{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T19:36:25Z","timestamp":1760297785780},"reference-count":41,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2007,5,30]],"date-time":"2007-05-30T00:00:00Z","timestamp":1180483200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biopolymers"],"published-print":{"date-parts":[[2007,9]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Nanometer distances in nucleic acids can be measured by EPR using two 1\u2010oxyl\u20102,2,5,5\u2010tetramethylpyrroline radicals, with each label attached via a methylene group to a phosphorothioate\u2010substituted backbone position as one of two phosphorothioate diastereomers (R<jats:sub>P<\/jats:sub> and S<jats:sub>P<\/jats:sub>). Correlating the internitroxide distance to the geometry of the parent molecule requires computational analysis of the label conformers. Here, we report sixteen 4\u2010ns MD simulations on a DNA duplex d(CTACTGCTTTAG) .d(CTAAAGCAGTAG) with label pairs at C7\/C19, T5\/A17, and T2\/T14, respectively. For each labeled duplex, four simulations were performed with S<jats:sub>P<\/jats:sub>\/S<jats:sub>P<\/jats:sub>, R<jats:sub>P<\/jats:sub>\/R<jats:sub>P<\/jats:sub>, S<jats:sub>P<\/jats:sub>\/R<jats:sub>P<\/jats:sub>, and R<jats:sub>P<\/jats:sub>\/S<jats:sub>P<\/jats:sub> labels, with initial all <jats:italic>trans<\/jats:italic> label conformations. Another set of four simulations was performed for the 7\/19\u2010labeled duplex using a different label starting conformation. The average internitroxide distance \u3008<jats:italic>r<\/jats:italic><jats:sub>MD<\/jats:sub>\u3009 was within 0.2 \u00c5 for the two sets of simulations for the 7\/19\u2010labeled duplex, indicating sufficient sampling of conformational space. For all three labeled duplexes studied, \u3008<jats:italic>r<\/jats:italic><jats:sub>MD<\/jats:sub>\u3009 agreed with experimental values, as well as with average distances obtained from an efficient conformer search algorithm (NASNOX). The simulations also showed that the labels have conformational preferences determined by the linker chemistry and label\u2013DNA interactions. These results establish computational algorithms that allow use of the 1\u2010oxyl\u20102,2,5,5\u2010tetramethylpyrroline label for mapping global structures of nucleic acids. \u00a9 2007 Wiley Periodicals, Inc. Biopolymers 87: 40\u201350, 2007.<\/jats:p><jats:p>This article was originally published online as an accepted preprint. The \u201cPublished Online\u201d date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com<\/jats:p>","DOI":"10.1002\/bip.20769","type":"journal-article","created":{"date-parts":[[2007,5,30]],"date-time":"2007-05-30T20:16:39Z","timestamp":1180556199000},"page":"40-50","source":"Crossref","is-referenced-by-count":31,"title":["Computation of nitroxide\u2013nitroxide distances in spin\u2010labeled DNA duplexes"],"prefix":"10.1002","volume":"87","author":[{"given":"Eric A.","family":"Price","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brian T.","family":"Sutch","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qi","family":"Cai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter Z.","family":"Qin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ian S.","family":"Haworth","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2007,5,30]]},"reference":[{"key":"e_1_2_6_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2006.08.008"},{"key":"e_1_2_6_3_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.291.5502.266"},{"key":"e_1_2_6_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/78956"},{"key":"e_1_2_6_5_2","first-page":"5725","volume-title":"In Encyclopedia of Analytical Chemistry","author":"Fajer P. 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