Effect of DNA Local Conformation on the Affinity and Binding Specificity of bis-Netropsins to DNA
The interaction of short nucleotide duplexes with bis-netropsins, in which netropsin fragments are linked tail-to-tail via cis-diammineplatinum group ([arrow left]Nt-Pt(NH^sub 3^ )-Nt[arrow right]) or aliphatic pentamethylene chain ([arrow left]Nt-(CH^sub 2^ )^sub 5^ -Nt[arrow right]), has been stud...
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Veröffentlicht in: | Molecular biology (New York) 2002-09, Vol.36 (5), p.726-735 |
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description | The interaction of short nucleotide duplexes with bis-netropsins, in which netropsin fragments are linked tail-to-tail via cis-diammineplatinum group ([arrow left]Nt-Pt(NH^sub 3^ )-Nt[arrow right]) or aliphatic pentamethylene chain ([arrow left]Nt-(CH^sub 2^ )^sub 5^ -Nt[arrow right]), has been studied. Both bis-netropsins have been shown to bind to DNA oligomer 5"-CCTATATCC-3" (I) as a hairpin with parallel orientation of netropsin fragments in 1:1 stoichiometry. Monodentate binding has been detected upon binding of bis-netropsins to other duplexes of sequences 5"-CCXCC-3" [where X = TTATT (II), TTAÐnT (III), TTTTT (IV), and AATTT (V)] along with the binding of bis-netropsins as a hairpin. The formation of dimeric antiparallel motif between the halves of two bound bis-netropsin molecules has been observed in the complexes of [arrow left]Nt-(CH^sub 2^ )^sub 5^ -Nt[arrow right] with DNA oligomers IV and V. The ratio of binding constant of bis-netropsin as a hairpin (Ðs^sub 2^) to monodentate binding constant (Ðs^sub 1^) has been shown to correlate with the width and/or conformational lability of DNA in the binding site. The share of bis-netropsin bound as a hairpin decreases in the order: TATAT > TTATT > TTAAT > TTTTT > AATTT, whereas the contribution of monodentate binding rises. The minimal strong binding site for [arrow left]Nt-Pt(NH^sub 3^ )-Nt[arrow right] and [arrow left]Nt-(CH^sub 2^ )^sub 5^ -Nt[arrow right] binding as a hairpin has been found to be DNA duplex 5"-CGTATACG-3".[PUBLICATION ABSTRACT] |
doi_str_mv | 10.1023/A:1020639917565 |
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Both bis-netropsins have been shown to bind to DNA oligomer 5"-CCTATATCC-3" (I) as a hairpin with parallel orientation of netropsin fragments in 1:1 stoichiometry. Monodentate binding has been detected upon binding of bis-netropsins to other duplexes of sequences 5"-CCXCC-3" [where X = TTATT (II), TTAÐnT (III), TTTTT (IV), and AATTT (V)] along with the binding of bis-netropsins as a hairpin. The formation of dimeric antiparallel motif between the halves of two bound bis-netropsin molecules has been observed in the complexes of [arrow left]Nt-(CH^sub 2^ )^sub 5^ -Nt[arrow right] with DNA oligomers IV and V. The ratio of binding constant of bis-netropsin as a hairpin (Ðs^sub 2^) to monodentate binding constant (Ðs^sub 1^) has been shown to correlate with the width and/or conformational lability of DNA in the binding site. The share of bis-netropsin bound as a hairpin decreases in the order: TATAT > TTATT > TTAAT > TTTTT > AATTT, whereas the contribution of monodentate binding rises. The minimal strong binding site for [arrow left]Nt-Pt(NH^sub 3^ )-Nt[arrow right] and [arrow left]Nt-(CH^sub 2^ )^sub 5^ -Nt[arrow right] binding as a hairpin has been found to be DNA duplex 5"-CGTATACG-3".[PUBLICATION ABSTRACT]</description><identifier>ISSN: 0026-8933</identifier><identifier>EISSN: 1608-3245</identifier><identifier>DOI: 10.1023/A:1020639917565</identifier><language>eng</language><publisher>New York: Springer Nature B.V</publisher><subject>Binding sites</subject><ispartof>Molecular biology (New York), 2002-09, Vol.36 (5), p.726-735</ispartof><rights>MAIK "Nauka/Interperiodica" 2002</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids></links><search><creatorcontrib>Surovaya, A N</creatorcontrib><creatorcontrib>Grokhovsky, S L</creatorcontrib><creatorcontrib>Burckhardt, G</creatorcontrib><creatorcontrib>Fritzsche, H</creatorcontrib><creatorcontrib>Zimmer, Ch</creatorcontrib><creatorcontrib>Gursky, G V</creatorcontrib><title>Effect of DNA Local Conformation on the Affinity and Binding Specificity of bis-Netropsins to DNA</title><title>Molecular biology (New York)</title><description>The