Ff gene 5 single-stranded DNA-binding protein assembles on nucleotides constrained by a DNA hairpin.
Identifieur interne : 002262 ( PubMed/Checkpoint ); précédent : 002261; suivant : 002263Ff gene 5 single-stranded DNA-binding protein assembles on nucleotides constrained by a DNA hairpin.
Auteurs : Jin-Der Wen [États-Unis] ; Donald M. GraySource :
- Biochemistry [ 0006-2960 ] ; 2004.
Descripteurs français
- KwdFr :
- ADN simple brin (génétique), ADN simple brin (métabolisme), ADN viral (métabolisme), Assemblage viral (génétique), Banque de gènes, Conformation d'acide nucléique, Deoxyribonuclease BamHI (), Dicarbonate de diéthyle (), Dimérisation, Données de séquences moléculaires, Famille multigénique, Fixation compétitive, Hydrolyse, Inovirus (génétique), Inovirus (physiologie), Protéines de liaison à l'ADN (génétique), Protéines de liaison à l'ADN (métabolisme), Protéines virales (génétique), Protéines virales (métabolisme), Sulfates organiques (), Séquence nucléotidique.
- MESH :
- génétique : ADN simple brin, Assemblage viral, Inovirus, Protéines de liaison à l'ADN, Protéines virales.
- métabolisme : ADN simple brin, ADN viral, Protéines de liaison à l'ADN, Protéines virales.
- physiologie : Inovirus.
- Banque de gènes, Conformation d'acide nucléique, Deoxyribonuclease BamHI, Dicarbonate de diéthyle, Dimérisation, Données de séquences moléculaires, Famille multigénique, Fixation compétitive, Hydrolyse, Sulfates organiques, Séquence nucléotidique.
English descriptors
- KwdEn :
- Base Sequence, Binding, Competitive, DNA, Single-Stranded (genetics), DNA, Single-Stranded (metabolism), DNA, Viral (metabolism), DNA-Binding Proteins (genetics), DNA-Binding Proteins (metabolism), Deoxyribonuclease BamHI (chemistry), Diethyl Pyrocarbonate (chemistry), Dimerization, Gene Library, Hydrolysis, Inovirus (genetics), Inovirus (physiology), Molecular Sequence Data, Multigene Family, Nucleic Acid Conformation, Sulfuric Acid Esters (chemistry), Viral Proteins (genetics), Viral Proteins (metabolism), Virus Assembly (genetics).
- MESH :
- chemical , chemistry : Deoxyribonuclease BamHI, Diethyl Pyrocarbonate, Sulfuric Acid Esters.
- chemical , genetics : DNA, Single-Stranded, DNA-Binding Proteins, Viral Proteins.
- chemical , metabolism : DNA, Single-Stranded, DNA, Viral, DNA-Binding Proteins, Viral Proteins.
- genetics : Inovirus, Virus Assembly.
- physiology : Inovirus.
- Base Sequence, Binding, Competitive, Dimerization, Gene Library, Hydrolysis, Molecular Sequence Data, Multigene Family, Nucleic Acid Conformation.
Abstract
The gene 5 protein (g5p) encoded by filamentous Ff phages is an ssDNA-binding protein, which binds to and sequesters the nascent ssDNA phage genome in the process of phage morphogenesis. The g5p also binds with high affinity to DNA and RNA sequences that form G-quadruplex structures. However, sequences that would form G-quadruplexes are absent in single copies of the phage genome. Using SELEX (systematic evolution of ligands by exponential enrichment), we have now identified a family of DNA hairpin structures to which g5p binds with high affinity. After eight rounds of selection from a library of 58-mers, 26 of 35 sequences of this family contained two regions of complete or partial complementarity. This family of DNA hairpins is represented by the sequence: 5'-d(CGGGATCCAACGTTTTCACCAGATCTACCTCCTCGGGATCCCAAGAGGCAGAATTCGC)-3' (named U-4), where complementary regions are italicized or underlined. Diethyl pyrocarbonate modification, UV-melting profiles, and BamH I digestion experiments revealed that the italicized sequences form an intramolecular hairpin, and the underlined sequences form intermolecular base pairs so that a dimer exists at higher oligomer concentrations. Gel shift assays and end boundary experiments demonstrated that g5p assembles on the hairpin of U-4 to give a discrete, intermediate complex prior to saturation of the oligomer at high g5p concentrations. Thus, biologically relevant sequences at which g5p initiates assembly might be typified better by DNA hairpins than by G-quadruplexes. Moreover, the finding that hairpins of U-4 can dimerize emphasizes the unexpected nature of sequence-dependent structures that can be recognized by the g5p ssDNA-binding protein.
