{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T10:24:56Z","timestamp":1787048696504,"version":"build-2736575974"},"reference-count":54,"publisher":"American Chemical Society (ACS)","issue":"7","license":[{"start":{"date-parts":[[2022,12,23]],"date-time":"2022-12-23T00:00:00Z","timestamp":1671753600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2022,12,23]],"date-time":"2022-12-23T00:00:00Z","timestamp":1671753600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2022,12,23]],"date-time":"2022-12-23T00:00:00Z","timestamp":1671753600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100009647","name":"University Grants Commission- Nepal","doi-asserted-by":"publisher","award":["PhD-78\/79-S&T-15"],"award-info":[{"award-number":["PhD-78\/79-S&T-15"]}],"id":[{"id":"10.13039\/501100009647","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002222","name":"The World Academy of Sciences","doi-asserted-by":"publisher","award":["RG 20-316"],"award-info":[{"award-number":["RG 20-316"]}],"id":[{"id":"10.13039\/501100002222","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,4,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Methyl CpG binding proteins (MBPs) are transcription factors that recognize the methylated CpG sites in DNA and mediate the DNA methylation signal into various downstream cellular processes. The C2H2 zinc finger (ZF) protein, Kaiso, also an MBP, preferentially binds to two symmetrically methylated CpG sites in DNA sequences via C-terminal C2H2 ZF domains and mediates the transcription regulation process. Investigation of the molecular mechanism of the recognition of methylated DNA (meDNA) by Kaiso is important to understand how this protein reads and translates this methylation signal into downstream transcription outcomes. Despite previous studies in Kaiso-meDNA interactions, detailed structural investigations on the sequence-specific interaction of Kaiso with the meDNA sequence are still lacking. In this work, we used molecular modeling and molecular dynamics (MD) simulation-based computational approaches to investigate the recognition of various methylated DNA sequences by Kaiso. Our MD simulation results show that the Kaiso-meDNA interaction is sequence specific. The recognition of meDNA by Kaiso is enhanced in the MeECad sequence compared to the MeCG2 sequence. Compared to the 5\u2032-flanking T\/A pair in MeCG2, both MeCG2_mutCG and MeECad sequences show that a C\/G base pair allows GLU535 of Kaiso to preferably recognize and bind the core mCpG site. The core mCGmCG site is crucial for the recognition process and formation of a stable complex. Our results reveal that the 5\u2032-flanking nucleotides are also important for the enhanced binding and recognition of methylated sites.<\/jats:p>","DOI":"10.1021\/acs.jcim.2c01294","type":"journal-article","created":{"date-parts":[[2022,12,23]],"date-time":"2022-12-23T11:47:14Z","timestamp":1671796034000},"page":"2095-2103","source":"Crossref","is-referenced-by-count":8,"title":["A 5\u2032-Flanking C\/G Pair at the Core Region Enhances\nthe Recognition and Binding of Kaiso to Methylated DNA"],"prefix":"10.1021","volume":"63","author":[{"given":"Bidhya","family":"Thapa","sequence":"first","affiliation":[{"name":"Tribhuvan University , , , ,","place":["Kirtipur, Kathmandu, Nepal, 44613"]},{"name":"Tribhuvan University , , , ,","place":["Bagbazar, Kathmandu, Nepal, 44613"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Narayan P.","family":"Adhikari","sequence":"additional","affiliation":[{"name":"Tribhuvan University , , , ,","place":["Kirtipur, Kathmandu, Nepal, 44613"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3140-0723","authenticated-orcid":true,"given":"Purushottam B.","family":"Tiwari","sequence":"additional","affiliation":[{"name":"Georgetown University , , ,","place":["Washington, DC, United States, 