The B-Z conformational transition in folded oligodeoxynucleotides: loop size and stability of Z-hairpins.
Identifieur interne : 002A54 ( PubMed/Curation ); précédent : 002A53; suivant : 002A55The B-Z conformational transition in folded oligodeoxynucleotides: loop size and stability of Z-hairpins.
Auteurs : L E Xodo [Italie] ; G. Manzini ; F. Quadrifoglio ; G A Van Der Marel ; J H Van BoomSource :
- Biochemistry [ 0006-2960 ] ; 1988.
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Abstract
The capacity to assume a left-handed conformation and the thermodynamics of loop formation in concentrated aqueous NaClO4 have been investigated for the following palindromic sequences: d-(CGCGCGAAAAACGCGCG) (A5), d(CGCGCGTTTTTCGCGCG) (T5), d(CGCGCGTACGCGCG) (TA), and d(CGCGCGATCGCGCG) (AT). The results show that (a) each oligomer assumes a Z conformation upon exposure to increasing NaClO4 concentrations; the salt concentration at the transition midpoint is 1.8 M for both A5 and T5 and 3 and 3.5 M for TA and AT, respectively; (b) in high salt the four oligomers exist, over a wide range of nucleotide concentrations (up to 10(-3) M) and of temperature (greater than 0 degrees C), as unimolecular hairpin structures; (c) hairpins TA and AT exhibit, in buffer A, a lower thermal stability with respect to A5 and T5 (delta T about 16 degrees C), contrary to what is observed at low ionic strength; (d) on hairpin formation, the enthalpic term is about -52 kcal/mol for the two 17-mers and -38 kcal/mol for the two 14-mers, while the change in entropy is found to be around -150 eu for A5 and T5 and -115 eu for TA and AT. This thermodynamic picture suggests that a two-residue loop for TA and AT, found at low ionic strength [see preceding paper (Xodo, L.E., Manzini, G., Quadrifoglio, F., van der Marel, G.A., & van Boom, J.H. (1988) Biochemistry (preceding paper in this issue)], is substituted by a longer one including two additional residues from a missing dC.dG base pairing at the top of the stem.
DOI: 10.1021/bi00417a019
PubMed: 3219338
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Quadrifoglio</name></author><author><name sortKey="Van Der Marel, G A" sort="Van Der Marel, G A" uniqKey="Van Der Marel G" first="G A" last="Van Der Marel">G A Van Der Marel</name></author><author><name sortKey="Van Boom, J H" sort="Van Boom, J H" uniqKey="Van Boom J" first="J H" last="Van Boom">J H Van Boom</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="1988">1988</date><idno type="RBID">pubmed:3219338</idno><idno type="pmid">3219338</idno><idno type="doi">10.1021/bi00417a019</idno><idno type="wicri:Area/PubMed/Corpus">002A54</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002A54</idno><idno type="wicri:Area/PubMed/Curation">002A54</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002A54</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">The B-Z conformational transition in folded oligodeoxynucleotides: loop size and stability of Z-hairpins.</title><author><name sortKey="Xodo, L E" sort="Xodo, L E" uniqKey="Xodo L" first="L E" last="Xodo">L E Xodo</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Biophysics and Macromolecular Chemistry, University of Trieste, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Biochemistry, Biophysics and Macromolecular Chemistry, University of Trieste</wicri:regionArea></affiliation></author><author><name sortKey="Manzini, G" sort="Manzini, G" uniqKey="Manzini G" first="G" last="Manzini">G. Manzini</name></author><author><name sortKey="Quadrifoglio, F" sort="Quadrifoglio, F" uniqKey="Quadrifoglio F" first="F" last="Quadrifoglio">F. Quadrifoglio</name></author><author><name sortKey="Van Der Marel, G A" sort="Van Der Marel, G A" uniqKey="Van Der Marel G" first="G A" last="Van Der Marel">G A Van Der Marel</name></author><author><name sortKey="Van Boom, J H" sort="Van Boom, J H" uniqKey="Van Boom J" first="J H" last="Van Boom">J H Van Boom</name></author></analytic><series><title level="j">Biochemistry</title><idno type="ISSN">0006-2960</idno><imprint><date when="1988" type="published">1988</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Circular Dichroism</term><term>DNA</term><term>Drug Stability</term><term>Kinetics</term><term>Nucleic Acid Conformation</term><term>Oligodeoxyribonucleotides</term><term>Thermodynamics</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN</term><term>Cinétique</term><term>Conformation d'acide nucléique</term><term>Dichroïsme circulaire</term><term>Oligodésoxyribonucléotides</term><term>Stabilité de médicament</term><term>Séquence nucléotidique</term><term>Thermodynamique</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA</term><term>Oligodeoxyribonucleotides</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Circular Dichroism</term><term>Drug Stability</term><term>Kinetics</term><term>Nucleic Acid Conformation</term><term>Thermodynamics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Cinétique</term><term>Conformation d'acide nucléique</term><term>Dichroïsme circulaire</term><term>Oligodésoxyribonucléotides</term><term>Stabilité de médicament</term><term>Séquence nucléotidique</term><term>Thermodynamique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The capacity to assume a left-handed conformation and the thermodynamics of loop formation in concentrated aqueous NaClO4 have been investigated for the following palindromic sequences: d-(CGCGCGAAAAACGCGCG) (A5), d(CGCGCGTTTTTCGCGCG) (T5), d(CGCGCGTACGCGCG) (TA), and