{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T01:15:31Z","timestamp":1780535731300,"version":"3.54.1"},"reference-count":60,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,5,17]],"date-time":"2017-05-17T00:00:00Z","timestamp":1494979200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2017,5,17]],"date-time":"2017-05-17T00:00:00Z","timestamp":1494979200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Here we describe AGCGA-quadruplexes, an unexpected addition to the well-known tetrahelical families, G-quadruplexes and i-motifs, that have been a focus of intense research due to their potential biological impact in G- and C-rich DNA regions, respectively. High-resolution structures determined by solution-state nuclear magnetic resonance (NMR) spectroscopy demonstrate that AGCGA-quadruplexes comprise four 5\u2032-AGCGA-3\u2032 tracts and are stabilized by G-A and G-C base pairs forming GAGA- and GCGC-quartets, respectively. Residues in the core of the structure are connected with edge-type loops. Sequences of alternating 5\u2032-AGCGA-3\u2032 and 5\u2032-GGG-3\u2032 repeats could be expected to form G-quadruplexes, but are shown herein to form AGCGA-quadruplexes instead. Unique structural features of AGCGA-quadruplexes together with lower sensitivity to cation and pH variation imply their potential biological relevance in regulatory regions of genes responsible for basic cellular processes that are related to neurological disorders, cancer and abnormalities in bone and cartilage development.<\/jats:p>","DOI":"10.1038\/ncomms15355","type":"journal-article","created":{"date-parts":[[2017,5,17]],"date-time":"2017-05-17T10:45:40Z","timestamp":1495017940000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":62,"title":["Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions"],"prefix":"10.1038","volume":"8","author":[{"given":"Voj\u010d","family":"Kocman","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1570-8602","authenticated-orcid":false,"given":"Janez","family":"Plavec","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,5,17]]},"reference":[{"key":"BFncomms15355_CR1","doi-asserted-by":"publisher","first-page":"5893","DOI":"10.1039\/c1cs15153c","volume":"40","author":"J Choi","year":"2011","unstructured":"Choi, J. & Majima, T. Conformational changes of non-B DNA. Chem. Soc. Rev. 40, 5893\u20135909 (2011).","journal-title":"Chem. Soc. Rev."},{"key":"BFncomms15355_CR2","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1038\/334364a0","volume":"334","author":"D Sen","year":"1988","unstructured":"Sen, D. & Gilbert, W. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature 334, 364\u2013366 (1988).","journal-title":"Nature"},{"key":"BFncomms15355_CR3","doi-asserted-by":"publisher","first-page":"871","DOI":"10.1016\/0092-8674(89)90610-7","volume":"59","author":"JR Williamson","year":"1989","unstructured":"Williamson, J. R., Raghuraman, M. K. & Cech, T. R. Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell 59, 871\u2013880 (1989).","journal-title":"Cell"},{"key":"BFncomms15355_CR4","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1038\/363561a0","volume":"363","author":"K Gehring","year":"1993","unstructured":"Gehring, K., Leroy, J. L. & Gueron, M. A tetrameric DNA structure with protonated cytosine\u00b7cytosine base pairs. Nature 363, 561\u2013565 (1993).","journal-title":"Nature"},{"key":"BFncomms15355_CR5","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1016\/j.ymeth.2013.06.004","volume":"64","author":"AI Karsisiotis","year":"2013","unstructured":"Karsisiotis, A. I., O\u2019Kane, C. & Webba da Silva, M. DNA quadruplex folding formalism\u2013A tutorial on quadruplex topologies. Methods. 64, 28\u201335 (2013).","journal-title":"Methods."},{"key":"BFncomms15355_CR6","doi-asserted-by":"publisher","first-page":"1107","DOI":"10.1111\/j.1742-4658.2009.07464.x","volume":"277","author":"AT Phan","year":"2010","unstructured":"Phan, A. T. Human telomeric G-quadruplex: structures of DNA and RNA sequences. FEBS J. 277, 1107\u20131117 (2010).","journal-title":"FEBS J."