20057"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0999-4975","authenticated-orcid":true,"given":"Prem P.","family":"Chapagain","sequence":"additional","affiliation":[{"name":"Florida International University , , , ,","place":["Miami, Florida, United States, 33199"]},{"name":"Florida International University , , , ,","place":["Miami, Florida, United\nStates, 33199"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2022,12,23]]},"reference":[{"key":"2026081804435059900_cit1","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1016\/j.tibs.2005.12.008","article-title":"Genomic DNA methylation:\nthe mark and its mediators","volume":"31","author":"Klose","year":"2006","journal-title":"Trends Biochem.\nSci."},{"key":"2026081804435059900_cit2","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1038\/321209a0","article-title":"CpG-rich\nislands and the function of DNA methylation","volume":"321","author":"Bird","year":"1986","journal-title":"Nature"},{"key":"2026081804435059900_cit3","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1016\/0092-8674(92)90526-I","article-title":"The essentials\nof DNA methylation","volume":"70","author":"Bird","year":"1992","journal-title":"Cell"},{"key":"2026081804435059900_cit4","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1101\/gad.947102","article-title":"DNA methylation\npatterns and epigenetic memory","volume":"16","author":"Bird","year":"2002","journal-title":"Genes Dev."},{"key":"2026081804435059900_cit5","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1002\/jcb.22253","article-title":"DNA methylation-mediated epigenetic\ncontrol","volume":"108","author":"Rottach","year":"2009","journal-title":"J. Cell. Biochem."},{"key":"2026081804435059900_cit6","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1002\/jcp.21224","article-title":"DNA methylation:\nthe nuts and bolts of repression","volume":"213","author":"Miranda","year":"2007","journal-title":"J. Cell. Physiol."},{"key":"2026081804435059900_cit7","first-page":"271","article-title":"DNA methylation and\nX-chromosome inactivation","volume":"1","author":"Blasi","year":"1983","journal-title":"Mol. Biol. Med."},{"key":"2026081804435059900_cit8","doi-asserted-by":"publisher","first-page":"362","DOI":"10.1038\/366362a0","article-title":"Role for DNA\nmethylation in genomic\nimprinting","volume":"366","author":"Li","year":"1993","journal-title":"Nature"},{"key":"2026081804435059900_cit9","doi-asserted-by":"publisher","first-page":"1068","DOI":"10.1126\/science.1063852","article-title":"The role of DNA methylation\nin mammalian epigenetics","volume":"293","author":"Jones","year":"2001","journal-title":"Science"},{"key":"2026081804435059900_cit10","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1038\/nrg1655","article-title":"DNA methylation\nand human disease","volume":"6","author":"Robertson","year":"2005","journal-title":"Nat. Rev. Genet."},{"key":"2026081804435059900_cit11","doi-asserted-by":"publisher","first-page":"1509","DOI":"10.1007\/s00018-008-7324-y","article-title":"Methyl-CpG\nbinding proteins: specialized transcriptional\nrepressors or structural components of chromatin?","volume":"65","author":"Clouaire","year":"2008","journal-title":"Cell. Mol. Life Sci."},{"key":"2026081804435059900_cit12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1046\/j.1432-1327.2001.01869.x","article-title":"Methyl-CpG-binding proteins: Targeting\nspecific gene\nrepression","volume":"268","author":"Ballestar","year":"2001","journal-title":"Eur. J. 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Sci."},{"key":"2026081804435059900_cit20","doi-asserted-by":"publisher","first-page":"2555","DOI":"10.3390\/molecules23102555","article-title":"Zinc finger\nreaders of methylated DNA","volume":"23","author":"Hudson","year":"2018","journal-title":"Molecules"},{"key":"2026081804435059900_cit21","doi-asserted-by":"publisher","first-page":"3614","DOI":"10.1128\/MCB.19.5.3614","article-title":"The catenin p120\nctn interacts with Kaiso, a novel\nBTB\/POZ domain zinc finger transcription factor","volume":"19","author":"Daniel","year":"1999","journal-title":"Mol. Cell. Biol."