{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T13:57:06Z","timestamp":1776866226758,"version":"3.51.2"},"reference-count":163,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2022,10,7]],"date-time":"2022-10-07T00:00:00Z","timestamp":1665100800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province","award":["2022E10022"],"award-info":[{"award-number":["2022E10022"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170650"],"award-info":[{"award-number":["32170650"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Guangzhou and Guangdong Key Project","award":["202007030002"],"award-info":[{"award-number":["202007030002"]}]},{"name":"Guangzhou and Guangdong Key Project","award":["2018B030335001"],"award-info":[{"award-number":["2018B030335001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Multiple types of non-canonical nucleic acid structures play essential roles in DNA recombination and replication, transcription, and genomic instability and have been associated with several human diseases. Thus, an increasing number of experimental and bioinformatics methods have been developed to identify these structures. To date, most reviews have focused on the features of non-canonical DNA\/RNA structure formation, experimental approaches to mapping these structures, and the association of these structures with diseases. In addition, two reviews of computational algorithms for the prediction of non-canonical nucleic acid structures have been published. One of these reviews focused only on computational approaches for G4 detection until 2020. The other mainly summarized the computational tools for predicting cruciform, H-DNA and Z-DNA, in which the algorithms discussed were published before 2012. Since then, several experimental and computational methods have been developed. However, a systematic review including the conformation, sequencing mapping methods and computational prediction strategies for these structures has not yet been published. The purpose of this review is to provide an updated overview of conformation, current sequencing technologies and computational identification methods for non-canonical nucleic acid structures, as well as their strengths and weaknesses. We expect that this review will aid in understanding how these structures are characterised and how they contribute to related biological processes and diseases.<\/jats:p>","DOI":"10.1093\/bib\/bbac441","type":"journal-article","created":{"date-parts":[[2022,10,8]],"date-time":"2022-10-08T12:27:38Z","timestamp":1665232058000},"source":"Crossref","is-referenced-by-count":5,"title":["An updated overview of experimental and computational approaches to identify non-canonical DNA\/RNA structures with emphasis on G-quadruplexes and R-loops"],"prefix":"10.1093","volume":"23","author":[{"given":"Xiaohui","family":"Shi","sequence":"first","affiliation":[{"name":"Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The first Affiliated Hospital of WMU; Beijing Institutes of Life Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences , Ouhai District, Wenzhou 325000, China"}]},{"given":"Huajing","family":"Teng","sequence":"additional","affiliation":[{"name":"Department of Radiation Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) at Peking University Cancer Hospital and Institute , Ouhai District, Wenzhou 325000, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1992-2681","authenticated-orcid":false,"given":"Zhongsheng","family":"Sun","sequence":"additional","affiliation":[{"name":"Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The first Affiliated Hospital of WMU; Beijing Institutes of Life Science, Chinese Academy of Sciences; CAS Center for Excellence in Biotic Interactions and State Key Laboratory of Integrated Management of Pest Insects and Rodents, University of Chinese Academy of Sciences; Institute of Genomic Medicine, Wenzhou Medical University; IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital); Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences , Ouhai District, Wenzhou 325000, China"}]}],"member":"286","published-online":{"date-parts":[[2022,10,7]]},"reference":[{"key":"2022112111202675700_ref1","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/171737a0","article-title":"Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid","volume":"171","author":"JD","year":"1953","journal-title":"Nature"},{"key":"2022112111202675700_ref2","doi-asserted-by":"crossref","first-page":"1264","DOI":"10.1101\/gr.231688.117","article-title":"Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis","volume":"28","author":"Georgakopoulos-Soares","year":"2018","journal-title":"Genome Res"},{"key":"2022112111202675700_ref3","doi-asserted-by":"crossref","first-page":"3785","DOI":"10.1093\/nar\/gki697","article-title":"Advances in mechanisms of genetic instability related to hereditary neurological diseases","volume":"33","author":"Wells","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref4","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1107\/S0907444903003251","article-title":"A glossary of DNA structures from A to Z","volume":"59","author":"Ghosh","year":"2003","journal-title":"Acta Crystallogr Sect D Biol Crystallogr"},{"key":"2022112111202675700_ref5","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.2741\/2744","article-title":"Discovery of alternative DNA structures: a heroic decade (1979\u20131989)","volume":"13","author":"Mirkin","year":"2008","journal-title":"Front Biosci"},{"key":"2022112111202675700_ref6","doi-asserted-by":"crossref","first-page":"5237","DOI":"10.1073\/pnas.94.10.5237","article-title":"Characteristic enrichment of DNA repeats in different genomes","volume":"94","author":"Cox","year":"1997","journal-title":"Proc Natl Acad Sci"},{"key":"2022112111202675700_ref7","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/j.dnarep.2014.03.017","article-title":"Impact of alternative DNA structures on DNA damage, DNA repair, and genetic instability","volume":"19","author":"Wang","year":"2014","journal-title":"DNA Repair (Amst)"},{"key":"2022112111202675700_ref8","doi-asserted-by":"crossref","first-page":"e1568","DOI":"10.1002\/wrna.1568","article-title":"The role of RNA G-quadruplexes in human diseases and therapeutic