{"doi":"10.1093/nar/gkg212","title":"Hybridization kinetics and thermodynamics of molecular beacons","abstract":null,"journal":"Nucleic Acids Research","year":2003,"id":625256,"datarank":0.8652481493690659,"base_score":5.768320995793772,"endowment":5.768320995793772,"self_citation_contribution":0.8652481493690659,"citation_network_contribution":0.0,"self_endowment_contribution":0.8652481493690659,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":319,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1597651,"name":"A. Tsourkas","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Hybridization kinetics and thermodynamics of molecular beacons","abstract":"Molecular beacons are increasingly being used in many applications involving nucleic acid detection and quantification. The stem-loop structure of molecular beacons provides a competing reaction for probe-target hybridization that serves to increase probe specificity, which is particularly useful when single-base discrimination is desired. To fully realize the potential of molecular beacons, it is necessary to optimize their structure. Here we report a systematic study of the thermodynamic and kinetic parameters that describe the molecular beacon structure-function relationship. Both probe and stem lengths are shown to have a significant impact on the binding specificity and hybridization kinetic rates of molecular beacons. Specifically, molecular beacons with longer stem lengths have an improved ability to discriminate between targets over a broader range of temperatures. However, this is accompanied by a decrease in the rate of molecular beacon-target hybridization. Molecular beacons with longer probe lengths tend to have lower dissociation constants, increased kinetic rate constants, and decreased specificity. Molecular beacons with very short stems have a lower signal-to-background ratio than molecular beacons with longer stems. These features have significant implications for the design of molecular beacons for various applications.","is_dataset_classified":null,"base_score":5.768320995793772,"endowment":5.768320995793772,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"12582252","pmcid":"PMC150230","openalex_id":"https://openalex.org/W2109007387","authors":[],"funders":[],"total_grants":0,"fwci":12.4695,"citation_percentile":0.99015129,"influential_citations":0,"citation_trend":[{"year":2012,"count":16},{"year":2013,"count":21},{"year":2014,"count":13},{"year":2015,"count":14},{"year":2016,"count":12},{"year":2017,"count":12},{"year":2018,"count":13},{"year":2019,"count":12},{"year":2020,"count":15},{"year":2021,"count":10},{"year":2022,"count":16},{"year":2023,"count":5},{"year":2024,"count":13},{"year":2025,"count":11},{"year":2026,"count":6}],"oa_status":"bronze","license":null,"oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/31/4/1319/7038350/gkg212.pdf","host_type":"journal"},{"url":"https://academic.oup.com/nar/article-pdf/31/4/1319/7038350/gkg212.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/nar/article-pdf/31/4/1319/7038350/gkg212.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/gkg212","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/12582252","host_type":"repository"},{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.616.612","host_type":""},{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.637.6918","host_type":""},{"url":"http://europepmc.org/pmc/articles/PMC150230","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/150230","host_type":"repository"}],"fields_of_study":["Molecular Junctions and Nanostructures","Nanopore and Nanochannel Transport Studies","Advanced biosensing and bioanalysis techniques","DNA Probes","Kinetics","Nucleic Acid Conformation","Nucleic Acid Denaturation","Nucleic Acid Hybridization","Temperature","Thermodynamics"],"mesh_terms":["Kinetics","Nucleic Acid Conformation","Nucleic Acid Denaturation","Nucleic Acid Hybridization","Temperature","Thermodynamics","DNA Probes"],"keywords":["Biology","Molecular beacon","Kinetics","Thermodynamics","Computational biology","Genetics","DNA","Physics","Oligonucleotide"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Reduced inequalities"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-04T06:16:17.526565Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}