},{"key":"2026081804435059900_cit22","doi-asserted-by":"publisher","first-page":"1613","DOI":"10.1101\/gad.198501","article-title":"The p120 catenin\npartner Kaiso is a DNA methylation-dependent transcriptional repressor","volume":"15","author":"Prokhortchouk","year":"2001","journal-title":"Genes Dev."},{"key":"2026081804435059900_cit23","doi-asserted-by":"publisher","first-page":"2911","DOI":"10.1093\/nar\/gkf398","article-title":"The p120 ctn-binding\npartner Kaiso is a bi-modal DNA-binding protein that recognizes both\na sequence-specific consensus and methylated CpG dinucleotides","volume":"30","author":"Daniel","year":"2002","journal-title":"Nucleic acids res."},{"key":"2026081804435059900_cit24","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1016\/j.molcel.2003.08.008","article-title":"N-CoR mediates\nDNA methylation-dependent repression through a methyl CpG binding\nprotein Kaiso","volume":"12","author":"Yoon","year":"2003","journal-title":"Mol. cell"},{"key":"2026081804435059900_cit25","doi-asserted-by":"publisher","first-page":"7188","DOI":"10.1128\/MCB.24.16.7188-7196.2004","article-title":"Regulation\nof the rapsyn promoter by Kaiso and \u03b4-catenin","volume":"24","author":"Rodova","year":"2004","journal-title":"Mol. Cell. Biol."},{"key":"2026081804435059900_cit26","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1756-8935-6-13","article-title":"ZBTB33\nbinds unmethylated regions of the genome associated with actively\nexpressed genes","volume":"6","author":"Blattler","year":"2013","journal-title":"Epigenetics Chromatin"},{"key":"2026081804435059900_cit27","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1016\/j.yexcr.2005.01.007","article-title":"The catenin p120ctn\ninhibits Kaiso-mediated transcriptional\nrepression of the \u03b2-catenin\/TCF target gene matrilysin","volume":"305","author":"Spring","year":"2005","journal-title":"Exp. Cell Res."},{"key":"2026081804435059900_cit28","doi-asserted-by":"publisher","first-page":"4110","DOI":"10.1091\/mbc.e08-03-0283","article-title":"p120 and Kaiso regulate\nHelicobacter pylori-induced expression of matrix metalloproteinase-7","volume":"19","author":"Ogden","year":"2008","journal-title":"Mol. Biol. 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Mech."},{"key":"2026081804435059900_cit32","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1016\/j.bbcan.2018.10.005","article-title":"Dancing\nfrom bottoms\nup-roles of the POZ-ZF transcription factor Kaiso in cancer","volume":"1871","author":"Pierre","year":"2019","journal-title":"Biochim. Biophys. Acta Rev. Cancer"},{"key":"2026081804435059900_cit33","doi-asserted-by":"publisher","first-page":"7258","DOI":"10.1158\/0008-5472.CAN-08-0344","article-title":"Kaiso contributes to\nDNA methylation-dependent silencing of tumor suppressor genes in colon\ncancer cell lines","volume":"68","author":"Lopes","year":"2008","journal-title":"Cancer Res."},{"key":"2026081804435059900_cit34","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0037864","article-title":"Nuclear Kaiso expression is associated\nwith high grade\nand triple-negative invasive breast cancer","volume":"7","author":"Vermeulen","year":"2012","journal-title":"PloS One"},{"key":"2026081804435059900_cit35","doi-asserted-by":"publisher","first-page":"e2689","DOI":"10.1038\/cddis.2017.92","article-title":"Kaiso depletion\nattenuates the growth and survival of triple negative breast cancer\ncells","volume":"8","author":"Bassey-Archibong","year":"2017","journal-title":"Cell Death Dis."