strategies","volume":"11","author":"Kharel","year":"2020","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"2022112111202675700_ref9","doi-asserted-by":"crossref","first-page":"8627","DOI":"10.1093\/nar\/gkv862","article-title":"G-quadruplexes and their regulatory roles in biology","volume":"43","author":"Rhodes","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref10","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1016\/j.biochi.2008.02.011","article-title":"DNA triple helices: biological consequences and therapeutic potential","volume":"90","author":"Jain","year":"2008","journal-title":"Biochimie"},{"key":"2022112111202675700_ref11","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/nrg3961","article-title":"R loops: new modulators of genome dynamics and function","volume":"16","author":"Santos-Pereira","year":"2015","journal-title":"Nat Rev Genet"},{"key":"2022112111202675700_ref12","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1007\/s12551-019-00534-1","article-title":"Z-DNA in the genome: from structure to disease","volume":"11","author":"Ravichandran","year":"2019","journal-title":"Biophys Rev"},{"key":"2022112111202675700_ref13","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1038\/s41580-019-0206-3","article-title":"Regulatory R-loops as facilitators of gene expression and genome stability","volume":"21","author":"Niehrs","year":"2020","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2022112111202675700_ref14","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1038\/nrm.2017.3","article-title":"DNA G-quadruplexes in the human genome: detection, functions and therapeutic potential","volume":"18","author":"H\u00e4nsel-Hertsch","year":"2017","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2022112111202675700_ref15","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1016\/j.tibtech.2017.06.012","article-title":"G-quadruplexes: prediction, characterization, and biological application","volume":"35","author":"Kwok","year":"2017","journal-title":"Trends Biotechnol"},{"key":"2022112111202675700_ref16","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1038\/s41580-020-0236-x","article-title":"The regulation and functions of DNA and RNA G-quadruplexes","volume":"21","author":"Varshney","year":"2020","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2022112111202675700_ref17","doi-asserted-by":"crossref","first-page":"9","DOI":"10.3390\/ncrna4020009","article-title":"Strengths and weaknesses of the current strategies to map and characterize R-loops","volume":"4","author":"Vanoosthuyse","year":"2018","journal-title":"Non-Coding RNA"},{"key":"2022112111202675700_ref18","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1016\/S0021-9258(17)49903-0","article-title":"The balancing act of R-loop biology: the good, the bad, and the ugly","volume":"295","author":"Hegazy","year":"2020","journal-title":"J Biol Chem"},{"key":"2022112111202675700_ref19","doi-asserted-by":"crossref","DOI":"10.15252\/embj.2020106394","article-title":"Best practices for the visualization, mapping, and manipulation of R-loops","volume":"40","author":"Ch\u00e9din","year":"2021","journal-title":"EMBO J"},{"key":"2022112111202675700_ref20","doi-asserted-by":"crossref","first-page":"11706","DOI":"10.1093\/nar\/gkaa841","article-title":"Detection of genomic G-quadruplexes in living cells using a small artificial protein","volume":"48","author":"Zheng","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref21","doi-asserted-by":"crossref","first-page":"3116","DOI":"10.1038\/s41598-018-21514-7","article-title":"Identification of G-quadruplex clusters by high-throughput sequencing of whole-genome amplified products with a G-quadruplex ligand","volume":"8","author":"Yoshida","year":"2018","journal-title":"Sci Rep"},{"key":"2022112111202675700_ref22","doi-asserted-by":"crossref","first-page":"4730","DOI":"10.1038\/s41467-018-07224-8","article-title":"Transcriptome-wide identification of transient RNA G-quadruplexes in human cells","volume":"9","author":"Yang","year":"2018","journal-title":"Nat Commun"},{"key":"2022112111202675700_ref23","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1186\/s13059-020-02142-9","article-title":"RNA G-quadruplex structures exist and function in vivo in plants","volume":"21","author":"Yang","year":"2020","journal-title":"Genome Biol"},{"key":"2022112111202675700_ref24","doi-asserted-by":"crossref","first-page":"e84","DOI":"10.1093\/nar\/gkaa500","article-title":"qDRIP: a method to quantitatively assess RNA\u2013DNA hybrid formation genome-wide","volume":"48","author":"Crossley","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref25","doi-asserted-by":"crossref","first-page":"eabe3516","DOI":"10.1126\/sciadv.abe3516","article-title":"Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor","volume":"7","author":"Wang","year":"2021","journal-title":"Sci Adv"},{"key":"2022112111202675700_ref26","doi-asserted-by":"crossref","first-page":"470","DOI":"10.2174\/1574893614666190126143438","article-title":"Computational approaches to predict the non-canonical DNAs","volume":"14","author":"Parveen","year":"2019","journal-title":"Curr Bioinform"},{"key":"2022112111202675700_ref27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkz1097","article-title":"A guide to computational methods for G-quadruplex prediction","volume":"48","author":"Puig Lombardi","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref28","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2020.568546","article-title":"PENGUINN: Precise exploration of nuclear G-quadruplexes using interpretable neural networks","volume":"11","author":"Klimentova","year":"2020","journal-title":"Front Genet"},{"key":"2022112111202675700_ref29","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1080\/15476286.2020.1740470","article-title":"rG4-seeker enables high-confidence identification of novel and non-canonical rG4 motifs from rG4-seq experiments","volume":"17","author":"Chow","year":"2020","journal-title":"RNA Biol"},{"key":"2022112111202675700_ref30","doi-asserted-by":"crossref","first-page":"e16","DOI":"10.1093\/nar\/gkr1075","article-title":"Quantitative model of R-loop forming structures reveals a novel level of RNA-DNA interactome