{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T10:53:08Z","timestamp":1769770388918,"version":"3.49.0"},"reference-count":81,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2006,9,28]],"date-time":"2006-09-28T00:00:00Z","timestamp":1159401600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,9,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Methodologies to detect DNA sequences with high sensitivity and specificity have tremendous potential as molecular diagnostic agents. Most current methods exploit the ability of single-stranded DNA (ssDNA) to base pair with high specificity to a complementary molecule. However, recent advances in robust techniques for recognition of DNA in the major and minor groove have made possible the direct detection of double-stranded DNA (dsDNA), without the need for denaturation, renaturation, or hybridization. This review will describe the progress in adapting polyamides, triplex DNA, and engineered zinc finger DNA-binding proteins as dsDNA diagnostic systems. In particular, the sequence-enabled reassembly (SEER) method, involving the use of custom zinc finger proteins, offers the potential for direct detection of dsDNA in cells, with implications for cell-based diagnostics and therapeutics.<\/jats:p>\n                  <jats:p\/>","DOI":"10.1039\/b611169f","type":"journal-article","created":{"date-parts":[[2006,9,28]],"date-time":"2006-09-28T07:03:35Z","timestamp":1159427015000},"page":"551-560","source":"Crossref","is-referenced-by-count":91,"title":["Direct detection of double-stranded DNA: molecular methods and applications for DNA diagnostics"],"prefix":"10.1093","volume":"2","author":[{"given":"Indraneel","family":"Ghosh","sequence":"first","affiliation":[{"name":"Department of Chemistry, University of Arizona a , Tucson, Arizona 85721 ghosh@email.arizona.edu 520-621-6331"}]},{"given":"Cliff I","family":"Stains","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Arizona a , Tucson, Arizona 85721 ghosh@email.arizona.edu 520-621-6331"}]},{"given":"Aik T","family":"Ooi","sequence":"additional","affiliation":[{"name":"Genome Center and Department of Pharmacology, University of California b , Davis, CA 95616 djsegal@ucdavis.edu 530-754-9658 530-754-9134"}]},{"given":"David J","family":"Segal","sequence":"additional","affiliation":[{"name":"Genome Center and Department of Pharmacology, University of California b , Davis, CA 95616 djsegal@ucdavis.edu 530-754-9658 530-754-9134"}]}],"member":"286","published-online":{"date-parts":[[2006,9,28]]},"reference":[{"key":"2026012914051237900_cit1","first-page":"3","volume":"45","author":"Atkins","year":"2004","journal-title":"J. Appl. Genet."},{"key":"2026012914051237900_cit2","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1007\/s10123-003-0143-y","volume":"6","author":"Lopez","year":"2003","journal-title":"Int. Microbiol."},{"key":"2026012914051237900_cit3","doi-asserted-by":"crossref","first-page":"545","DOI":"10.2174\/0929867003373373","volume":"8","author":"Nielsen","year":"2001","journal-title":"Curr. Med. Chem."},{"key":"2026012914051237900_cit4","doi-asserted-by":"crossref","first-page":"2833","DOI":"10.1242\/jcs.00633","volume":"116","author":"Levsky","year":"2003","journal-title":"J. Cell Sci."},{"key":"2026012914051237900_cit5","doi-asserted-by":"crossref","first-page":"2215","DOI":"10.1016\/S0968-0896(01)00262-0","volume":"9","author":"Dervan","year":"2001","journal-title":"Bioorg. Med. Chem."},{"key":"2026012914051237900_cit6","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1007\/s001090050112","volume":"75","author":"Chan","year":"1997","journal-title":"J. Mol. Med."},{"key":"2026012914051237900_cit7","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1016\/S0958-1669(01)00272-5","volume":"12","author":"Segal","year":"2001","journal-title":"Curr. Opin. Biotechnol."},{"key":"2026012914051237900_cit8","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1038\/nrg1809","volume":"7","author":"Hoheisel","year":"2006","journal-title":"Nat. Rev. Genet."},{"key":"2026012914051237900_cit9","first-page":"111","volume":"573","author":"la Vega","year":"2005","journal-title":"Mutat. Res."},{"key":"2026012914051237900_cit10","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1586\/14737159.3.5.649","volume":"3","author":"Stender","year":"2003","journal-title":"Expert. Rev. Mol. Diagn."},{"key":"2026012914051237900_cit11","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1038\/90236","volume":"19","author":"Howorka","year":"2001","journal-title":"Nat. Biotechnol."},{"key":"2026012914051237900_cit12","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/85696","volume":"19","author":"Vercoutere","year":"2001","journal-title":"Nat. Biotechnol."