},{"key":"BFncomms15355_CR7","doi-asserted-by":"publisher","first-page":"5402","DOI":"10.1093\/nar\/gkl655","volume":"34","author":"S Burge","year":"2006","unstructured":"Burge, S., Parkinson, G. N., Hazel, P., Todd, A. K. & Neidle, S. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res. 34, 5402\u20135415 (2006).","journal-title":"Nucleic Acids Res."},{"key":"BFncomms15355_CR8","doi-asserted-by":"publisher","first-page":"7429","DOI":"10.1093\/nar\/gkm711","volume":"35","author":"DJ Patel","year":"2007","unstructured":"Patel, D. J., Phan, A. T. & Kuryavyi, V. Human telomere, oncogenic promoter and 5\u2032-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res. 35, 7429\u20137455 (2007).","journal-title":"Nucleic Acids Res."},{"key":"BFncomms15355_CR9","doi-asserted-by":"publisher","first-page":"5017","DOI":"10.1021\/ja310251r","volume":"135","author":"VT Mukundan","year":"2013","unstructured":"Mukundan, V. T. & Phan, A. T. Bulges in G-quadruplexes: broadening the definition of G-quadruplex-forming sequences. J. Am. Chem. Soc. 135, 5017\u20135028 (2013).","journal-title":"J. Am. Chem. Soc."},{"key":"BFncomms15355_CR10","doi-asserted-by":"publisher","first-page":"e1003468","DOI":"10.1371\/journal.pgen.1003468","volume":"9","author":"N Maizels","year":"2013","unstructured":"Maizels, N. & Gray, L. T. The G4 genome. PLOS Genet. 9, e1003468 (2013).","journal-title":"PLOS Genet."},{"key":"BFncomms15355_CR11","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1038\/nbt.3295","volume":"33","author":"VS Chambers","year":"2015","unstructured":"Chambers, V. S. et al. High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nat. Biotechnol. 33, 877\u2013881 (2015).","journal-title":"Nat. Biotechnol."},{"key":"BFncomms15355_CR12","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1038\/nchem.1548","volume":"5","author":"G Biffi","year":"2013","unstructured":"Biffi, G., Tannahill, D., McCafferty, J. & Balasubramanian, S. Quantitative visualization of DNA G-quadruplex structures in human cells. Nat. Chem. 5, 182\u2013186 (2013).","journal-title":"Nat. Chem."},{"key":"BFncomms15355_CR13","doi-asserted-by":"publisher","first-page":"1299","DOI":"10.1039\/b922050j","volume":"46","author":"A Rajendran","year":"2010","unstructured":"Rajendran, A., Nakano, S. & Sugimoto, N. Molecular crowding of the cosolutes induces an intramolecular i-motif structure of triplet repeat DNA oligomers at neutral pH. Chem. Commun. 46, 1299\u20131301 (2010).","journal-title":"Chem. Commun."},{"key":"BFncomms15355_CR14","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1021\/bi401523b","volume":"53","author":"YP Bhavsar-Jog","year":"2014","unstructured":"Bhavsar-Jog, Y. P., Van Dornshuld, E., Brooks, T. A., Tschumper, G. S. & Wadkins, R. M. Epigenetic modification, dehydration, and molecular crowding effects on the thermodynamics of i-motif structure formation from C-rich DNA. Biochemistry 53, 1586\u20131594 (2014).","journal-title":"Biochemistry"},{"key":"BFncomms15355_CR15","doi-asserted-by":"publisher","first-page":"17944","DOI":"10.1038\/srep17944","volume":"5","author":"A Kovanda","year":"2015","unstructured":"Kovanda, A., Zalar, M., Sket, P., Plavec, J. & Rogelj, B. Anti-sense DNA d(GGCCCC)n expansions in C9ORF72 form i-motifs and protonated hairpins. Sci. Rep. 5, 17944 (2015).","journal-title":"Sci. Rep."},{"key":"BFncomms15355_CR16","doi-asserted-by":"publisher","first-page":"10950","DOI":"10.1021\/jacs.6b05036","volume":"138","author":"B Roy","year":"2016","unstructured":"Roy, B. et al. Interaction of individual structural domains of hnRNP LL with the BCL2 promoter i-motif DNA. J. Am. Chem. Soc. 138, 10950\u201310962 (2016).","journal-title":"J. Am. Chem. Soc."},{"key":"BFncomms15355_CR17","doi-asserted-by":"publisher","first-page":"5831","DOI":"10.1038\/ncomms6831","volume":"5","author":"V Kocman","year":"2014","unstructured":"Kocman, V. & Plavec, J. A tetrahelical DNA fold adopted by tandem repeats of alternating GGG and GCG tracts. Nat. Commun. 