complexity","volume":"40","author":"Wongsurawat","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref31","doi-asserted-by":"crossref","first-page":"D119","DOI":"10.1093\/nar\/gkw1054","article-title":"R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops","volume":"45","author":"Jenjaroenpun","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref32","doi-asserted-by":"crossref","first-page":"W527","DOI":"10.1093\/nar\/gkv344","article-title":"QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences","volume":"43","author":"Jenjaroenpun","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref33","doi-asserted-by":"crossref","first-page":"6014","DOI":"10.1038\/s41467-021-26312-w","article-title":"Direct genome-wide identification of G-quadruplex structures by whole-genome resequencing","volume":"12","author":"Tu","year":"2021","journal-title":"Nat Commun"},{"key":"2022112111202675700_ref34","doi-asserted-by":"crossref","first-page":"1946","DOI":"10.1109\/TCBB.2021.3073595","article-title":"G4detector: convolutional neural network to predict DNA G-quadruplexes","volume":"19","author":"Barshai","year":"2022","journal-title":"IEEE\/ACM Trans Comput Biol Bioinforma"},{"key":"2022112111202675700_ref35","doi-asserted-by":"crossref","first-page":"e1009308","DOI":"10.1371\/journal.pcbi.1009308","article-title":"DeepG4: a deep learning approach to predict cell-type specific active G-quadruplex regions","volume":"17","author":"Rocher","year":"2021","journal-title":"PLoS Comput Biol"},{"key":"2022112111202675700_ref36","first-page":"293","article-title":"Untersuchungen \u00fcber die Guanyls\u00e4ure","volume":"26","author":"Bang","year":"1910","journal-title":"Biochem Z"},{"key":"2022112111202675700_ref37","doi-asserted-by":"crossref","first-page":"2013","DOI":"10.1073\/pnas.48.12.2013","article-title":"Helix formation by guanylic acid","volume":"48","author":"Gellert","year":"1962","journal-title":"Proc Natl Acad Sci"},{"key":"2022112111202675700_ref38","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1038\/344410a0","article-title":"A sodium-potassium switch in the formation of four-stranded G4-DNA","volume":"344","author":"Sen","year":"1990","journal-title":"Nature"},{"key":"2022112111202675700_ref39","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1038\/334364a0","article-title":"Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis","volume":"334","author":"Sen","year":"1988","journal-title":"Nature"},{"key":"2022112111202675700_ref40","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/351331a0","article-title":"Tetramerization of an RNA oligonucleotide containing a GGGG sequence","volume":"351","author":"Kim","year":"1991","journal-title":"Nature"},{"key":"2022112111202675700_ref41","doi-asserted-by":"crossref","first-page":"8572","DOI":"10.1073\/pnas.141229498","article-title":"In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei","volume":"98","author":"Schaffitzel","year":"2001","journal-title":"Proc Natl Acad Sci"},{"key":"2022112111202675700_ref42","doi-asserted-by":"crossref","first-page":"2507","DOI":"10.15252\/embj.201488398","article-title":"Determinants of G quadruplex-induced epigenetic instability in REV1-deficient cells","volume":"33","author":"Schiavone","year":"2014","journal-title":"EMBO J"},{"key":"2022112111202675700_ref43","doi-asserted-by":"crossref","first-page":"2495","DOI":"10.1073\/pnas.79.8.2495","article-title":"Higher order DNA structure in macronuclear chromatin of the hypotrichous ciliate Oxytricha nova","volume":"79","author":"Lipps","year":"1982","journal-title":"Proc Natl Acad Sci"},{"key":"2022112111202675700_ref44","doi-asserted-by":"crossref","first-page":"7429","DOI":"10.1093\/nar\/gkm711","article-title":"Human telomere, oncogenic promoter and 5\u2032-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics","volume":"35","author":"Patel","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref45","doi-asserted-by":"crossref","first-page":"1989","DOI":"10.1093\/nar\/gkw079","article-title":"G-quadruplexes and helicases","volume":"44","author":"Mendoza","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref46","doi-asserted-by":"crossref","first-page":"2294","DOI":"10.1073\/pnas.73.7.2294","article-title":"Hybridization of RNA to double-stranded DNA: formation of R-loops","volume":"73","author":"Thomas","year":"1976","journal-title":"Proc Natl Acad Sci"},{"key":"2022112111202675700_ref47","doi-asserted-by":"crossref","first-page":"3526","DOI":"10.1073\/pnas.92.8.3526","article-title":"Overexpression of RNase H partially complements the growth defect of an Escherichia coli delta topA mutant: R-loop formation is a major problem in the absence of DNA topoisomerase I","volume":"92","author":"Drolet","year":"1995","journal-title":"Proc Natl Acad Sci"},{"key":"2022112111202675700_ref48","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1016\/j.cell.2019.08.055","article-title":"R loops: from physiological to pathological roles","volume":"179","author":"Garc\u00eda-Muse","year":"2019","journal-title":"Cell"},{"key":"2022112111202675700_ref49","doi-asserted-by":"crossref","first-page":"1327","DOI":"10.1101\/gad.280834.116","article-title":"S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation","volume":"30","author":"Wahba","year":"2016","journal-title":"Genes Dev"},{"key":"2022112111202675700_ref50","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1038\/s41477-017-0004-x","article-title":"The R-loop is a common chromatin feature of the Arabidopsis genome","volume":"3","author":"Xu","year":"2017","journal-title":"Nat Plants"},{"key":"2022112111202675700_ref51","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.molcel.2016.05.032","article-title":"Prevalent, dynamic, and conserved R-loop structures associate with specific epigenomic signatures in mammals","volume":"63","author":"Sanz","year":"2016","journal-title":"Mol Cell"},{"key":"2022112111202675700_ref52","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1016\/j.molcel.2017.05.014","article-title":"Histone mutants separate R loop formation from genome instability induction","volume":"66","author":"Garc\u00eda-Pichardo","year":"2017","journal-title":"Mol Cell"},{"key":"2022112111202675700_ref53","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1016\/j.cell.2005.06.008","article-title":"Inactivation of the SR protein splicing factor ASF\/SF2 results in genomic instability","volume":"122","author":"Li","year":"2005","journal-title":"Cell"},{"key":"2022112111202675700_ref54","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1038\/ni919","article-title":"R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells","volume":"4","author":"Yu","year":"2003","journal-title":"Nat