},{"key":"2026012914051237900_cit13","doi-asserted-by":"crossref","first-page":"5932","DOI":"10.1021\/ja049384+","volume":"126","author":"Nam","year":"2004","journal-title":"J. Am. Chem. Soc."},{"key":"2026012914051237900_cit14","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1007\/s10895-006-0098-4","volume":"16","author":"Dore","year":"2006","journal-title":"J. Fluoresc."},{"key":"2026012914051237900_cit15","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1586\/14737159.4.2.251","volume":"4","author":"Hellyer","year":"2004","journal-title":"Expert. Rev. Mol. Diagn."},{"key":"2026012914051237900_cit16","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1586\/14737159.5.4.477","volume":"5","author":"Demidov","year":"2005","journal-title":"Expert. Rev. Mol. Diagn."},{"key":"2026012914051237900_cit17","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1586\/14737159.6.3.433","volume":"6","author":"Bissonnette","year":"2006","journal-title":"Expert. Rev. Mol. Diagn."},{"key":"2026012914051237900_cit18","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1586\/14737159.3.2.153","volume":"3","author":"Jain","year":"2003","journal-title":"Expert. Rev. Mol. Diagn."},{"key":"2026012914051237900_cit19","first-page":"254","volume":"18","author":"Zhao","year":"2005","journal-title":"Clin. Lab. Sci."},{"key":"2026012914051237900_cit20","doi-asserted-by":"crossref","first-page":"1376","DOI":"10.1073\/pnas.82.5.1376","volume":"82","author":"Kopka","year":"1985","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026012914051237900_cit21","doi-asserted-by":"crossref","first-page":"9892","DOI":"10.1021\/ja00075a004","volume":"115","author":"Mrksich","year":"1993","journal-title":"J. Am. Chem. Soc."},{"key":"2026012914051237900_cit22","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1038\/35106","volume":"391","author":"White","year":"1998","journal-title":"Nature"},{"key":"2026012914051237900_cit23","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1016\/S1097-2765(00)00099-X","volume":"6","author":"Janssen","year":"2000","journal-title":"Mol. Cell"},{"key":"2026012914051237900_cit24","doi-asserted-by":"crossref","first-page":"3218","DOI":"10.1093\/emboj\/20.12.3218","volume":"20","author":"Maeshima","year":"2001","journal-title":"EMBO J."},{"key":"2026012914051237900_cit25","doi-asserted-by":"crossref","first-page":"16685","DOI":"10.1021\/ja054650k","volume":"127","author":"Fechter","year":"2005","journal-title":"J. Am. Chem. Soc."},{"key":"2026012914051237900_cit26","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1021\/ja021011q","volume":"125","author":"Rucker","year":"2003","journal-title":"J. Am. Chem. Soc."},{"key":"2026012914051237900_cit27","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1073\/pnas.0509843102","volume":"103","author":"Warren","year":"2006","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026012914051237900_cit28","doi-asserted-by":"crossref","first-page":"7749","DOI":"10.1093\/nar\/15.19.7749","volume":"15","author":"Doan","year":"1987","journal-title":"Nucleic Acids Res."},{"key":"2026012914051237900_cit29","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1126\/science.3118463","volume":"238","author":"Moser","year":"1987","journal-title":"Science"},{"key":"2026012914051237900_cit30","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1089\/oli.1.1998.8.215","volume":"8","author":"Cheng","year":"1998","journal-title":"Antisense Nucleic Acid Drug Dev."},{"key":"2026012914051237900_cit31","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1007\/s004120050367","volume":"108","author":"Johnson","year":"1999","journal-title":"Chromosoma"},{"key":"2026012914051237900_cit32","doi-asserted-by":"crossref","first-page":"10603","DOI":"10.1073\/pnas.96.19.10603","volume":"96","author":"Escude","year":"1999","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026012914051237900_cit33","doi-asserted-by":"crossref","first-page":"e125","DOI":"10.1093\/nar\/gng125","volume":"31","author":"Geron-Landre","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2026012914051237900_cit34","doi-asserted-by":"crossref","first-page":"5343","DOI":"10.1111\/j.1742-4658.2005.04932.x","volume":"272","author":"Geron-Landre","year":"2005","journal-title":"FEBS J."},{"key":"2026012914051237900_cit35","doi-asserted-by":"crossref","first-page":"12657","DOI":"10.1021\/ja0530218","volume":"127","author":"Li","year":"2005","journal-title":"J. Am. Chem. Soc."},{"key":"2026012914051237900_cit36","doi-asserted-by":"crossref","first-page":"1523","DOI":"10.1002\/1521-3773(20010417)40:8<1523::AID-ANIE1523>3.0.CO;2-A","volume":"40","author":"Roulon","year":"2001","journal-title":"Angew. Chem., Int. Ed."