},{"key":"2026081804435059900_cit36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2407-9-178","article-title":"Cytoplasmic\nKaiso is associated with poor prognosis in non-small cell lung cancer","volume":"9","author":"Dai","year":"2009","journal-title":"BMC Cancer"},{"key":"2026081804435059900_cit37","doi-asserted-by":"publisher","first-page":"1836","DOI":"10.1016\/j.ajpath.2012.08.008","article-title":"Nuclear Kaiso indicates aggressive prostate cancers and promotes\nmigration and invasiveness of prostate cancer cells","volume":"181","author":"Jones","year":"2012","journal-title":"Am. J. Pathol."},{"key":"2026081804435059900_cit38","doi-asserted-by":"publisher","first-page":"5677","DOI":"10.18632\/oncotarget.6801","article-title":"Kaiso, a transcriptional\nrepressor, promotes cell migration and invasion of prostate cancer\ncells through regulation of miR-31 expression","volume":"7","author":"Wang","year":"2016","journal-title":"Oncotarget"},{"key":"2026081804435059900_cit39","doi-asserted-by":"publisher","first-page":"2374","DOI":"10.1101\/gad.202200.112","article-title":"An atomic model of\nZfp57 recognition of CpG methylation within a specific DNA sequence","volume":"26","author":"Liu","year":"2012","journal-title":"Genes Dev."},{"key":"2026081804435059900_cit40","doi-asserted-by":"publisher","first-page":"15229","DOI":"10.1073\/pnas.1213726109","article-title":"Molecular basis\nfor recognition of methylated and specific DNA sequences by the zinc\nfinger protein Kaiso","volume":"109","author":"Buck-Koehntop","year":"2012","journal-title":"Proc. Natl. Acad. Sci.\nU.S.A."},{"key":"2026081804435059900_cit41","doi-asserted-by":"publisher","first-page":"4859","DOI":"10.1093\/nar\/gku134","article-title":"Structural basis for\nKlf4 recognition of methylated DNA","volume":"42","author":"Liu","year":"2014","journal-title":"Nucleic\nAcids Res."},{"key":"2026081804435059900_cit42","doi-asserted-by":"publisher","first-page":"2109","DOI":"10.1021\/acs.biochem.8b00065","article-title":"CH\u00b7\u00b7\u00b7\nO hydrogen bonds mediate highly specific recognition of methylated\nCpG sites by the zinc finger protein Kaiso","volume":"57","author":"Nikolova","year":"2018","journal-title":"Biochem."},{"key":"2026081804435059900_cit43","doi-asserted-by":"publisher","first-page":"1909","DOI":"10.1021\/acs.biochem.0c00253","article-title":"A conformational\nswitch in the zinc finger protein Kaiso mediates differential readout\nof specific and methylated DNA sequences","volume":"59","author":"Nikolova","year":"2020","journal-title":"Biochem."},{"key":"2026081804435059900_cit44","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1016\/j.molcel.2012.03.017","article-title":"Integrative\ngenomics identifies the corepressor SMRT as a gatekeeper of adipogenesis\nthrough the transcription factors C\/EBP\u03b2 and KAISO","volume":"46","author":"Raghav","year":"2012","journal-title":"Mol. 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Chem."},{"key":"2026081804435059900_cit53","doi-asserted-by":"publisher","first-page":"8577","DOI":"10.1063\/1.470117","article-title":"A smooth particle\nmesh Ewald method","volume":"103","author":"Essmann","year":"1995","journal-title":"J. Chem. Phys."},{"key":"2026081804435059900_cit54","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: visual\nmolecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.2c01294","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/63\/7\/2095\/8909065\/ci2c01294.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/63\/7\/2095\/8909065\/ci2c01294.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T09:32:22Z","timestamp":1787045542000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article\/63\/7\/2095\/850314\/A-5-Flanking-C-G-Pair-at-the-Core-Region-Enhances"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,23]]},"references-count":54,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2022,12,23]]},"published-print":{"date-parts":[[2023,4,10]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.2c01294","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,12,23]]}}}