Exploring Hoogsteen and Reversed-Hoogsteen Duplex and Triplex Formation with Tricyclo-DNA Purine Sequences
The duplex- and triplex-formation properties of the tricyclo-DNA purine decamer 5′p-gagaaggaaa-3′ as a single strand or as part of a hairpin duplex with corresponding parallel and antiparallel pyrimidine DNA and RNA complements, as well as with antiparallel purine DNA and RNA complements, were inves...
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| Veröffentlicht in: | Chembiochem : a European journal of chemical biology 2004-08, Vol.5 (8), p.1114-1118 |
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| container_title | Chembiochem : a European journal of chemical biology |
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| creator | Renneberg, Dorte Leumann, Christian J |
| description | The duplex- and triplex-formation properties of the tricyclo-DNA purine decamer 5′p-gagaaggaaa-3′ as a single strand or as part of a hairpin duplex with corresponding parallel and antiparallel pyrimidine DNA and RNA complements, as well as with antiparallel purine DNA and RNA complements, were investigated by UV melting curve analysis, circular dichroism spectroscopy, and gel mobility shift experiments. It was found that tricyclo-DNA forms very stable duplexes with the pyrimidine RNA and DNA complements not only in the Watson-Crick pairing mode, but also in the Hoogsteen one. Below pH 6.0, the tc-DNA/DNA and tc-DNA/RNA Hoogsteen duplexes were found to be more stable than the corresponding Watson-Crick DNA duplexes. Triplexes of the hairpin structure with parallel pyrimidine complements revealed even stronger Hoogsteen pairing relative to the duplexes, presumably due to structural preorganization phenomena. Triplex formation with antiparallel pyrimidine and purine third strands (reversed-Hoogsteen motif) could not be observed and seem to be unstable. |
| doi_str_mv | 10.1002/cbic.200400069 |
| format | Article |
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It was found that tricyclo-DNA forms very stable duplexes with the pyrimidine RNA and DNA complements not only in the Watson-Crick pairing mode, but also in the Hoogsteen one. Below pH 6.0, the tc-DNA/DNA and tc-DNA/RNA Hoogsteen duplexes were found to be more stable than the corresponding Watson-Crick DNA duplexes. Triplexes of the hairpin structure with parallel pyrimidine complements revealed even stronger Hoogsteen pairing relative to the duplexes, presumably due to structural preorganization phenomena. Triplex formation with antiparallel pyrimidine and purine third strands (reversed-Hoogsteen motif) could not be observed and seem to be unstable.</description><identifier>ISSN: 1439-4227</identifier><identifier>EISSN: 1439-7633</identifier><identifier>EISSN: 1439-4227</identifier><identifier>DOI: 10.1002/cbic.200400069</identifier><identifier>PMID: 15300836</identifier><language>eng</language><publisher>Weinheim: Wiley-VCH Verlag</publisher><subject>Base Sequence ; Circular Dichroism ; DNA - chemistry ; DNA recognition ; DNA triple-helix ; Hoogsteen pairing ; oligonucleotides ; Purines - chemistry ; Watson-Crick pairing</subject><ispartof>Chembiochem : a European journal of chemical biology, 2004-08, Vol.5 (8), p.1114-1118</ispartof><rights>Copyright © 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4349-a7288ca1069439427fb2e3f8ab5b2506fcaac3a10c266e7be93c35ec12dffb413</citedby><cites>FETCH-LOGICAL-c4349-a7288ca1069439427fb2e3f8ab5b2506fcaac3a10c266e7be93c35ec12dffb413</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fcbic.200400069$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fcbic.200400069$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>315,781,785,1418,27929,27930,45579,45580</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15300836$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Renneberg, Dorte</creatorcontrib><creatorcontrib>Leumann, Christian J</creatorcontrib><title>Exploring Hoogsteen and Reversed-Hoogsteen Duplex and Triplex Formation with Tricyclo-DNA Purine Sequences</title><title>Chembiochem : a European journal of chemical biology</title><addtitle>ChemBioChem</addtitle><description>The duplex- and triplex-formation properties of the tricyclo-DNA purine decamer 5′p-gagaaggaaa-3′ as a single strand or as part of a hairpin duplex with corresponding parallel and antiparallel pyrimidine DNA and RNA complements, as well as with antiparallel purine DNA and RNA complements, were investigated by UV melting curve analysis, circular dichroism spectroscopy, and gel mobility shift experiments. It was found that tricyclo-DNA forms very stable duplexes with the pyrimidine RNA and DNA complements not only in the Watson-Crick pairing mode, but also in the Hoogsteen one. Below pH 6.0, the tc-DNA/DNA and tc-DNA/RNA Hoogsteen duplexes were found to be more stable than the corresponding Watson-Crick DNA duplexes. Triplexes of the hairpin structure with parallel pyrimidine complements revealed even stronger Hoogsteen pairing relative to the duplexes, presumably due to structural preorganization phenomena. Triplex formation with antiparallel pyrimidine and purine third strands (reversed-Hoogsteen motif) could not be observed and seem to be unstable.