guide_RNA","note":"general description of the item"}],"openQuestions":["Does the underlying registry concept mean guide RNA broadly, specifically CRISPR guide RNA, or specifically RNA-editing guide RNA?","Does an existing Vercy RNA or CRISPR world model already own this concept, requiring a link rather than a separate publication?","Which additional guide mechanisms, if any, belong within this registry entry rather than neighbouring RNA categories?","Which mechanism-specific architecture and target-recognition constraints have sufficient primary evidence to become model requirements?","Which preparation quality, stability and specificity acceptance criteria are justified for each intended use, given that no universal thresholds have been established here?"],"resources":{"spec":"/models/things/publications/thing-q4039747/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q4039747/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T10:07:49Z","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 2026-10-08T18:56:48+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass"},"score":1.0}}