},{"key":"2026012914051237900_cit37","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1089\/gte.2005.9.111","volume":"9","author":"Daksis","year":"2005","journal-title":"Genet. Test."},{"key":"2026012914051237900_cit38","doi-asserted-by":"crossref","first-page":"4201","DOI":"10.1093\/nar\/9.16.4201","volume":"9","author":"Cassuto","year":"1981","journal-title":"Nucleic Acids Res."},{"key":"2026012914051237900_cit39","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1006\/jmbi.1993.1038","volume":"229","author":"Rao","year":"1993","journal-title":"J. Mol. Biol."},{"key":"2026012914051237900_cit40","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1126\/science.1962210","volume":"254","author":"Nielsen","year":"1991","journal-title":"Science"},{"key":"2026012914051237900_cit41","doi-asserted-by":"crossref","first-page":"2478","DOI":"10.1101\/gr.2789604","volume":"14","author":"Shigemori","year":"2004","journal-title":"Genome Res."},{"key":"2026012914051237900_cit42","doi-asserted-by":"crossref","first-page":"8484","DOI":"10.1021\/ja060069s","volume":"128","author":"Baker","year":"2006","journal-title":"J. Am. Chem. Soc."},{"key":"2026012914051237900_cit43","doi-asserted-by":"crossref","first-page":"e59","DOI":"10.1093\/nar\/gkl218","volume":"34","author":"Schatz","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2026012914051237900_cit44","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1101\/gr.1635204","volume":"14","author":"Chan","year":"2004","journal-title":"Genome Res."},{"key":"2026012914051237900_cit45","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0065-2660(06)56001-8","volume":"56","author":"Lundin","year":"2006","journal-title":"Adv. Genet."},{"key":"2026012914051237900_cit46","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.1126\/science.1058040","volume":"291","author":"Venter","year":"2001","journal-title":"Science"},{"key":"2026012914051237900_cit47","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1021\/bc050307t","volume":"17","author":"Thompson","year":"2006","journal-title":"Bioconjugate Chem."},{"key":"2026012914051237900_cit48","doi-asserted-by":"crossref","first-page":"1979","DOI":"10.1021\/ac9913311","volume":"72","author":"Taylor","year":"2000","journal-title":"Anal. Chem."},{"key":"2026012914051237900_cit49","doi-asserted-by":"crossref","first-page":"1685","DOI":"10.1083\/jcb.135.6.1685","volume":"135","author":"Robinett","year":"1996","journal-title":"J. Cell Biol."},{"key":"2026012914051237900_cit50","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/1471-2156-7-36","volume":"7","author":"Gonzalez-Serricchio","year":"2006","journal-title":"BMC Genet."},{"key":"2026012914051237900_cit51","doi-asserted-by":"crossref","first-page":"3620","DOI":"10.1021\/bi0517032","volume":"45","author":"Ooi","year":"2006","journal-title":"Biochemistry"},{"key":"2026012914051237900_cit52","doi-asserted-by":"crossref","first-page":"9761","DOI":"10.1021\/ja060681j","volume":"128","author":"Stains","year":"2006","journal-title":"J. Am. Chem. Soc."},{"key":"2026012914051237900_cit53","doi-asserted-by":"crossref","first-page":"10782","DOI":"10.1021\/ja051969w","volume":"127","author":"Stains","year":"2005","journal-title":"J. Am. Chem. Soc."},{"key":"2026012914051237900_cit54","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1146\/annurev.biophys.29.1.183","volume":"29","author":"Wolfe","year":"2000","journal-title":"Annu. Rev. Biophys. Biomol. Struct."},{"key":"2026012914051237900_cit55","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1038\/nbt0202-135","volume":"20","author":"Beerli","year":"2002","journal-title":"Nat. Biotechnol."},{"key":"2026012914051237900_cit56","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1146\/annurev.biochem.70.1.313","volume":"70","author":"Pabo","year":"2001","journal-title":"Annu. Rev. Biochem."},{"key":"2026012914051237900_cit57","doi-asserted-by":"crossref","first-page":"29466","DOI":"10.1074\/jbc.M102604200","volume":"276","author":"Dreier","year":"2001","journal-title":"J. Biol. Chem."},{"key":"2026012914051237900_cit58","doi-asserted-by":"crossref","first-page":"35588","DOI":"10.1074\/jbc.M506654200","volume":"280","author":"Dreier","year":"2005","journal-title":"J. Biol. Chem."},{"key":"2026012914051237900_cit59","doi-asserted-by":"crossref","first-page":"2758","DOI":"10.1073\/pnas.96.6.2758","volume":"96","author":"Segal","year":"1999","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026012914051237900_cit60","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1016\/j.bbrc.2005.07.089","volume":"335","author":"Mani","year":"2005","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2026012914051237900_cit61","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/S1046-2023(02)00009-9","volume":"26","author":"Segal","year":"2002","journal-title":"Methods"},{"key":"2026012914051237900_cit62","first-page":"447","volume":"185","author":"Remy","year":"2002","journal-title":"Methods Mol. Biol."