Immunol"},{"key":"2022112111202675700_ref55","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1016\/j.molcel.2017.10.008","article-title":"R-ChIP using inactive RNase H reveals dynamic coupling of R-loops with transcriptional pausing at gene promoters","volume":"68","author":"Chen","year":"2017","journal-title":"Mol Cell"},{"key":"2022112111202675700_ref56","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1073\/pnas.1810409116","article-title":"DNA damage and genome instability by G-quadruplex ligands are mediated by R loops in human cancer cells","volume":"116","author":"De Magis","year":"2019","journal-title":"Proc Natl Acad Sci"},{"key":"2022112111202675700_ref57","doi-asserted-by":"crossref","first-page":"6036","DOI":"10.1021\/acs.analchem.7b00625","article-title":"Real-time detection reveals responsive cotranscriptional formation of persistent intramolecular DNA and intermolecular DNA:RNA hybrid G-quadruplexes stabilized by R-loop","volume":"89","author":"Zhao","year":"2017","journal-title":"Anal Chem"},{"key":"2022112111202675700_ref58","doi-asserted-by":"crossref","first-page":"3124","DOI":"10.1128\/MCB.00139-09","article-title":"G clustering is important for the initiation of transcription-induced R-loops in vitro, whereas high G density without clustering is sufficient thereafter","volume":"29","author":"Roy","year":"2009","journal-title":"Mol Cell Biol"},{"key":"2022112111202675700_ref59","doi-asserted-by":"crossref","first-page":"1618","DOI":"10.1101\/gad.1200804","article-title":"Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA","volume":"18","author":"Duquette","year":"2004","journal-title":"Genes Dev"},{"key":"2022112111202675700_ref60","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1038\/282680a0","article-title":"Molecular structure of a left-handed double helical DNA fragment at atomic resolution","volume":"282","author":"Wang","year":"1979","journal-title":"Nature"},{"key":"2022112111202675700_ref61","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1038\/nature04088","article-title":"Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases","volume":"437","author":"Ha","year":"2005","journal-title":"Nature"},{"key":"2022112111202675700_ref62","doi-asserted-by":"crossref","first-page":"4424","DOI":"10.2741\/2399","article-title":"Z-DNA, an active element in the genome","volume":"12","author":"Wang","year":"2007","journal-title":"Front Biosci"},{"key":"2022112111202675700_ref63","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/0092-8674(85)90316-2","article-title":"Transcriptional block caused by a negative supercoiling induced structural change in an alternating CG sequence","volume":"40","author":"Peck","year":"1985","journal-title":"Cell"},{"key":"2022112111202675700_ref64","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1093\/dnares\/dsw031","article-title":"Z-DNA-forming sites identified by ChIP-Seq are associated with actively transcribed regions in the human genome","volume":"23","author":"Shin","year":"2016","journal-title":"DNA Res"},{"key":"2022112111202675700_ref65","doi-asserted-by":"crossref","first-page":"2677","DOI":"10.1073\/pnas.0511084103","article-title":"Z-DNA-forming sequences generate large-scale deletions in mammalian cells","volume":"103","author":"Wang","year":"2006","journal-title":"Proc Natl Acad Sci"},{"key":"2022112111202675700_ref66","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1073\/pnas.41.3.181","article-title":"POSSIBLE SEPARATION OF INTERTWINED NUCLEIC ACID CHAINS BY TRANSFER-TWIST","volume":"41","author":"Platt","year":"1955","journal-title":"Proc Natl Acad Sci"},{"key":"2022112111202675700_ref67","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1016\/0014-5793(83)80628-0","article-title":"Evidence of cruciform structures in superhelical DNA provided by two-dimensional gel electrophoresis","volume":"153","author":"Lyamichev","year":"1983","journal-title":"FEBS Lett"},{"key":"2022112111202675700_ref68","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1038\/289466a0","article-title":"Cruciform structures in supercoiled DNA","volume":"289","author":"Panayotatos","year":"1981","journal-title":"Nature"},{"key":"2022112111202675700_ref69","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1016\/S0092-8674(00)80275-5","article-title":"Frpo: a novel single-stranded DNA promoter for transcription and for primer RNA synthesis of DNA replication","volume":"89","author":"Masai","year":"1997","journal-title":"Cell"},{"key":"2022112111202675700_ref70","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1126\/science.2456617","article-title":"An E. coli promoter that regulates transcription by DNA superhelix-induced cruciform extrusion","volume":"241","author":"Horwitz","year":"1988","journal-title":"Science (80-)"},{"key":"2022112111202675700_ref71","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/0022-2836(87)90337-8","article-title":"Superhelical DNA with local substructures","volume":"195","author":"White","year":"1987","journal-title":"J Mol Biol"},{"key":"2022112111202675700_ref72","doi-asserted-by":"crossref","first-page":"2612","DOI":"10.1101\/gad.1724708","article-title":"Meeting DNA palindromes head-to-head","volume":"22","author":"Smith","year":"2008","journal-title":"Genes Dev"},{"key":"2022112111202675700_ref73","doi-asserted-by":"crossref","first-page":"906","DOI":"10.1086\/342928","article-title":"Recombination between palindromes P5 and P1 on the human Y chromosome causes massive deletions and spermatogenic failure","volume":"71","author":"Repping","year":"2002","journal-title":"Am J Hum Genet"},{"key":"2022112111202675700_ref74","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1128\/MMBR.00026-10","article-title":"Folded DNA in action: Hairpin formation and biological functions in prokaryotes","volume":"74","author":"Bikard","year":"2010","journal-title":"Microbiol Mol Biol Rev"},{"key":"2022112111202675700_ref75","doi-asserted-by":"crossref","first-page":"3269","DOI":"10.1093\/nar\/16.8.3269","article-title":"Early melting of supercoiled DNA","volume":"16","author":"YuL","year":"1988","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref76","doi-asserted-by":"crossref","first-page":"9464","DOI":"10.1073\/pnas.85.24.9464","article-title":"Stable