5, 5831 (2014).","journal-title":"Nat. Commun."},{"key":"BFncomms15355_CR18","doi-asserted-by":"publisher","first-page":"1713","DOI":"10.1093\/nar\/gkp026","volume":"37","author":"J Kypr","year":"2009","unstructured":"Kypr, J., Kejnovska, I., Renciuk, D. & Vorlickova, M. Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res. 37, 1713\u20131725 (2009).","journal-title":"Nucleic Acids Res."},{"key":"BFncomms15355_CR19","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1002\/(SICI)1097-0282(199707)42:1<113::AID-BIP10>3.0.CO;2-O","volume":"42","author":"B Schneider","year":"1997","unstructured":"Schneider, B., Neidle, S. & Berman, H. M. Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers 42, 113\u2013124 (1997).","journal-title":"Biopolymers"},{"key":"BFncomms15355_CR20","doi-asserted-by":"publisher","first-page":"1872","DOI":"10.1021\/jp311180u","volume":"117","author":"M Krepl","year":"2013","unstructured":"Krepl, M., Otyepka, M., Banas, P. & Sponer, J. Effect of guanine to inosine substitution on stability of canonical DNA and RNA duplexes: molecular dynamics thermodynamics integration study. J. Phys. Chem. B 117, 1872\u20131879 (2013).","journal-title":"J. Phys. Chem. B"},{"key":"BFncomms15355_CR21","doi-asserted-by":"publisher","first-page":"596","DOI":"10.1002\/dvg.20656","volume":"48","author":"R Witschi","year":"2010","unstructured":"Witschi, R. et al. Hoxb8-Cre mice: a tool for brain-sparing conditional gene deletion. Genesis 48, 596\u2013602 (2010).","journal-title":"Genesis"},{"key":"BFncomms15355_CR22","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1016\/j.ajhg.2015.07.014","volume":"97","author":"AJ Tanaka","year":"2015","unstructured":"Tanaka, A. J. et al. Mutations in SPATA5 are associated with microcephaly, intellectual disability, seizures, and hearing loss. Am. J. Hum. Genet. 97, 457\u2013464 (2015).","journal-title":"Am. J. Hum. Genet."},{"key":"BFncomms15355_CR23","doi-asserted-by":"publisher","first-page":"1744","DOI":"10.1002\/ajmg.a.36450","volume":"164A","author":"S Tunovic","year":"2014","unstructured":"Tunovic, S., Barkovich, J., Sherr, E. H. & Slavotinek, A. M. De novo ANKRD11 and KDM1A gene mutations in a male with features of KBG syndrome and Kabuki syndrome. Am. J. Med. Genet. A 164A, 1744\u20131749 (2014).","journal-title":"Am. J. Med. Genet. A"},{"key":"BFncomms15355_CR24","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1186\/s13229-016-0079-7","volume":"7","author":"SR Berkowicz","year":"2016","unstructured":"Berkowicz, S. R. et al. Brinp1 (\u2212\/\u2212) mice exhibit autism-like behaviour, altered memory, hyperactivity and increased parvalbumin-positive cortical interneuron density. Mol. Autism 7, 22 (2016).","journal-title":"Mol. Autism"},{"key":"BFncomms15355_CR25","doi-asserted-by":"publisher","first-page":"2411","DOI":"10.1093\/hmg\/4.12.2411","volume":"4","author":"F Quan","year":"1995","unstructured":"Quan, F., Janas, J. & Popovich, B. W. A novel CAG repeat configuration in the SCA1 gene - implications for the molecular diagnostics of spinocerebellar ataxia type-1. Hum. Mol. Genet. 4, 2411\u20132413 (1995).","journal-title":"Hum. Mol. Genet."},{"key":"BFncomms15355_CR26","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1007\/s10048-015-0450-4","volume":"16","author":"AW Yang","year":"2015","unstructured":"Yang, A. W., Sachs, A. J. & Nystuen, A. M. Deletion of Inpp5a causes ataxia and cerebellar degeneration in mice. Neurogenetics 16, 277\u2013285 (2015).","journal-title":"Neurogenetics"},{"key":"BFncomms15355_CR27","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1186\/s12861-015-0093-6","volume":"15","author":"O Machon","year":"2015","unstructured":"Machon, O., Masek, J., Machonova, O., Krauss, S. & Kozmik, Z. Meis2 is essential for cranial and cardiac neural crest development. BMC Dev. Biol. 15, 40 (2015).","journal-title":"BMC Dev. Biol."