},{"key":"2026012914051237900_cit63","doi-asserted-by":"crossref","first-page":"5658","DOI":"10.1021\/ja994421w","volume":"122","author":"Ghosh","year":"2000","journal-title":"J. Am. Chem. Soc."},{"key":"2026012914051237900_cit64","doi-asserted-by":"crossref","first-page":"11146","DOI":"10.1021\/ja036126o","volume":"125","author":"Gao","year":"2003","journal-title":"J. Am. Chem. Soc."},{"key":"2026012914051237900_cit65","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1038\/nbt0602-619","volume":"20","author":"Galarneau","year":"2002","journal-title":"Nat. Biotechnol."},{"key":"2026012914051237900_cit66","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/0092-8674(92)90526-I","volume":"70","author":"Bird","year":"1992","journal-title":"Cell"},{"key":"2026012914051237900_cit67","doi-asserted-by":"crossref","first-page":"1499","DOI":"10.1093\/nar\/8.7.1499","volume":"8","author":"Bird","year":"1980","journal-title":"Nucleic Acids Res."},{"key":"2026012914051237900_cit68","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/ng1089","volume":"33 Suppl","author":"Jaenisch","year":"2003","journal-title":"Nat. Genet."},{"key":"2026012914051237900_cit69","doi-asserted-by":"crossref","first-page":"2990","DOI":"10.1093\/nar\/22.15.2990","volume":"22","author":"Clark","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"2026012914051237900_cit70","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1016\/0006-291X(70)90211-1","volume":"41","author":"Furuichi","year":"1970","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2026012914051237900_cit71","doi-asserted-by":"crossref","first-page":"9821","DOI":"10.1073\/pnas.93.18.9821","volume":"93","author":"Herman","year":"1996","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026012914051237900_cit72","doi-asserted-by":"crossref","first-page":"2532","DOI":"10.1093\/nar\/25.12.2532","volume":"25","author":"Xiong","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2026012914051237900_cit73","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1006\/abio.1995.1204","volume":"226","author":"Raizis","year":"1995","journal-title":"Anal. Biochem."},{"key":"2026012914051237900_cit74","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1006\/meth.1999.0883","volume":"19","author":"Thomassin","year":"1999","journal-title":"Methods"},{"key":"2026012914051237900_cit75","doi-asserted-by":"crossref","first-page":"10021","DOI":"10.1074\/jbc.272.15.10021","volume":"272","author":"Rein","year":"1997","journal-title":"J. Biol. Chem."},{"key":"2026012914051237900_cit76","doi-asserted-by":"crossref","first-page":"632, 634, 636","DOI":"10.2144\/02333rv01","volume":"33","author":"Fraga","year":"2002","journal-title":"Biotechniques"},{"key":"2026012914051237900_cit77","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/S1046-2023(02)00060-9","volume":"27","author":"Warnecke","year":"2002","journal-title":"Methods"},{"key":"2026012914051237900_cit78","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.copbio.2004.12.001","volume":"16","author":"Tanke","year":"2005","journal-title":"Curr. Opin. Biotechnol."},{"key":"2026012914051237900_cit79","doi-asserted-by":"crossref","first-page":"6064","DOI":"10.1093\/nar\/gkg815","volume":"31","author":"Uil","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2026012914051237900_cit80","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1016\/j.tibtech.2005.06.005","volume":"23","author":"Kolb","year":"2005","journal-title":"Trends Biotechnol."},{"key":"2026012914051237900_cit81","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1016\/S0960-894X(02)00935-6","volume":"13","author":"Vrudhula","year":"2003","journal-title":"Bioorg. Med. Chem. Lett."}],"container-title":["Molecular BioSystems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/molecular-omics\/article-pdf\/2\/11\/551\/66233887\/b611169f.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/molecular-omics\/article-pdf\/2\/11\/551\/66233887\/b611169f.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,29]],"date-time":"2026-01-29T19:08:13Z","timestamp":1769713693000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/molecular-omics\/article\/2\/11\/551\/8384697"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,9,28]]},"references-count":81,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2006,9,28]]}},"URL":"https:\/\/doi.org\/10.1039\/b611169f","relation":{},"ISSN":["1742-2051","1742-206X"],"issn-type":[{"value":"1742-2051","type":"electronic"},{"value":"1742-206X","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,10,17]]},"published":{"date-parts":[[2006,9,28]]}}}