DOI: 10.1021/bi030177g
PubMed: 14992600
Affiliations:
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pubmed:14992600Le document en format XML
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The g5p also binds with high affinity to DNA and RNA sequences that form G-quadruplex structures. However, sequences that would form G-quadruplexes are absent in single copies of the phage genome. Using SELEX (systematic evolution of ligands by exponential enrichment), we have now identified a family of DNA hairpin structures to which g5p binds with high affinity. After eight rounds of selection from a library of 58-mers, 26 of 35 sequences of this family contained two regions of complete or partial complementarity. This family of DNA hairpins is represented by the sequence: 5'-d(CGGGATCCAACGTTTTCACCAGATCTACCTCCTCGGGATCCCAAGAGGCAGAATTCGC)-3' (named U-4), where complementary regions are italicized or underlined. Diethyl pyrocarbonate modification, UV-melting profiles, and BamH I digestion experiments revealed that the italicized sequences form an intramolecular hairpin, and the underlined sequences form intermolecular base pairs so that a dimer exists at higher oligomer concentrations. Gel shift assays and end boundary experiments demonstrated that g5p assembles on the hairpin of U-4 to give a discrete, intermediate complex prior to saturation of the oligomer at high g5p concentrations. Thus, biologically relevant sequences at which g5p initiates assembly might be typified better by DNA hairpins than by G-quadruplexes. Moreover, the finding that hairpins of U-4 can dimerize emphasizes the unexpected nature of sequence-dependent structures that can be recognized by the g5p ssDNA-binding protein.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">14992600</PMID><DateCompleted><Year>2004</Year><Month>06</Month><Day>29</Day></DateCompleted><DateRevised><Year>2013</Year><Month>11</Month><Day>21</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0006-2960</ISSN><JournalIssue CitedMedium="Print"><Volume>43</Volume><Issue>9</Issue><PubDate><Year>2004</Year><Month>Mar</Month><Day>09</Day></PubDate></JournalIssue><Title>Biochemistry</Title><ISOAbbreviation>Biochemistry</ISOAbbreviation></Journal><ArticleTitle>Ff gene 5 single-stranded DNA-binding protein assembles on nucleotides constrained by a DNA hairpin.</ArticleTitle><Pagination><MedlinePgn>2622-34</MedlinePgn></Pagination><Abstract><AbstractText>The gene 5 protein (g5p) encoded by filamentous Ff phages is an ssDNA-binding protein, which binds to and sequesters the nascent ssDNA phage genome in the process of phage morphogenesis. The g5p also binds with high affinity to DNA and RNA sequences that form G-quadruplex structures. However, sequences that would form G-quadruplexes are absent in single copies of the phage genome. Using SELEX (systematic evolution of ligands by exponential enrichment), we have now identified a family of DNA hairpin structures to which g5p binds with high affinity. After eight rounds of selection from a library of 58-mers, 26 of 35 sequences of this family contained two regions of complete or partial complementarity. This family of DNA hairpins is represented by the sequence: 5'-d(CGGGATCCAACGTTTTCACCAGATCTACCTCCTCGGGATCCCAAGAGGCAGAATTCGC)-3' (named U-4), where complementary regions are italicized or underlined. Diethyl pyrocarbonate modification, UV-melting profiles, and BamH I digestion experiments revealed that the italicized sequences form an intramolecular hairpin, and the underlined sequences form intermolecular base pairs so that a dimer exists at higher oligomer concentrations. Gel shift assays and end boundary experiments demonstrated that g5p assembles on the hairpin of U-4 to give a discrete, intermediate complex prior to saturation of the oligomer at high g5p concentrations. Thus, biologically relevant sequences at which g5p initiates assembly might be typified better by DNA hairpins than by G-quadruplexes. Moreover, the finding that hairpins of U-4 can dimerize emphasizes the unexpected nature of sequence-dependent structures that can be recognized by the g5p ssDNA-binding protein.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wen</LastName><ForeName>Jin-Der</ForeName><Initials>JD</Initials><AffiliationInfo><Affiliation>Department of Molecular and Cell Biology, The University of Texas at Dallas, Box 830688, Richardson, Texas 75083-0688, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gray</LastName><ForeName>Donald M</ForeName><Initials>DM</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 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MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015245" MajorTopicYN="N">Deoxyribonuclease BamHI</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004047" MajorTopicYN="N">Diethyl Pyrocarbonate</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019281" MajorTopicYN="N">Dimerization</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015723" MajorTopicYN="N">Gene Library</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006868" MajorTopicYN="N">Hydrolysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017912" MajorTopicYN="N">Inovirus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000502" 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MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2004</Year><Month>3</Month><Day>3</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2004</Year><Month>6</Month><Day>30</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2004</Year><Month>3</Month><Day>3</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">14992600</ArticleId><ArticleId IdType="doi">10.1021/bi030177g</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Gray, Donald M" sort="Gray, Donald M" uniqKey="Gray D" first="Donald M" last="Gray">Donald M. Gray</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Wen, Jin Der" sort="Wen, Jin Der" uniqKey="Wen J" first="Jin-Der" last="Wen">Jin-Der Wen</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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