},{"key":"BFncomms15355_CR28","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1016\/S0378-1119(03)00715-7","volume":"315","author":"J Aruga","year":"2003","unstructured":"Aruga, J., Yokota, N. & Mikoshiba, K. Human SLITRK family genes: genomic organization and expression profiling in normal brain and brain tumor tissue. Gene 315, 87\u201394 (2003).","journal-title":"Gene"},{"key":"BFncomms15355_CR29","doi-asserted-by":"publisher","first-page":"4074","DOI":"10.1038\/ncomms5074","volume":"5","author":"D Hadley","year":"2014","unstructured":"Hadley, D. et al. The impact of the metabotropic glutamate receptor and other gene family interaction networks on autism. Nat. Commun. 5, 4074 (2014).","journal-title":"Nat. Commun."},{"key":"BFncomms15355_CR30","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1002\/emmm.201202106","volume":"5","author":"A Sudarov","year":"2013","unstructured":"Sudarov, A., Gooden, F., Tseng, D., Gan, W. B. & Ross, M. E. Lis1 controls dynamics of neuronal filopodia and spines to impact synaptogenesis and social behaviour. EMBO Mol. Med. 5, 591\u2013607 (2013).","journal-title":"EMBO Mol. Med."},{"key":"BFncomms15355_CR31","doi-asserted-by":"publisher","first-page":"1989","DOI":"10.1002\/dvdy.22686","volume":"240","author":"J Saarimaki-Vire","year":"2011","unstructured":"Saarimaki-Vire, J., Alitalo, A. & Partanen, J. Analysis of Cdh22 expression and function in the developing mouse brain. Dev. Dyn. 240, 1989\u20132001 (2011).","journal-title":"Dev. Dyn."},{"key":"BFncomms15355_CR32","doi-asserted-by":"publisher","first-page":"850","DOI":"10.1038\/ejhg.2012.245","volume":"21","author":"PR Moya","year":"2013","unstructured":"Moya, P. R. et al. Rare missense neuronal cadherin gene (CDH2) variants in specific obsessive-compulsive disorder and Tourette disorder phenotypes. Eur. J. Hum. Genet. 21, 850\u2013854 (2013).","journal-title":"Eur. J. Hum. Genet."},{"key":"BFncomms15355_CR33","doi-asserted-by":"publisher","first-page":"600","DOI":"10.1016\/j.tig.2013.08.001","volume":"29","author":"N Oksenberg","year":"2013","unstructured":"Oksenberg, N. & Ahituv, N. The role of AUTS2 in neurodevelopment and human evolution. Trends Genet. 29, 600\u2013608 (2013).","journal-title":"Trends Genet."},{"key":"BFncomms15355_CR34","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1016\/j.neulet.2013.10.041","volume":"557 Pt B","author":"Q Mei","year":"2013","unstructured":"Mei, Q. et al. Expression of proline-rich coiled-coil 2B protein in developing rat brains. Neurosci. Lett. 557 Pt B, 171\u2013176 (2013).","journal-title":"Neurosci. Lett."},{"key":"BFncomms15355_CR35","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1016\/j.ymgme.2013.10.012","volume":"111","author":"SC Quinonez","year":"2014","unstructured":"Quinonez, S. C. & Innis, J. W. Human HOX gene disorders. Mol. Gen. Metab. 111, 4\u201315 (2014).","journal-title":"Mol. Gen. Metab."},{"key":"BFncomms15355_CR36","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/S0014-5793(02)02579-6","volume":"517","author":"J Fitzgerald","year":"2002","unstructured":"Fitzgerald, J., Ting, S. T. & Bateman, J. F. WARP is a new member of the von Willebrand factor A-domain superfamily of extracellular matrix proteins. FEBS Lett. 517, 61\u201366 (2002).","journal-title":"FEBS Lett."},{"key":"BFncomms15355_CR37","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1177\/0022034513513588","volume":"93","author":"SA Frazier-Bowers","year":"2014","unstructured":"Frazier-Bowers, S. A. et al. Novel mutations in PTH1R associated with primary failure of eruption and osteoarthritis. J. Dent. Res. 93, 134\u2013139 (2014).","journal-title":"J. Dent. Res."},{"key":"BFncomms15355_CR38","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1177\/0022034508328168","volume":"88","author":"SK Lee","year":"2009","unstructured":"Lee, S. K. et al. A novel mutation in the DSPP gene associated with dentinogenesis imperfecta type II. J. Dent. Res. 88, 51\u201355 (2009).","journal-title":"J. Dent. Res."