DNA unwinding, not \u2018breathing,\u2019 accounts for single-strand-specific nuclease hypersensitivity of specific A+T-rich sequences","volume":"85","author":"Kowalski","year":"1988","journal-title":"Proc Natl Acad Sci"},{"key":"2022112111202675700_ref77","doi-asserted-by":"crossref","first-page":"9551","DOI":"10.1021\/bi00493a009","article-title":"Torsional stress stabilizes extended base unpairing in suppressor sites flanking immunoglobulin heavy chain enhancer","volume":"29","author":"Kohwi-Shigematsu","year":"1990","journal-title":"Biochemistry"},{"key":"2022112111202675700_ref78","volume-title":"DNA Structure and Function","author":"Drakesmith","year":"1994"},{"key":"2022112111202675700_ref79","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1016\/S0022-2836(03)00037-8","article-title":"Unpaired structures in SCA10 (ATTCT)n\u00b7(AGAAT)n repeats","volume":"326","author":"Potaman","year":"2003","journal-title":"J Mol Biol"},{"key":"2022112111202675700_ref80","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1016\/0006-3002(57)90091-4","article-title":"Studies on the formation of two- and three-stranded polyribonucleotides","volume":"26","author":"Felsenfeld","year":"1957","journal-title":"Biochim Biophys Acta"},{"key":"2022112111202675700_ref81","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1126\/science.2421408","article-title":"Design of sequence-specific DNA-binding molecules","volume":"232","author":"Dervan","year":"1986","journal-title":"Science (80-)"},{"key":"2022112111202675700_ref82","doi-asserted-by":"crossref","first-page":"1791","DOI":"10.1126\/science.3175620","article-title":"Single strands, triple strands, and kinks in H-DNA","volume":"241","author":"Htun","year":"1988","journal-title":"Science (80-)"},{"key":"2022112111202675700_ref83","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1146\/annurev.bb.23.060194.002545","article-title":"H-DNA and related structures","volume":"23","author":"Mirkin","year":"1994","journal-title":"Annu Rev Biophys Biomol Struct"},{"key":"2022112111202675700_ref84","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/S0167-4781(99)00149-9","article-title":"Triple helix formation and the antigene strategy for sequence-specific control of gene expression","volume":"1489","author":"Praseuth","year":"1999","journal-title":"Biochim Biophys Acta Gene Struct Expr"},{"key":"2022112111202675700_ref85","doi-asserted-by":"crossref","first-page":"5041","DOI":"10.1021\/bi9601013","article-title":"Alternative structures in duplex DNA formed within the trinucleotide repeats of the myotonic dystrophy and fragile X loci","volume":"35","author":"Pearson","year":"1996","journal-title":"Biochemistry"},{"key":"2022112111202675700_ref86","doi-asserted-by":"crossref","first-page":"4788","DOI":"10.2741\/2427","article-title":"Slipped strand DNA structures","volume":"12","author":"Sinden","year":"2007","journal-title":"Front Biosci"},{"key":"2022112111202675700_ref87","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1016\/S1097-2765(00)80474-8","article-title":"Sticky DNA","volume":"3","author":"Sakamoto","year":"1999","journal-title":"Mol Cell"},{"key":"2022112111202675700_ref88","doi-asserted-by":"crossref","first-page":"39217","DOI":"10.1074\/jbc.M205209200","article-title":"Sticky DNA, a long GAA\u00b7GAA\u00b7TTC triplex that is formed intramolecularly, in the sequence of Intron 1 of the frataxin gene","volume":"277","author":"Vetcher","year":"2002","journal-title":"J Biol Chem"},{"key":"2022112111202675700_ref89","doi-asserted-by":"crossref","first-page":"2286","DOI":"10.1128\/MCB.24.6.2286-2295.2004","article-title":"Replication stalling at Friedreich\u2019s ataxia (GAA) n repeats in vivo","volume":"24","author":"Krasilnikova","year":"2004","journal-title":"Mol Cell Biol"},{"key":"2022112111202675700_ref90","doi-asserted-by":"crossref","first-page":"14588","DOI":"10.1074\/jbc.273.23.14588","article-title":"Inhibitory effects of expanded GAA\u00b7TTC triplet repeats from Intron I of the Friedreich ataxia gene on transcription and replicationin vivo","volume":"273","author":"Ohshima","year":"1998","journal-title":"J Biol Chem"},{"key":"2022112111202675700_ref91","doi-asserted-by":"crossref","first-page":"6444","DOI":"10.1074\/jbc.M309596200","article-title":"Structure-dependent recombination hot spot activity of GAA\u00b7TTC sequences from Intron 1 of the Friedreich\u2019s ataxia gene","volume":"279","author":"Napierala","year":"2004","journal-title":"J Biol Chem"},{"key":"2022112111202675700_ref92","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1038\/nchembio.780","article-title":"Small-molecule\u2013induced DNA damage identifies alternative DNA structures in human genes","volume":"8","author":"Rodriguez","year":"2012","journal-title":"Nat Chem Biol"},{"key":"2022112111202675700_ref93","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1038\/ng.3662","article-title":"G-quadruplex structures mark human regulatory chromatin","volume":"48","author":"H\u00e4nsel-Hertsch","year":"2016","journal-title":"Nat Genet"},{"key":"2022112111202675700_ref94","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1038\/nprot.2017.150","article-title":"Genome-wide mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and high-throughput sequencing","volume":"13","author":"H\u00e4nsel-Hertsch","year":"2018","journal-title":"Nat Protoc"},{"key":"2022112111202675700_ref95","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1016\/j.chembiol.2016.08.013","article-title":"Conformation selective antibody enables genome profiling and leads to discovery of parallel G-quadruplex in human telomeres","volume":"23","author":"Liu","year":"2016","journal-title":"Cell Chem Biol"},{"key":"2022112111202675700_ref96","doi-asserted-by":"crossref","first-page":"1796","DOI":"10.1038\/ncomms2792","article-title":"G-quadruplex structures are stable and detectable in human genomic DNA","volume":"4","author":"Lam","year":"2013","journal-title":"Nat Commun"},{"key":"2022112111202675700_ref97","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/nchembio.1475","article-title":"G quadruplexes are genomewide targets of transcriptional helicases XPB and XPD","volume":"10","author":"Gray","year":"2014","journal-title":"Nat Chem Biol"},{"key":"2022112111202675700_ref98","doi-asserted-by":"crossref","first-page":"27029","DOI":"10.1016\/S0021-9258(18)47121-9","article-title":"A