d(CGCGCGATCGCGCG) (AT). The results show that (a) each oligomer assumes a Z conformation upon exposure to increasing NaClO4 concentrations; the salt concentration at the transition midpoint is 1.8 M for both A5 and T5 and 3 and 3.5 M for TA and AT, respectively; (b) in high salt the four oligomers exist, over a wide range of nucleotide concentrations (up to 10(-3) M) and of temperature (greater than 0 degrees C), as unimolecular hairpin structures; (c) hairpins TA and AT exhibit, in buffer A, a lower thermal stability with respect to A5 and T5 (delta T about 16 degrees C), contrary to what is observed at low ionic strength; (d) on hairpin formation, the enthalpic term is about -52 kcal/mol for the two 17-mers and -38 kcal/mol for the two 14-mers, while the change in entropy is found to be around -150 eu for A5 and T5 and -115 eu for TA and AT. This thermodynamic picture suggests that a two-residue loop for TA and AT, found at low ionic strength [see preceding paper (Xodo, L.E., Manzini, G., Quadrifoglio, F., van der Marel, G.A., & van Boom, J.H. (1988) Biochemistry (preceding paper in this issue)], is substituted by a longer one including two additional residues from a missing dC.dG base pairing at the top of the stem.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">3219338</PMID><DateCompleted><Year>1989</Year><Month>03</Month><Day>23</Day></DateCompleted><DateRevised><Year>2019</Year><Month>06</Month><Day>13</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0006-2960</ISSN><JournalIssue CitedMedium="Print"><Volume>27</Volume><Issue>17</Issue><PubDate><Year>1988</Year><Month>Aug</Month><Day>23</Day></PubDate></JournalIssue><Title>Biochemistry</Title><ISOAbbreviation>Biochemistry</ISOAbbreviation></Journal><ArticleTitle>The B-Z conformational transition in folded oligodeoxynucleotides: loop size and stability of Z-hairpins.</ArticleTitle><Pagination><MedlinePgn>6327-31</MedlinePgn></Pagination><Abstract><AbstractText>The capacity to assume a left-handed conformation and the thermodynamics of loop formation in concentrated aqueous NaClO4 have been investigated for the following palindromic sequences: d-(CGCGCGAAAAACGCGCG) (A5), d(CGCGCGTTTTTCGCGCG) (T5), d(CGCGCGTACGCGCG) (TA), and d(CGCGCGATCGCGCG) (AT). The results show that (a) each oligomer assumes a Z conformation upon exposure to increasing NaClO4 concentrations; the salt concentration at the transition midpoint is 1.8 M for both A5 and T5 and 3 and 3.5 M for TA and AT, respectively; (b) in high salt the four oligomers exist, over a wide range of nucleotide concentrations (up to 10(-3) M) and of temperature (greater than 0 degrees C), as unimolecular hairpin structures; (c) hairpins TA and AT exhibit, in buffer A, a lower thermal stability with respect to A5 and T5 (delta T about 16 degrees C), contrary to what is observed at low ionic strength; (d) on hairpin formation, the enthalpic term is about -52 kcal/mol for the two 17-mers and -38 kcal/mol for the two 14-mers, while the change in entropy is found to be around -150 eu for A5 and T5 and -115 eu for TA and AT. This thermodynamic picture suggests that a two-residue loop for TA and AT, found at low ionic strength [see preceding paper (Xodo, L.E., Manzini, G., Quadrifoglio, F., van der Marel, G.A., & van Boom, J.H. (1988) Biochemistry (preceding paper in this issue)], is substituted by a longer one including two additional residues from a missing dC.dG base pairing at the top of the stem.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xodo</LastName><ForeName>L E</ForeName><Initials>LE</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Biophysics and Macromolecular Chemistry, University of Trieste, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Manzini</LastName><ForeName>G</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Quadrifoglio</LastName><ForeName>F</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>van der Marel</LastName><ForeName>G A</ForeName><Initials>GA</Initials></Author><Author ValidYN="Y"><LastName>van Boom</LastName><ForeName>J H</ForeName><Initials>JH</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Biochemistry</MedlineTA><NlmUniqueID>0370623</NlmUniqueID><ISSNLinking>0006-2960</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009838">Oligodeoxyribonucleotides</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002942" MajorTopicYN="N">Circular Dichroism</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="Y">DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004355" MajorTopicYN="N">Drug Stability</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007700" MajorTopicYN="N">Kinetics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009690" MajorTopicYN="Y">Nucleic Acid Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009838" MajorTopicYN="Y">Oligodeoxyribonucleotides</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013816" MajorTopicYN="N">Thermodynamics</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>1988</Year><Month>8</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>1988</Year><Month>8</Month><Day>23</Day><Hour>0</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>1988</Year><Month>8</Month><Day>23</Day><Hour>0</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">3219338</ArticleId><ArticleId IdType="doi">10.1021/bi00417a019</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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