Torsional constant of 27-mer DNA oligomers of different sequences
We have studied the torsional elastic constant ( α) of short DNA (27mer) oligomers of various sequence by fluorescence polarization anysotropy (FPA) measurements. The lowest α values were found in samples with sequence rich in AA dinucleotides or containing the alternating d(A–T)·d(A–T) motif. The t...
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| Veröffentlicht in: | Biophysical chemistry 2001-12, Vol.94 (1), p.175-184 |
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| creator | Pedone, Francesco Mazzei, Filomena Matzeu, Mirella Barone, Flavia |
| description | We have studied the torsional elastic constant (
α) of short DNA (27mer) oligomers of various sequence by fluorescence polarization anysotropy (FPA) measurements. The lowest
α values were found in samples with sequence rich in AA dinucleotides or containing the alternating d(A–T)·d(A–T) motif. The torsional rigidity of our DNA samples was compared to that calculated according to the current values of twist angle fluctuations derived for ten dinucleotide steps by recent analyses of DNA crystal structure database. The values of torsional rigidity derived from crystals are higher than our experimental ones, obtained by FPA analysis, suggesting that packing force in crystals may notably hinder the dinucleotide twist angle fluctuations that occur in solution. This behaviour is more evident for samples containing AA, TA and AT steps. In all the samples there is about a twofold change of the
α value in the 10–40
°C range. An activation enthalpy (Δ
H
#) of about 17.4 kJ mol
−1, on average, was obtained for the temperature dependence of eight of the ten samples studied. A correlation with the stacking energy is discussed. |
| doi_str_mv | 10.1016/S0301-4622(01)00232-0 |
| format | Article |
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α) of short DNA (27mer) oligomers of various sequence by fluorescence polarization anysotropy (FPA) measurements. The lowest
α values were found in samples with sequence rich in AA dinucleotides or containing the alternating d(A–T)·d(A–T) motif. The torsional rigidity of our DNA samples was compared to that calculated according to the current values of twist angle fluctuations derived for ten dinucleotide steps by recent analyses of DNA crystal structure database. The values of torsional rigidity derived from crystals are higher than our experimental ones, obtained by FPA analysis, suggesting that packing force in crystals may notably hinder the dinucleotide twist angle fluctuations that occur in solution. This behaviour is more evident for samples containing AA, TA and AT steps. In all the samples there is about a twofold change of the
α value in the 10–40
°C range. An activation enthalpy (Δ
H
#) of about 17.4 kJ mol
−1, on average, was obtained for the temperature dependence of eight of the ten samples studied. A correlation with the stacking energy is discussed.</description><identifier>ISSN: 0301-4622</identifier><identifier>EISSN: 1873-4200</identifier><identifier>DOI: 10.1016/S0301-4622(01)00232-0</identifier><identifier>PMID: 11744198</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Base Sequence ; Base stacking ; Biopolymers - chemistry ; Circular Dichroism ; Dinucleotide step rigidity ; DNA - chemistry ; Fluorescence polarization anisotropy ; Fluorescence Polarization Immunoassay ; Molecular Sequence Data ; Nucleic Acid Conformation</subject><ispartof>Biophysical chemistry, 2001-12, Vol.94 (1), p.175-184</ispartof><rights>2001 Elsevier Science B.V.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c361t-acde0b84ec24d12f20c11c2efea44fc0f64f2946256ae472c864aff21a519a213</citedby><cites>FETCH-LOGICAL-c361t-acde0b84ec24d12f20c11c2efea44fc0f64f2946256ae472c864aff21a519a213</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/S0301-4622(01)00232-0$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3548,27922,27923,45993</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/11744198$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Pedone, Francesco</creatorcontrib><creatorcontrib>Mazzei, Filomena</creatorcontrib><creatorcontrib>Matzeu, Mirella</creatorcontrib><creatorcontrib>Barone, Flavia</creatorcontrib><title>Torsional constant of 27-mer DNA oligomers of different sequences</title><title>Biophysical chemistry</title><addtitle>Biophys Chem</addtitle><description>We have studied the torsional elastic constant (
α) of short DNA (27mer) oligomers of various sequence by fluorescence polarization anysotropy (FPA) measurements. The lowest
α values were found in samples with sequence rich in AA dinucleotides or containing the alternating d(A–T)·d(A–T) motif. The torsional rigidity of our DNA samples was compared to that calculated according to the current values of twist angle fluctuations derived for ten dinucleotide steps by recent analyses of DNA crystal structure database. The values of torsional rigidity derived from crystals are higher than our experimental ones, obtained by FPA analysis, suggesting that packing force in crystals may notably hinder the dinucleotide twist angle fluctuations that occur in solution. This behaviour is more evident for samples containing AA, TA and AT steps. In all the samples there is about a twofold change of the