novel K(+)-dependent DNA synthesis arrest site in a commonly occurring sequence motif in eukaryotes","volume":"269","author":"Woodford","year":"1994","journal-title":"J Biol Chem"},{"key":"2022112111202675700_ref99","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1093\/nar\/27.2.537","article-title":"A DNA polymerase stop assay for G-quadruplex-interactive compounds","volume":"27","author":"Han","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref100","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1038\/nbt.3295","article-title":"High-throughput sequencing of DNA G-quadruplex structures in the human genome","volume":"33","author":"Chambers","year":"2015","journal-title":"Nat Biotechnol"},{"key":"2022112111202675700_ref101","doi-asserted-by":"crossref","first-page":"3862","DOI":"10.1093\/nar\/gkz179","article-title":"Whole genome experimental maps of DNA G-quadruplexes in multiple species","volume":"47","author":"Marsico","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref102","doi-asserted-by":"crossref","first-page":"aaf5371","DOI":"10.1126\/science.aaf5371","article-title":"RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria","volume":"353","author":"Guo","year":"2016","journal-title":"Science (80-)"},{"key":"2022112111202675700_ref103","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1038\/nmeth.3965","article-title":"rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome","volume":"13","author":"Kwok","year":"2016","journal-title":"Nat Methods"},{"key":"2022112111202675700_ref104","doi-asserted-by":"crossref","DOI":"10.1126\/science.aaf5371","article-title":"RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria","volume":"353","author":"Guo","year":"2016","journal-title":"Science (80-)"},{"key":"2022112111202675700_ref105","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1016\/j.molcel.2012.01.017","article-title":"R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters","volume":"45","author":"Ginno","year":"2012","journal-title":"Mol Cell"},{"key":"2022112111202675700_ref106","doi-asserted-by":"crossref","first-page":"e28306","DOI":"10.7554\/eLife.28306","article-title":"Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq","volume":"6","author":"Dumelie","year":"2017","journal-title":"Elife"},{"key":"2022112111202675700_ref107","doi-asserted-by":"crossref","first-page":"23547","DOI":"10.1074\/jbc.M009676200","article-title":"Investigating the structure of human RNase H1 by site-directed mutagenesis","volume":"276","author":"Wu","year":"2001","journal-title":"J Biol Chem"},{"key":"2022112111202675700_ref108","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.1016\/j.celrep.2019.09.052","article-title":"Mapping native R-loops genome-wide using a targeted nuclease approach","volume":"29","author":"Yan","year":"2019","journal-title":"Cell Rep"},{"key":"2022112111202675700_ref109","doi-asserted-by":"crossref","first-page":"2271","DOI":"10.1016\/j.jmb.2020.02.014","article-title":"Ultra-deep coverage single-molecule R-loop footprinting reveals principles of R-loop formation","volume":"432","author":"Malig","year":"2020","journal-title":"J Mol Biol"},{"key":"2022112111202675700_ref110","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1101\/gr.219394.116","article-title":"RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases","volume":"27","author":"Hal\u00e1sz","year":"2017","journal-title":"Genome Res"},{"key":"2022112111202675700_ref111","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1016\/j.jmb.2017.12.016","article-title":"The affinity of the S9.6 antibody for double-stranded RNAs impacts the accurate mapping of R-loops in fission yeast","volume":"430","author":"Hartono","year":"2018","journal-title":"J Mol Biol"},{"key":"2022112111202675700_ref112","doi-asserted-by":"crossref","first-page":"e0178875","DOI":"10.1371\/journal.pone.0178875","article-title":"The monoclonal S9.6 antibody exhibits highly variable binding affinities towards different R-loop sequences","volume":"12","author":"K\u00f6nig","year":"2017","journal-title":"PLoS One"},{"key":"2022112111202675700_ref113","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1016\/j.cels.2017.01.013","article-title":"Permanganate\/S1 nuclease footprinting reveals non-B DNA structures with regulatory potential across a mammalian genome","volume":"4","author":"Kouzine","year":"2017","journal-title":"Cell Syst"},{"key":"2022112111202675700_ref114","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1038\/s41592-020-0797-9","article-title":"Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ","volume":"17","author":"Wu","year":"2020","journal-title":"Nat Methods"},{"key":"2022112111202675700_ref115","doi-asserted-by":"crossref","first-page":"11063","DOI":"10.1073\/pnas.1106501108","article-title":"Multiplexed RNA structure characterization with selective 2\u2032-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)","volume":"108","author":"Lucks","year":"2011","journal-title":"Proc Natl Acad Sci"},{"key":"2022112111202675700_ref116","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1002\/9780470559277.ch120019","article-title":"SHAPE\u2013seq: high-throughput RNA structure analysis","volume":"4","author":"Mortimer","year":"2012","journal-title":"Curr Protoc Chem Biol"},{"key":"2022112111202675700_ref117","doi-asserted-by":"crossref","first-page":"e165","DOI":"10.1093\/nar\/gku909","article-title":"SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing","volume":"42","author":"Loughrey","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref118","doi-asserted-by":"crossref","first-page":"1746","DOI":"10.1093\/nar\/gkw006","article-title":"Re-evaluation of G-quadruplex propensity with G4Hunter","volume":"44","author":"Bedrat","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref119","doi-asserted-by":"crossref","first-page":"14535","DOI":"10.1038\/s41598-017-14017-4","article-title":"Machine learning model for sequence-driven DNA G-quadruplex formation","volume":"7","author":"Sahakyan","year":"2017","journal-title":"Sci Rep"},{"key":"2022112111202675700_ref120","doi-asserted-by":"crossref","first-page":"3373","DOI":"10.1093\/bioinformatics\/btx413","article-title":"Pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R","volume":"33","author":"Hon","year":"2017","journal-title":"Bioinformatics"},{"key":"2022112111202675700_ref121","first-page":"357","volume-title":"Proc. 