},{"key":"BFncomms15355_CR39","doi-asserted-by":"crossref","unstructured":"Stanley, E. R. & Chitu, V. CSF-1 receptor signaling in myeloid cells. Cold Spring Harb. Perspect Biol. 6, (2014).","DOI":"10.1101\/cshperspect.a021857"},{"key":"BFncomms15355_CR40","first-page":"49","volume":"20","author":"JM Garcia-Castellano","year":"2000","unstructured":"Garcia-Castellano, J. M., Diaz-Herrera, P. & Morcuende, J. A. Is bone a target-tissue for the nervous system? New advances on the understanding of their interactions. Iowa Orthop. J. 20, 49\u201358 (2000).","journal-title":"Iowa Orthop. J."},{"key":"BFncomms15355_CR41","doi-asserted-by":"publisher","first-page":"6770","DOI":"10.18632\/oncotarget.2252","volume":"5","author":"N Zatula","year":"2014","unstructured":"Zatula, N. et al. The BCL9-2 proto-oncogene governs estrogen receptor alpha expression in breast tumorigenesis. Oncotarget 5, 6770\u20136787 (2014).","journal-title":"Oncotarget"},{"key":"BFncomms15355_CR42","doi-asserted-by":"publisher","first-page":"899","DOI":"10.1038\/onc.2013.23","volume":"33","author":"MD Arensman","year":"2014","unstructured":"Arensman, M. D. et al. WNT7B mediates autocrine Wnt\/beta-catenin signaling and anchorage-independent growth in pancreatic adenocarcinoma. Oncogene 33, 899\u2013908 (2014).","journal-title":"Oncogene"},{"key":"BFncomms15355_CR43","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1007\/s11033-014-3779-0","volume":"42","author":"K Larsen","year":"2015","unstructured":"Larsen, K., Momeni, J., Farajzadeh, L. & Bendixen, C. Cloning and characterization of the porcine DBC1 gene encoding deleted in bladder cancer. Mol. Biol. Rep. 42, 383\u2013391 (2015).","journal-title":"Mol. Biol. Rep."},{"key":"BFncomms15355_CR44","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1016\/j.molcel.2015.09.005","volume":"60","author":"O Anczukow","year":"2015","unstructured":"Anczukow, O. et al. SRSF1-regulated alternative splicing in breast cancer. Mol. Cell 60, 105\u2013117 (2015).","journal-title":"Mol. Cell"},{"key":"BFncomms15355_CR45","doi-asserted-by":"publisher","first-page":"11548","DOI":"10.1074\/jbc.271.19.11548","volume":"271","author":"K Sugimoto","year":"1996","unstructured":"Sugimoto, K. et al. Molecular cloning and characterization of a newly identified member of the cadherin family, PB-cadherin. J. Biol. Chem. 271, 11548\u201311556 (1996).","journal-title":"J. Biol. Chem."},{"key":"BFncomms15355_CR46","doi-asserted-by":"publisher","first-page":"5931","DOI":"10.1113\/jphysiol.2012.245563","volume":"590","author":"CM Fuller","year":"2012","unstructured":"Fuller, C. M. Time for TMEM? J. Physiol. 590, 5931\u20135932 (2012).","journal-title":"J. Physiol."},{"key":"BFncomms15355_CR47","first-page":"004","volume":"S2","author":"DL Daniels","year":"2013","unstructured":"Daniels, D. L. et al. Mutual Exclusivity of MED12\/MED12L, MED13\/13L, and CDK8\/19 Paralogs Revealed within the CDK-Mediator Kinase Module. J. Proteomics Bioinform. S2, 004 (2013).","journal-title":"J. Proteomics Bioinform."},{"key":"BFncomms15355_CR48","doi-asserted-by":"publisher","first-page":"1340","DOI":"10.1038\/sj.onc.1209169","volume":"25","author":"S Morgan-Lappe","year":"2006","unstructured":"Morgan-Lappe, S. et al. RNAi-based screening of the human kinome identifies Akt-cooperating kinases: a new approach to designing efficacious multitargeted kinase inhibitors. Oncogene 25, 1340\u20131348 (2006).","journal-title":"Oncogene"},{"key":"BFncomms15355_CR49","doi-asserted-by":"publisher","first-page":"292","DOI":"10.7150\/ijbs.3.292","volume":"3","author":"J Rollins","year":"2007","unstructured":"Rollins, J., Veras, I., Cabarcas, S., Willis, I. & Schramm, L. Human Maf1 negatively regulates RNA polymerase III transcription via the TFIIB family members Brf1 and Brf2. Int. J. Biol. Sci. 3, 292\u2013302 (2007).","journal-title":"Int. J. Biol. Sci."},{"key":"BFncomms15355_CR50","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1038\/nmeth0511-379","volume":"8","author":"M Baker","year":"2011","unstructured":"Baker, M. Long noncoding RNAs: the search for function. Nat. Methods. 8, 379\u2013383 (2011).","journal-title":"Nat. Methods."