{"doi":"10.1093/nar/gkaa1249","title":"Conformational constraints of cyclopentane peptide nucleic acids facilitate tunable binding to DNA","abstract":"We report a series of synthetic, nucleic acid mimics with highly customizable thermodynamic binding to DNA. Incorporation of helix-promoting cyclopentanes into peptide nucleic acids (PNAs) increases the melting temperatures (Tm) of PNA+DNA duplexes by approximately +5°C per cyclopentane. Sequential addition of cyclopentanes allows the Tm of PNA + DNA duplexes to be systematically fine-tuned from +5 to +50°C compared with the unmodified PNA. Containing only nine nucleobases and an equal number of cyclopentanes, cpPNA-9 binds to complementary DNA with a Tm around 90°C. Additional experiments reveal that the cpPNA-9 sequence specifically binds to DNA duplexes containing its complementary sequence and functions as a PCR clamp. An X-ray crystal structure of the cpPNA-9-DNA duplex revealed that cyclopentanes likely induce a right-handed helix in the PNA with conformations that promote DNA binding.","journal":"Nucleic Acids Research","year":2020,"id":98900,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":31,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9504,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":289171,"name":"Istvan Botos","orcid":"0000-0002-7702-6749","position":1,"is_corresponding":false},{"id":487249,"name":"Victor Clausse","orcid":"0000-0002-9080-4365","position":2,"is_corresponding":false},{"id":487250,"name":"Herman Nikolayevskiy","orcid":"0000-0002-4658-4182","position":3,"is_corresponding":false},{"id":487793,"name":"Elizabeth E. Rastede","orcid":null,"position":4,"is_corresponding":false},{"id":487794,"name":"Munira F. Fouz","orcid":null,"position":5,"is_corresponding":false},{"id":487251,"name":"Sharlyn J. Mazur","orcid":"0000-0002-6378-0791","position":6,"is_corresponding":false},{"id":383718,"name":"Daniel H. Appella","orcid":"0000-0001-7195-7764","position":7,"is_corresponding":false},{"id":487248,"name":"Hongchao Zheng","orcid":"0000-0003-2205-175X","position":0,"is_corresponding":true}],"reference_count":51,"raw_metadata":null,"created_at":"2026-07-18T22:36:58.511143Z","pmid":"33406227","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":[]}