Construction and analysis of monomobile DNA junctions.
Identifieur interne : 002907 ( PubMed/Checkpoint ); précédent : 002906; suivant : 002908Construction and analysis of monomobile DNA junctions.
Auteurs : J H Chen ; M E Churchill ; T D Tullius ; N R Kallenbach ; N C SeemanSource :
- Biochemistry [ 0006-2960 ] ; 1988.
Descripteurs français
- KwdFr :
- MESH :
- génétique : ADN.
- isolement et purification : ADN.
- Composition en bases nucléiques, Conformation d'acide nucléique, Hétéroduplexes d'acides nucléiques, Recombinaison génétique, Sites de fixation, Séquence nucléotidique, Thermodynamique, Électrophorèse sur gel de polyacrylamide.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA.
- chemical , isolation & purification : DNA.
- Base Composition, Base Sequence, Binding Sites, Electrophoresis, Polyacrylamide Gel, Nucleic Acid Conformation, Nucleic Acid Heteroduplexes, Recombination, Genetic, Thermodynamics.
Abstract
Immobile DNA junctions are complexes of oligomeric DNA strands that interact to yield branched structures in which the branch point cannot migrate. This is achieved by minimizing the sequence symmetry in the flanking arms, so that base pairs lock at the branch site. Here, we report the design, synthesis, and analysis of two semimobile junctions, structures in which a controlled extent of branch point migratory freedom is deliberately introduced. We have constructed two minimally symmetric four-arm semimobile junctions from synthetic deoxy 17-mers. These junctions, termed "monomobile", contain a single pair of base pairs (A-T or C-G) which can migrate at the site of branching, while the rest of the junction is immobile. We have demonstrated by gel electrophoresis techniques that these junctions form and that they have the predicted 1:1:1:1 stoichiometry. We have compared these junctions with the immobile junction on which they are based, by means of hydroxyl radical protection experiments. From these data, both migratory conformers can be seen to coexist in solution. The semimobile junction with the C-G base pair has the same crossover and stacking pattern observed for the immobile junction, while the junction with the A-T base pair has the opposite pattern. We conclude that crossover and stacking patterns are a direct consequence of the base pairs which flank the junction. In addition, the data indicate that the crossover pattern biases for these junctions are much greater than are the migratory biases.
DOI: 10.1021/bi00416a031
PubMed: 3191106
Affiliations:
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This is achieved by minimizing the sequence symmetry in the flanking arms, so that base pairs lock at the branch site. Here, we report the design, synthesis, and analysis of two semimobile junctions, structures in which a controlled extent of branch point migratory freedom is deliberately introduced. We have constructed two minimally symmetric four-arm semimobile junctions from synthetic deoxy 17-mers. These junctions, termed "monomobile", contain a single pair of base pairs (A-T or C-G) which can migrate at the site of branching, while the rest of the junction is immobile. We have demonstrated by gel electrophoresis techniques that these junctions form and that they have the predicted 1:1:1:1 stoichiometry. We have compared these junctions with the immobile junction on which they are based, by means of hydroxyl radical protection experiments. From these data, both migratory conformers can be seen to coexist in solution. The semimobile junction with the C-G base pair has the same crossover and stacking pattern observed for the immobile junction, while the junction with the A-T base pair has the opposite pattern. We conclude that crossover and stacking patterns are a direct consequence of the base pairs which flank the junction. In addition, the data indicate that the crossover pattern biases for these junctions are much greater than are the migratory biases.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">3191106</PMID><DateCompleted><Year>1989</Year><Month>01</Month><Day>09</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>16</Issue><PubDate><Year>1988</Year><Month>Aug</Month><Day>09</Day></PubDate></JournalIssue><Title>Biochemistry</Title><ISOAbbreviation>Biochemistry</ISOAbbreviation></Journal><ArticleTitle>Construction and analysis of monomobile DNA junctions.</ArticleTitle><Pagination><MedlinePgn>6032-8</MedlinePgn></Pagination><Abstract><AbstractText>Immobile DNA junctions are complexes of oligomeric DNA strands that interact to yield branched structures in which the branch point cannot migrate. This is achieved by minimizing the sequence symmetry in the flanking arms, so that base pairs lock at the branch site. Here, we report the design, synthesis, and analysis of two semimobile junctions, structures in which a controlled extent of branch point migratory freedom is deliberately introduced. We have constructed two minimally symmetric four-arm semimobile junctions from synthetic deoxy 17-mers. These junctions, termed "monomobile", contain a single pair of base pairs (A-T or C-G) which can migrate at the site of branching, while the rest of the junction is immobile. We have demonstrated by gel electrophoresis techniques that these junctions form and that they have the predicted 1:1:1:1 stoichiometry. We have compared these junctions with the immobile junction on which they are based, by means of hydroxyl radical protection experiments. From these data, both migratory conformers can be seen to coexist in solution. The semimobile junction with the C-G base pair has the same crossover and stacking pattern observed for the immobile junction, while the junction with the A-T base pair has the opposite pattern. We conclude that crossover and stacking patterns are a direct consequence of the base pairs which flank the junction. In addition, the data indicate that the crossover pattern biases for these junctions are much greater than are the migratory biases.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>J H</ForeName><Initials>JH</Initials><AffiliationInfo><Affiliation>Department of Biology, State University of New York, Albany 12222.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Churchill</LastName><ForeName>M E</ForeName><Initials>ME</Initials></Author><Author ValidYN="Y"><LastName>Tullius</LastName><ForeName>T D</ForeName><Initials>TD</Initials></Author><Author ValidYN="Y"><LastName>Kallenbach</LastName><ForeName>N R</ForeName><Initials>NR</Initials></Author><Author ValidYN="Y"><LastName>Seeman</LastName><ForeName>N C</ForeName><Initials>NC</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="N"><Grant><GrantID>CA-37444</GrantID><Acronym>CA</Acronym><Agency>NCI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>ES-00117</GrantID><Acronym>ES</Acronym><Agency>NIEHS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>GM-29554</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013487">Research Support, U.S. Gov't, P.H.S.</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="D009692">Nucleic Acid Heteroduplexes</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001482" MajorTopicYN="N">Base Composition</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="Y">DNA</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004591" MajorTopicYN="N">Electrophoresis, Polyacrylamide Gel</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009690" MajorTopicYN="Y">Nucleic Acid Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009692" MajorTopicYN="Y">Nucleic Acid Heteroduplexes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011995" MajorTopicYN="N">Recombination, Genetic</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>9</Day></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>1988</Year><Month>8</Month><Day>9</Day><Hour>0</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>1988</Year><Month>8</Month><Day>9</Day><Hour>0</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">3191106</ArticleId><ArticleId IdType="doi">10.1021/bi00416a031</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list></list><tree><noCountry><name sortKey="Chen, J H" sort="Chen, J H" uniqKey="Chen J" first="J H" last="Chen">J H Chen</name><name sortKey="Churchill, M E" sort="Churchill, M E" uniqKey="Churchill M" first="M E" last="Churchill">M E Churchill</name><name sortKey="Kallenbach, N R" sort="Kallenbach, N R" uniqKey="Kallenbach N" first="N R" last="Kallenbach">N R Kallenbach</name><name sortKey="Seeman, N C" sort="Seeman, N C" uniqKey="Seeman N" first="N C" last="Seeman">N C Seeman</name><name sortKey="Tullius, T D" sort="Tullius, T D" uniqKey="Tullius T" first="T D" last="Tullius">T D Tullius</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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