},{"key":"BFncomms15355_CR51","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1016\/j.cell.2013.06.020","volume":"154","author":"I Ulitsky","year":"2013","unstructured":"Ulitsky, I. & Bartel, D. P. lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26\u201346 (2013).","journal-title":"Cell"},{"key":"BFncomms15355_CR52","unstructured":"Case, D. A. et al. AMBER 14 (University of California (2014)."},{"key":"BFncomms15355_CR53","doi-asserted-by":"publisher","first-page":"3817","DOI":"10.1529\/biophysj.106.097782","volume":"92","author":"A Perez","year":"2007","unstructured":"Perez, A. et al. Refinement of the AMBER force field for nucleic acids: improving the description of alpha\/gamma conformers. Biophys. J. 92, 3817\u20133829 (2007).","journal-title":"Biophys. J."},{"key":"BFncomms15355_CR54","doi-asserted-by":"publisher","first-page":"2506","DOI":"10.1021\/ct300275s","volume":"8","author":"M Krepl","year":"2012","unstructured":"Krepl, M. et al. Reference simulations of noncanonical nucleic acids with different chi variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA. J. Chem. Theory Comput. 8, 2506\u20132520 (2012).","journal-title":"J. Chem. Theory Comput."},{"key":"BFncomms15355_CR55","doi-asserted-by":"publisher","first-page":"2339","DOI":"10.1021\/ct400154j","volume":"9","author":"M Zgarbova","year":"2013","unstructured":"Zgarbova, M. et al. Toward improved description of DNA backbone: revisiting epsilon and zeta torsion force field parameters. J. Chem. Theory Comput. 9, 2339\u20132354 (2013).","journal-title":"J. Chem. Theory Comput."},{"key":"BFncomms15355_CR56","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen, E. F. et al. UCSF chimera\u2013a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605\u20131612 (2004).","journal-title":"J. Comput. Chem."},{"key":"BFncomms15355_CR57","doi-asserted-by":"publisher","first-page":"3084","DOI":"10.1021\/ct400341p","volume":"9","author":"DR Roe","year":"2013","unstructured":"Roe, D. R. & Cheatham, T. E. III PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J. Chem. Theory Comput. 9, 3084\u20133095 (2013).","journal-title":"J. Chem. Theory Comput."},{"key":"BFncomms15355_CR58","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","volume":"98","author":"T Darden","year":"1993","unstructured":"Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: an N\u00b7log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089\u201310092 (1993).","journal-title":"J. Chem. Phys."},{"key":"BFncomms15355_CR59","doi-asserted-by":"publisher","first-page":"8577","DOI":"10.1063\/1.470117","volume":"103","author":"U Essmann","year":"1995","unstructured":"Essmann, U. et al. A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577\u20138593 (1995).","journal-title":"J. Chem. Phys."},{"key":"BFncomms15355_CR60","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","volume":"23","author":"JP Ryckaert","year":"1977","unstructured":"Ryckaert, J. P., Ciccotti, G. & Berendsen, H. J. C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327\u2013341 (1977).","journal-title":"J. Comput. Phys."}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/ncomms15355.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/ncomms15355","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/doifinder\/10.1038\/ncomms15355","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/www.nature.com\/articles\/ncomms15355.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,23]],"date-time":"2022-12-23T00:49:07Z","timestamp":1671756547000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/ncomms15355"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,5,17]]},"references-count":60,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,8,14]]}},"alternative-id":["BFncomms15355"],"URL":"https:\/\/doi.org\/10.1038\/ncomms15355","relation":{},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,5,17]]},"assertion":[{"value":"27 October 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 March 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 May 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"15355"}}