Base pair opening in three DNA-unwinding elements.
Identifieur interne : 002342 ( PubMed/Corpus ); précédent : 002341; suivant : 002343Base pair opening in three DNA-unwinding elements.
Auteurs : Daniel Coman ; Irina M. RussuSource :
- The Journal of biological chemistry [ 0021-9258 ] ; 2005.
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : Ammonia.
- chemical , chemistry : DNA, Bacterial.
- genetics : Base Pairing, Escherichia coli.
- Base Sequence, Conserved Sequence, DNA Replication, Kinetics, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Nucleic Acid Conformation, Protons.
Abstract
DNA-unwinding elements are specific base sequences that are located in the origin of DNA replication where they provide the start point for strand separation and unwinding of the DNA double helix. In the present work we have obtained the first characterization of the opening of individual base pairs in DNA-unwinding elements. The three DNA molecules investigated reproduce the 13-mer DNA-unwinding elements present in the Escherichia coli chromosome. The base sequences of the three 13-mers are conserved in the origins of replication of enteric bacterial chromosomes. The exchange of imino protons with solvent protons was measured for each DNA as a function of the concentration of exchange catalyst using nuclear magnetic resonance spectroscopy. The exchange rates provided the rates and the equilibrium constants for opening of individual base pairs in each DNA at 20 degrees C. The results reveal that the kinetics and energetics of the opening reactions for AT/TA base pairs are different in the three DNA-unwinding elements due to long range effects of the base sequence. These differences encompass the AT/TA base pairs that are conserved in various bacterial genomes. Furthermore, a qualitative correlation is observed between the kinetics and energetics of opening of AT/TA base pairs and the location of the corresponding DNA-unwinding element in the origin of DNA replication.
DOI: 10.1074/jbc.M502773200
PubMed: 15784615
Links to Exploration step
pubmed:15784615Le document en format XML
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<author><name sortKey="Coman, Daniel" sort="Coman, Daniel" uniqKey="Coman D" first="Daniel" last="Coman">Daniel Coman</name>
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<author><name sortKey="Russu, Irina M" sort="Russu, Irina M" uniqKey="Russu I" first="Irina M" last="Russu">Irina M. Russu</name>
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<term>Base Pairing (genetics)</term>
<term>Base Sequence</term>
<term>Conserved Sequence</term>
<term>DNA Replication</term>
<term>DNA, Bacterial (chemistry)</term>
<term>Escherichia coli (genetics)</term>
<term>Kinetics</term>
<term>Magnetic Resonance Spectroscopy</term>
<term>Molecular Sequence Data</term>
<term>Nucleic Acid Conformation</term>
<term>Protons</term>
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<keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Ammonia</term>
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<term>Conserved Sequence</term>
<term>DNA Replication</term>
<term>Kinetics</term>
<term>Magnetic Resonance Spectroscopy</term>
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<front><div type="abstract" xml:lang="en">DNA-unwinding elements are specific base sequences that are located in the origin of DNA replication where they provide the start point for strand separation and unwinding of the DNA double helix. In the present work we have obtained the first characterization of the opening of individual base pairs in DNA-unwinding elements. The three DNA molecules investigated reproduce the 13-mer DNA-unwinding elements present in the Escherichia coli chromosome. The base sequences of the three 13-mers are conserved in the origins of replication of enteric bacterial chromosomes. The exchange of imino protons with solvent protons was measured for each DNA as a function of the concentration of exchange catalyst using nuclear magnetic resonance spectroscopy. The exchange rates provided the rates and the equilibrium constants for opening of individual base pairs in each DNA at 20 degrees C. The results reveal that the kinetics and energetics of the opening reactions for AT/TA base pairs are different in the three DNA-unwinding elements due to long range effects of the base sequence. These differences encompass the AT/TA base pairs that are conserved in various bacterial genomes. Furthermore, a qualitative correlation is observed between the kinetics and energetics of opening of AT/TA base pairs and the location of the corresponding DNA-unwinding element in the origin of DNA replication.</div>
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<Title>The Journal of biological chemistry</Title>
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<ArticleTitle>Base pair opening in three DNA-unwinding elements.</ArticleTitle>
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<Abstract><AbstractText>DNA-unwinding elements are specific base sequences that are located in the origin of DNA replication where they provide the start point for strand separation and unwinding of the DNA double helix. In the present work we have obtained the first characterization of the opening of individual base pairs in DNA-unwinding elements. The three DNA molecules investigated reproduce the 13-mer DNA-unwinding elements present in the Escherichia coli chromosome. The base sequences of the three 13-mers are conserved in the origins of replication of enteric bacterial chromosomes. The exchange of imino protons with solvent protons was measured for each DNA as a function of the concentration of exchange catalyst using nuclear magnetic resonance spectroscopy. The exchange rates provided the rates and the equilibrium constants for opening of individual base pairs in each DNA at 20 degrees C. The results reveal that the kinetics and energetics of the opening reactions for AT/TA base pairs are different in the three DNA-unwinding elements due to long range effects of the base sequence. These differences encompass the AT/TA base pairs that are conserved in various bacterial genomes. Furthermore, a qualitative correlation is observed between the kinetics and energetics of opening of AT/TA base pairs and the location of the corresponding DNA-unwinding element in the origin of DNA replication.</AbstractText>
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