α value in the 10–40
°C range. An activation enthalpy (Δ
H
#) of about 17.4 kJ mol
−1, on average, was obtained for the temperature dependence of eight of the ten samples studied. A correlation with the stacking energy is discussed.</description><subject>Base Sequence</subject><subject>Base stacking</subject><subject>Biopolymers - chemistry</subject><subject>Circular Dichroism</subject><subject>Dinucleotide step rigidity</subject><subject>DNA - chemistry</subject><subject>Fluorescence polarization anisotropy</subject><subject>Fluorescence Polarization Immunoassay</subject><subject>Molecular Sequence Data</subject><subject>Nucleic Acid Conformation</subject><issn>0301-4622</issn><issn>1873-4200</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2001</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkE1LAzEQhoMotlZ_grIn0cPqTDb70ZOU-glFD9ZzSLMTiWw3NdkK_nuzbdGjuQwJz8ybeRg7RbhCwOL6FTLAVBScXwBeAvCMp7DHhliVWSo4wD4b_iIDdhTCB8RTARyyAWIpBI6rIZvMnQ_WtapJtGtDp9oucSbhZbokn9w-TxLX2HcXL6F_r60x5ClCgT7X1GoKx-zAqCbQya6O2Nv93Xz6mM5eHp6mk1mqswK7VOmaYFEJ0lzUyA0Hjag5GVJCGA2mEIaP42fzQpEoua4KoYzhqHIcK47ZiJ1v5668i9Ghk0sbNDWNasmtgyx5lpdVlUcw34LauxA8Gbnydqn8t0SQvTu5cSd7MTLWjTsJse9sF7BeLKn-69rJisDNFqC45pclL4O2vYPaetKdrJ39J-IHxl59Jg</recordid><startdate>20011211</startdate><enddate>20011211</enddate><creator>Pedone, Francesco</creator><creator>Mazzei, Filomena</creator><creator>Matzeu, Mirella</creator><creator>Barone, Flavia</creator><general>Elsevier B.V</general><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>7X8</scope></search><sort><creationdate>20011211</creationdate><title>Torsional constant of 27-mer DNA oligomers of different sequences</title><author>Pedone, Francesco ; Mazzei, Filomena ; Matzeu, Mirella ; Barone, Flavia</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c361t-acde0b84ec24d12f20c11c2efea44fc0f64f2946256ae472c864aff21a519a213</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2001</creationdate><topic>Base Sequence</topic><topic>Base stacking</topic><topic>Biopolymers - chemistry</topic><topic>Circular Dichroism</topic><topic>Dinucleotide step rigidity</topic><topic>DNA - chemistry</topic><topic>Fluorescence polarization anisotropy</topic><topic>Fluorescence Polarization Immunoassay</topic><topic>Molecular Sequence Data</topic><topic>Nucleic Acid Conformation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Pedone, Francesco</creatorcontrib><creatorcontrib>Mazzei, Filomena</creatorcontrib><creatorcontrib>Matzeu, Mirella</creatorcontrib><creatorcontrib>Barone, Flavia</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Biophysical chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Pedone, Francesco</au><au>Mazzei, Filomena</au><au>Matzeu, Mirella</au><au>Barone, Flavia</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Torsional constant of 27-mer DNA oligomers of different sequences</atitle><jtitle>Biophysical chemistry</jtitle><addtitle>Biophys Chem</addtitle><date>2001-12-11</date><risdate>2001</risdate><volume>94</volume><issue>1</issue><spage>175</spage><epage>184</epage><pages>175-184</pages><issn>0301-4622</issn><eissn>1873-4200</eissn><abstract>We have studied the torsional elastic constant (
α) of short DNA (27mer) oligomers of various sequence by fluorescence polarization anysotropy (FPA) measurements. The lowest
α values were found in samples with sequence rich in AA dinucleotides or containing the alternating d(A–T)·d(A–T) motif. The torsional rigidity of our DNA samples was compared to that calculated according to the current values of twist angle fluctuations derived for ten dinucleotide steps by recent analyses of DNA crystal structure database. The values of torsional rigidity derived from crystals are higher than our experimental ones, obtained by FPA analysis, suggesting that packing force in crystals may notably hinder the dinucleotide twist angle fluctuations that occur in solution. This behaviour is more evident for samples containing AA, TA and AT steps. In all the samples there is about a twofold change of the
α value in the 10–40
°C range. An activation enthalpy (Δ
H
#) of about 17.4 kJ mol
−1, on average, was obtained for the temperature dependence of eight of the ten samples studied. A correlation with the stacking energy is discussed.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>11744198</pmid><doi>10.1016/S0301-4622(01)00232-0</doi><tpages>10</tpages></addata></record> |
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| ispartof | Biophysical chemistry, 2001-12, Vol.94 (1), p.175-184 |
| issn | 0301-4622 1873-4200 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_72357885 |
| source | MEDLINE; ScienceDirect Journals (5 years ago - present) |
| subjects | Base Sequence Base stacking Biopolymers - chemistry Circular Dichroism Dinucleotide step rigidity DNA - chemistry Fluorescence polarization anisotropy Fluorescence Polarization Immunoassay Molecular Sequence Data Nucleic Acid Conformation |
| title | Torsional constant of 27-mer DNA oligomers of different sequences |
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