Ff Gene 5 Single-Stranded DNA-Binding Protein Assembles on Nucleotides Constrained by a DNA Hairpin†
Identifieur interne : 001A43 ( Istex/Curation ); précédent : 001A42; suivant : 001A44Ff Gene 5 Single-Stranded DNA-Binding Protein Assembles on Nucleotides Constrained by a DNA Hairpin†
Auteurs : Jin-Der Wen [États-Unis] ; Donald M. Gray [États-Unis]Source :
- Biochemistry [ 0006-2960 ] ; 2004.
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.
Url:
DOI: 10.1021/bi030177g
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: Pour aller vers cette notice dans l'étape Curation :001A43
Links to Exploration step
ISTEX:CA373B053D7ED48EBB94507E1A45BD9028356550Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title>Ff Gene 5 Single-Stranded DNA-Binding Protein Assembles on Nucleotides Constrained by a DNA Hairpin†</title><author><name sortKey="Wen, Jin Der" sort="Wen, Jin Der" uniqKey="Wen J" first="Jin-Der" last="Wen">Jin-Der Wen</name><affiliation wicri:level="2"><mods:affiliation>Department of Molecular and Cell Biology, The University of Texas at Dallas, Box 830688, Richardson, Texas 75083-0688</mods:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>Department of Molecular and Cell Biology, The University of Texas at Dallas, Box 830688, Richardson</wicri:cityArea></affiliation></author><author><name sortKey="Gray, Donald M" sort="Gray, Donald M" uniqKey="Gray D" first="Donald M." last="Gray">Donald M. Gray</name><affiliation wicri:level="2"><mods:affiliation>Department of Molecular and Cell Biology, The University of Texas at Dallas, Box 830688, Richardson, Texas 75083-0688</mods:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>Department of Molecular and Cell Biology, The University of Texas at Dallas, Box 830688, Richardson</wicri:cityArea></affiliation><affiliation wicri:level="1"><mods:affiliation> Corresponding author. Phone: (972) 883-2513. Fax: (972) 883-2409. E-mail: dongray@utdallas.edu.</mods:affiliation><country wicri:rule="url">États-Unis</country></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:CA373B053D7ED48EBB94507E1A45BD9028356550</idno><date when="2004" year="2004">2004</date><idno type="doi">10.1021/bi030177g</idno><idno type="url">https://api.istex.fr/ark:/67375/TPS-X652NCPH-C/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">001A43</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">001A43</idno><idno type="wicri:Area/Istex/Curation">001A43</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main">Ff Gene 5 Single-Stranded DNA-Binding Protein Assembles on Nucleotides
Constrained by a DNA Hairpin<ref type="bib" target="#bi030177gAF2">†</ref></title><author><name sortKey="Wen, Jin Der" sort="Wen, Jin Der" uniqKey="Wen J" first="Jin-Der" last="Wen">Jin-Der Wen</name><affiliation wicri:level="2"><mods:affiliation>Department of Molecular and Cell Biology, The University of Texas at Dallas, Box 830688, Richardson, Texas 75083-0688</mods:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>Department of Molecular and Cell Biology, The University of Texas at Dallas, Box 830688, Richardson</wicri:cityArea></affiliation></author><author><name sortKey="Gray, Donald M" sort="Gray, Donald M" uniqKey="Gray D" first="Donald M." last="Gray">Donald M. Gray</name><affiliation wicri:level="2"><mods:affiliation>Department of Molecular and Cell Biology, The University of Texas at Dallas, Box 830688, Richardson, Texas 75083-0688</mods:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>Department of Molecular and Cell Biology, The University of Texas at Dallas, Box 830688, Richardson</wicri:cityArea></affiliation><affiliation wicri:level="1"><mods:affiliation> Corresponding author. Phone: (972) 883-2513. Fax: (972) 883-2409. E-mail: dongray@utdallas.edu.</mods:affiliation><country wicri:rule="url">États-Unis</country></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Biochemistry</title><title level="j" type="abbrev">Biochemistry</title><idno type="ISSN">0006-2960</idno><idno type="eISSN">1520-4995</idno><imprint><publisher>American Chemical Society</publisher><date type="e-published">2004</date><date type="published">2004</date><biblScope unit="vol">43</biblScope><biblScope unit="issue">9</biblScope><biblScope unit="page" from="2622">2622</biblScope><biblScope unit="page" to="2634">2634</biblScope></imprint><idno type="ISSN">0006-2960</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0006-2960</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="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.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Istex/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001A43 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Istex/Curation/biblio.hfd -nk 001A43 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Istex
|étape= Curation
|type= RBID
|clé= ISTEX:CA373B053D7ED48EBB94507E1A45BD9028356550
|texte= Ff Gene 5 Single-Stranded DNA-Binding Protein Assembles on Nucleotides Constrained by a DNA Hairpin†
}}
| This area was generated with Dilib version V0.6.33. |  |