</description><subject>Base Sequence</subject><subject>Circular Dichroism</subject><subject>DNA - chemistry</subject><subject>DNA recognition</subject><subject>DNA triple-helix</subject><subject>Hoogsteen pairing</subject><subject>oligonucleotides</subject><subject>Purines - chemistry</subject><subject>Watson-Crick pairing</subject><issn>1439-4227</issn><issn>1439-7633</issn><issn>1439-4227</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkUFPGzEQha2qqFDolWPZE7cNY3vX3j3SAAEJ0YiAKnGxvM5satisg52F5N_XYSPojZNHM9-8Gc8j5JDCgAKwE1NZM2AAGQCI8gvZoxkvUyk4_7qNM8bkLvkewmNESsHpN7JLcw5QcLFHHs9Xi8Z5286SS-dmYYnYJrqdJrf4gj7gNP1In3WLBldv1Ttv3-IL5-d6aV2bvNrl303arE3j0rOb02TcRVlMJvjcYWswHJCdWjcBf2zffXJ_cX43vEyvf4-uhqfXqcl4VqZasqIwmsbvxPUzJuuKIa8LXeUVy0HURmvDY90wIVBWWHLDczSUTeu6yijfJ8e97sK7ODos1dwGg02jW3RdUEJIyTiwT0FaQCYllxEc9KDxLgSPtVp4O9d-rSiojQ1qY4N6tyE2_Nwqd9Ucpx_49u4RKHvg1Ta4_kRODX9dDf8XT_teG21Zvfdq_6RE3DZXf25Gio5HYyYfJmoS-aOer7VTeuZtUPcTBpQDjeeFXPJ_-XytOw</recordid><startdate>20040806</startdate><enddate>20040806</enddate><creator>Renneberg, Dorte</creator><creator>Leumann, Christian J</creator><general>Wiley-VCH Verlag</general><general>WILEY-VCH Verlag</general><general>WILEY‐VCH Verlag</general><scope>FBQ</scope><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7TM</scope><scope>7X8</scope></search><sort><creationdate>20040806</creationdate><title>Exploring Hoogsteen and Reversed-Hoogsteen Duplex and Triplex Formation with Tricyclo-DNA Purine Sequences</title><author>Renneberg, Dorte ; Leumann, Christian J</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4349-a7288ca1069439427fb2e3f8ab5b2506fcaac3a10c266e7be93c35ec12dffb413</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2004</creationdate><topic>Base Sequence</topic><topic>Circular Dichroism</topic><topic>DNA - chemistry</topic><topic>DNA recognition</topic><topic>DNA triple-helix</topic><topic>Hoogsteen pairing</topic><topic>oligonucleotides</topic><topic>Purines - chemistry</topic><topic>Watson-Crick pairing</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Renneberg, Dorte</creatorcontrib><creatorcontrib>Leumann, Christian J</creatorcontrib><collection>AGRIS</collection><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Chembiochem : a European journal of chemical biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Renneberg, Dorte</au><au>Leumann, Christian J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Exploring Hoogsteen and Reversed-Hoogsteen Duplex and Triplex Formation with Tricyclo-DNA Purine Sequences</atitle><jtitle>Chembiochem : a European journal of chemical biology</jtitle><addtitle>ChemBioChem</addtitle><date>2004-08-06</date><risdate>2004</risdate><volume>5</volume><issue>8</issue><spage>1114</spage><epage>1118</epage><pages>1114-1118</pages><issn>1439-4227</issn><eissn>1439-7633</eissn><eissn>1439-4227</eissn><abstract>The duplex- and triplex-formation properties of the tricyclo-DNA purine decamer 5′p-gagaaggaaa-3′ as a single strand or as part of a hairpin duplex with corresponding parallel and antiparallel pyrimidine DNA and RNA complements, as well as with antiparallel purine DNA and RNA complements, were investigated by UV melting curve analysis, circular dichroism spectroscopy, and gel mobility shift experiments. It was found that tricyclo-DNA forms very stable duplexes with the pyrimidine RNA and DNA complements not only in the Watson-Crick pairing mode, but also in the Hoogsteen one. Below pH 6.0, the tc-DNA/DNA and tc-DNA/RNA Hoogsteen duplexes were found to be more stable than the corresponding Watson-Crick DNA duplexes. Triplexes of the hairpin structure with parallel pyrimidine complements revealed even stronger Hoogsteen pairing relative to the duplexes, presumably due to structural preorganization phenomena. Triplex formation with antiparallel pyrimidine and purine third strands (reversed-Hoogsteen motif) could not be observed and seem to be unstable.</abstract><cop>Weinheim</cop><pub>Wiley-VCH Verlag</pub><pmid>15300836</pmid><doi>10.1002/cbic.200400069</doi><tpages>5</tpages></addata></record> |
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| ispartof | Chembiochem : a European journal of chemical biology, 2004-08, Vol.5 (8), p.1114-1118 |
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| source | MEDLINE; Access via Wiley Online Library |
| subjects | Base Sequence Circular Dichroism DNA - chemistry DNA recognition DNA triple-helix Hoogsteen pairing oligonucleotides Purines - chemistry Watson-Crick pairing |
| title | Exploring Hoogsteen and Reversed-Hoogsteen Duplex and Triplex Formation with Tricyclo-DNA Purine Sequences |
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