interaction of short nucleotide duplexes with bis-netropsins, in which netropsin fragments are linked tail-to-tail via cis-diammineplatinum group ([arrow left]Nt-Pt(NH^sub 3^ )-Nt[arrow right]) or aliphatic pentamethylene chain ([arrow left]Nt-(CH^sub 2^ )^sub 5^ -Nt[arrow right]), has been studied. Both bis-netropsins have been shown to bind to DNA oligomer 5"-CCTATATCC-3" (I) as a hairpin with parallel orientation of netropsin fragments in 1:1 stoichiometry. Monodentate binding has been detected upon binding of bis-netropsins to other duplexes of sequences 5"-CCXCC-3" [where X = TTATT (II), TTAÐnT (III), TTTTT (IV), and AATTT (V)] along with the binding of bis-netropsins as a hairpin. The formation of dimeric antiparallel motif between the halves of two bound bis-netropsin molecules has been observed in the complexes of [arrow left]Nt-(CH^sub 2^ )^sub 5^ -Nt[arrow right] with DNA oligomers IV and V. The ratio of binding constant of bis-netropsin as a hairpin (Ðs^sub 2^) to monodentate binding constant (Ðs^sub 1^) has been shown to correlate with the width and/or conformational lability of DNA in the binding site. The share of bis-netropsin bound as a hairpin decreases in the order: TATAT > TTATT > TTAAT > TTTTT > AATTT, whereas the contribution of monodentate binding rises. The minimal strong binding site for [arrow left]Nt-Pt(NH^sub 3^ )-Nt[arrow right] and [arrow left]Nt-(CH^sub 2^ )^sub 5^ -Nt[arrow right] binding as a hairpin has been found to be DNA duplex 5"-CGTATACG-3".[PUBLICATION ABSTRACT]</description><subject>Binding sites</subject><issn>0026-8933</issn><issn>1608-3245</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2002</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNpdkE1LAzEYhIMoWKtnr8GTl9V8bJKNt7WtH1Dqwd5Ldvu-mrJN1k168N-7RU_CwMAwPAxDyDVnd5wJeV8_jMa0tJYbpdUJmXDNqkKKUp2SCWNCF5WV8pxcpLRjjI8SE-IWiNBmGpHOVzVdxtZ1dBYDxmHvso-BjsqfQGtEH3z-pi5s6aMPWx8-6HsPrUffHvOR0PhUrCAPsU8-JJrjkXlJztB1Ca7-fErWT4v17KVYvj2_zupl0Qsuc6FKjYwZy9Api9JVTcO1qiwAuq2UjW0lNtAIVxpgAFaha5xBoQ0XAoyckttfbD_ErwOkvNn71ELXuQDxkDZcVIpVUphyrN78q-7iYQjjuI3R4zEVV0b-ALQWY4U</recordid><startdate>20020901</startdate><enddate>20020901</enddate><creator>Surovaya, A N</creator><creator>Grokhovsky, S L</creator><creator>Burckhardt, G</creator><creator>Fritzsche, H</creator><creator>Zimmer, Ch</creator><creator>Gursky, G V</creator><general>Springer Nature B.V</general><scope>3V.</scope><scope>7QP</scope><scope>7QR</scope><scope>7T5</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>RC3</scope></search><sort><creationdate>20020901</creationdate><title>Effect of DNA Local Conformation on the Affinity and Binding Specificity of bis-Netropsins to DNA</title><author>Surovaya, A N ; 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Both bis-netropsins have been shown to bind to DNA oligomer 5"-CCTATATCC-3" (I) as a hairpin with parallel orientation of netropsin fragments in 1:1 stoichiometry. Monodentate binding has been detected upon binding of bis-netropsins to other duplexes of sequences 5"-CCXCC-3" [where X = TTATT (II), TTAÐnT (III), TTTTT (IV), and AATTT (V)] along with the binding of bis-netropsins as a hairpin. The formation of dimeric antiparallel motif between the halves of two bound bis-netropsin molecules has been observed in the complexes of [arrow left]Nt-(CH^sub 2^ )^sub 5^ -Nt[arrow right] with DNA oligomers IV and V. The ratio of binding constant of bis-netropsin as a hairpin (Ðs^sub 2^) to monodentate binding constant (Ðs^sub 1^) has been shown to correlate with the width and/or conformational lability of DNA in the binding site. The share of bis-netropsin bound as a hairpin decreases in the order: TATAT > TTATT > TTAAT > TTTTT > AATTT, whereas the contribution of monodentate binding rises. The minimal strong binding site for [arrow left]Nt-Pt(NH^sub 3^ )-Nt[arrow right] and [arrow left]Nt-(CH^sub 2^ )^sub 5^ -Nt[arrow right] binding as a hairpin has been found to be DNA duplex 5"-CGTATACG-3".[PUBLICATION ABSTRACT]</abstract><cop>New York</cop><pub>Springer Nature B.V</pub><doi>10.1023/A:1020639917565</doi><tpages>10</tpages></addata></record> |
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title | Effect of DNA Local Conformation on the Affinity and Binding Specificity of bis-Netropsins to DNA |
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