10th ACM Int. Conf. Bioinformatics, Comput. Biol. Heal. Informatics","author":"Barshai","year":"2019"},{"key":"2022112111202675700_ref122","doi-asserted-by":"crossref","first-page":"D613","DOI":"10.1093\/nar\/gkp939","article-title":"The UCSC genome browser database: update 2010","volume":"38","author":"Rhead","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref123","doi-asserted-by":"crossref","first-page":"1590","DOI":"10.1101\/gr.158436.113","article-title":"GC skew at the 5\u2032 and 3\u2032 ends of human genes links R-loop formation to epigenetic regulation and transcription termination","volume":"23","author":"Ginno","year":"2013","journal-title":"Genome Res"},{"key":"2022112111202675700_ref124","doi-asserted-by":"crossref","first-page":"7566","DOI":"10.1093\/nar\/gky554","article-title":"Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers","volume":"46","author":"Kuznetsov","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref125","doi-asserted-by":"crossref","first-page":"e08007","DOI":"10.7554\/eLife.08007","article-title":"Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi\u2013Gouti\u00e8res syndrome","volume":"4","author":"Lim","year":"2015","journal-title":"Elife"},{"key":"2022112111202675700_ref126","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/s13072-015-0040-6","article-title":"RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships","volume":"8","author":"Nadel","year":"2015","journal-title":"Epigenetics Chromatin"},{"key":"2022112111202675700_ref127","doi-asserted-by":"crossref","first-page":"D303","DOI":"10.1093\/nar\/gkab1103","article-title":"R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation","volume":"50","author":"Lin","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref128","doi-asserted-by":"crossref","first-page":"D383","DOI":"10.1093\/nar\/gkq1170","article-title":"Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes","volume":"39","author":"Cer","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref129","doi-asserted-by":"crossref","first-page":"D94","DOI":"10.1093\/nar\/gks955","article-title":"Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools","volume":"41","author":"Cer","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref130","article-title":"Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool)","volume":"Chapter 18","author":"Cer","year":"2012","journal-title":"Curr. Protoc. Hum. Genet."},{"key":"2022112111202675700_ref131","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.ymeth.2013.08.004","article-title":"Methods to detect replication-dependent and replication-independent DNA structure-induced genetic instability","volume":"64","author":"Wang","year":"2013","journal-title":"Methods"},{"key":"2022112111202675700_ref132","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1016\/j.bbrc.2016.09.015","article-title":"Palindrome analyser\u2014a new web-based server for predicting and evaluating inverted repeats in nucleotide sequences","volume":"478","author":"Br\u00e1zda","year":"2016","journal-title":"Biochem Biophys Res Commun"},{"key":"2022112111202675700_ref133","doi-asserted-by":"crossref","first-page":"2438","DOI":"10.1016\/j.jmb.2017.06.013","article-title":"3D-NuS: a web server for automated modeling and visualization of non-canonical 3-D imensional nucleic acid structures","volume":"429","author":"Patro","year":"2017","journal-title":"J Mol Biol"},{"key":"2022112111202675700_ref134","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","article-title":"EMBOSS: the European molecular biology open software suite","volume":"16","author":"Rice","year":"2000","journal-title":"Trends Genet"},{"key":"2022112111202675700_ref135","doi-asserted-by":"crossref","first-page":"3406","DOI":"10.1093\/nar\/gkg595","article-title":"Mfold web server for nucleic acid folding and hybridization prediction","volume":"31","author":"Zuker","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref136","doi-asserted-by":"crossref","first-page":"1861","DOI":"10.1101\/gr.2542904","article-title":"Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes","volume":"14","author":"Warburton","year":"2004","journal-title":"Genome Res"},{"key":"2022112111202675700_ref137","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1093\/bioinformatics\/btt651","article-title":"A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences","volume":"30","author":"Sreeskandarajan","year":"2014","journal-title":"Bioinformatics"},{"key":"2022112111202675700_ref138","doi-asserted-by":"crossref","first-page":"e113349","DOI":"10.1371\/journal.pone.0113349","article-title":"detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation","volume":"9","author":"Ye","year":"2014","journal-title":"PLoS One"},{"key":"2022112111202675700_ref139","doi-asserted-by":"crossref","first-page":"6468","DOI":"10.1073\/pnas.77.11.6468","article-title":"The inverted repeat as a recognizable structural feature in supercoiled DNA molecules","volume":"77","author":"Lilley","year":"1980","journal-title":"Proc Natl Acad Sci"},{"key":"2022112111202675700_ref140","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1007\/s00294-010-0302-6","article-title":"The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome","volume":"56","author":"Strawbridge","year":"2010","journal-title":"Curr Genet"},{"key":"2022112111202675700_ref141","doi-asserted-by":"crossref","first-page":"2503","DOI":"10.1093\/bioinformatics\/bty142","article-title":"NeSSie: a tool for the identification of approximate DNA sequence symmetries","volume":"34","author":"Berselli","year":"2018","journal-title":"Bioinformatics"},{"key":"2022112111202675700_ref142","doi-asserted-by":"crossref","first-page":"3511","DOI":"10.1093\/nar\/gkl456","article-title":"Structural polymorphism exhibited by a quasipalindrome present in the locus control region (LCR) of the human -globin gene cluster","volume":"34","author":"Kaushik","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref143","doi-asserted-by":"crossref","first-page":"19134","DOI":"10.1038\/s41598-020-76203-1","article-title":"Deep learning approach for predicting functional Z-DNA regions using omics data","volume":"10","author":"Beknazarov","year":"2020","journal-title":"Sci Rep"},{"key":"2022112111202675700_ref144","doi-asserted-by":"crossref","first-page":"2379","DOI":"10.1039\/C9CC09771F","article-title":"Chemical biology of non-canonical structures of nucleic acids for therapeutic applications","volume":"56","author":"Tateishi-Karimata","year":"2020","journal-title":"Chem Commun"},{"key":"2022112111202675700_ref145","doi-asserted-by":"crossref","first-page":"11365","DOI":"10.1002\/anie.201703783","article-title":"Copper-alkyne complexation responsible for the nucleolar localization of quadruplex nucleic acid drugs labeled by click reactions","volume":"56","author":"Lefebvre","year":"2017","journal-title":"Angew Chem Int Ed"},{"key":"2022112111202675700_ref146","doi-asserted-by":"crossref","first-page":"2884","DOI":"10.3390\/ijms20122884","article-title":"Perspectives for applying G-quadruplex structures in neurobiology and neuropharmacology","volume":"20","author":"Asamitsu","year":"2019","journal-title":"Int J Mol Sci"},{"key":"2022112111202675700_ref147","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/s10142-007-0047-6","article-title":"The human genome-wide distribution of DNA palindromes","volume":"7","author":"Lu","year":"2007","journal-title":"Funct Integr Genomics"},{"key":"2022112111202675700_ref148","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1007\/s00018-009-0131-2","article-title":"Non-B DNA structure-induced genetic instability and evolution","volume":"67","author":"Zhao","year":"2010","journal-title":"Cell Mol Life Sci"},{"key":"2022112111202675700_ref149","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1261\/rna.058115.116","article-title":"Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq","volume":"23","author":"Nicholson","year":"2017","journal-title":"RNA"},{"key":"2022112111202675700_ref150","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1016\/j.cell.2012.05.003","article-title":"Comprehensive analysis of mRNA methylation reveals enrichment in 3\u2032 UTRs and near stop codons","volume":"149","author":"Meyer","year":"2012","journal-title":"Cell"},{"key":"2022112111202675700_ref151","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1038\/nsmb.1838","article-title":"iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution","volume":"17","author":"K\u00f6nig","year":"2010","journal-title":"Nat Struct Mol Biol"},{"key":"2022112111202675700_ref152","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1038\/nmeth.3810","article-title":"Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)","volume":"13","author":"Van Nostrand","year":"2016","journal-title":"Nat Methods"},{"key":"2022112111202675700_ref153","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1126\/science.4035359","article-title":"Z-DNA forms without an alternating purine-pyrimidine sequence in solution","volume":"230","author":"Feigon","year":"1985","journal-title":"Science (80-)"},{"key":"2022112111202675700_ref154","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1093\/nar\/27.2.543","article-title":"The intrinsic structure and stability of out-of-alternation base pairs in Z-DNA","volume":"27","author":"Eichman","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref155","doi-asserted-by":"crossref","first-page":"1977","DOI":"10.1093\/nar\/23.11.1977","article-title":"Occurrence of potential cruciform and H-DNA forming sequences in genomic DNA","volume":"23","author":"Schroth","year":"1995","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref156","first-page":"124","article-title":"Prediction of significant cruciform structures from sequence in topologically constrained DNA","author":"Lexa","year":"2012","journal-title":"Bioinformatics"},{"key":"2022112111202675700_ref157","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-60327-429-6_1","article-title":"UNAFold: software for nucleic acid folding and hybridization","author":"Markham","year":"2008","journal-title":"Methods Mol Biol"},{"key":"2022112111202675700_ref158","doi-asserted-by":"crossref","first-page":"3682","DOI":"10.1093\/nar\/gkg625","article-title":"TRACTS: a program to map oligopurine.oligopyrimidine and other binary DNA tracts","volume":"31","author":"Gal","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2022112111202675700_ref159","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1089\/oli.2006.16.196","article-title":"A Web-Based Search Engine for Triplex-forming Oligonucleotide Target Sequences","volume":"16","author":"Gaddis","year":"2006","journal-title":"Oligonucleotides"},{"key":"2022112111202675700_ref160","doi-asserted-by":"crossref","first-page":"S9","DOI":"10.1186\/1471-2164-10-S3-S9","article-title":"TTS Mapping: integrative WEB tool for analysis of triplex formation target DNA Sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome","volume":"10","author":"Jenjaroenpun","year":"2009","journal-title":"BMC Genomics"},{"key":"2022112111202675700_ref161","doi-asserted-by":"crossref","first-page":"2510","DOI":"10.1093\/bioinformatics\/btr439","article-title":"A dynamic programming algorithm for identification of triplex-forming sequences","volume":"27","author":"Lexa","year":"2011","journal-title":"Bioinformatics"},{"key":"2022112111202675700_ref162","doi-asserted-by":"crossref","first-page":"2737","DOI":"10.1002\/j.1460-2075.1986.tb04558.x","article-title":"A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences","volume":"5","author":"Ho","year":"1986","journal-title":"EMBO J"},{"key":"2022112111202675700_ref163","doi-asserted-by":"crossref","first-page":"11846","DOI":"10.1016\/S0021-9258(19)49776-7","article-title":"Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes","volume":"267","author":"Schroth","year":"1992","journal-title":"J Biol Chem"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/6\/bbac441\/47144540\/bbac441.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/6\/bbac441\/47144540\/bbac441.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,21]],"date-time":"2022-11-21T11:29:07Z","timestamp":1669030147000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbac441\/6751149"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,7]]},"references-count":163,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2022,11,19]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbac441","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,11]]},"published":{"date-parts":[[2022,10,7]]},"article-number":"bbac441"}}