Serveur d'exploration MERS

Attention, ce site est en cours de développement !
Attention, site généré par des moyens informatiques à partir de corpus bruts.
Les informations ne sont donc pas validées.

Studies of DNA bending and flexibility using gel electrophoresis

Identifieur interne : 001433 ( Istex/Curation ); précédent : 001432; suivant : 001434

Studies of DNA bending and flexibility using gel electrophoresis

Auteurs : Rodney E. Harrington [États-Unis]

Source :

RBID : ISTEX:211EDCC834B6D81056614084E93A2E7095B8CE57

English descriptors

Abstract

Gel electrophoretic methods have become established as primary tools in the study and elucidation of sequence‐directed curvature both in free DNA and in the operator DNA of several site‐specific nucleoprotein complexes. Results using them have been generally consistent with physical methods sensitive to DNA structure and conformation in those instances where direct comparisons can be made, and in a number of cases, gel methods have provided unique information not presently available from other techniques. Two basic strategies have been used: one based upon anomalous gel mobility effects; and a second based upon cyclization properties of curved DNA. Within each of these categories, various approaches have been used, some of which can lead, in favorable cases, to quantitative estimation of bending angles. In this review, the various gel‐based methods that have been used to date are critically discussed and the qualitative and quantitative information that can be obtained from them is evaluated. A number of possible structural models for DNA curvature are described and a distinction is drawn between static or fixed bending and bending due to anisotropic flexibility at specific sequence loci. The importance and roles of gel electrophoretic methods in providing experimental approaches to this question are discussed. It is suggested that both static curvature and anisotropic flexibility in operator DNA may provide much of the basis for indirect readout of sequence information by specific sitebinding regulatory proteins.

Url:
DOI: 10.1002/elps.11501401116

Links toward previous steps (curation, corpus...)


Links to Exploration step

ISTEX:211EDCC834B6D81056614084E93A2E7095B8CE57

Le document en format XML

<record>
<TEI wicri:istexFullTextTei="biblStruct">
<teiHeader>
<fileDesc>
<titleStmt>
<title xml:lang="en">Studies of DNA bending and flexibility using gel electrophoresis</title>
<author>
<name sortKey="Harrington, Rodney E" sort="Harrington, Rodney E" uniqKey="Harrington R" first="Rodney E." last="Harrington">Rodney E. Harrington</name>
<affiliation wicri:level="2">
<mods:affiliation>Department of Biochemistry, University of Nevada Reno, Reno, Nevada</mods:affiliation>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Nevada</region>
</placeName>
<wicri:cityArea>Department of Biochemistry, University of Nevada Reno, Reno</wicri:cityArea>
</affiliation>
<affiliation wicri:level="1">
<mods:affiliation>Correspondence address: Department of Biochemistry, University of Nevada Reno, Reno, NV 89557, USA===</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>Correspondence address: Department of Biochemistry, University of Nevada Reno, Reno, NV 89557</wicri:regionArea>
</affiliation>
</author>
</titleStmt>
<publicationStmt>
<idno type="wicri:source">ISTEX</idno>
<idno type="RBID">ISTEX:211EDCC834B6D81056614084E93A2E7095B8CE57</idno>
<date when="1993" year="1993">1993</date>
<idno type="doi">10.1002/elps.11501401116</idno>
<idno type="url">https://api.istex.fr/ark:/67375/WNG-F3665HX5-V/fulltext.pdf</idno>
<idno type="wicri:Area/Istex/Corpus">001433</idno>
<idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">001433</idno>
<idno type="wicri:Area/Istex/Curation">001433</idno>
</publicationStmt>
<sourceDesc>
<biblStruct>
<analytic>
<title level="a" type="main">Studies of DNA bending and flexibility using gel electrophoresis</title>
<author>
<name sortKey="Harrington, Rodney E" sort="Harrington, Rodney E" uniqKey="Harrington R" first="Rodney E." last="Harrington">Rodney E. Harrington</name>
<affiliation wicri:level="2">
<mods:affiliation>Department of Biochemistry, University of Nevada Reno, Reno, Nevada</mods:affiliation>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Nevada</region>
</placeName>
<wicri:cityArea>Department of Biochemistry, University of Nevada Reno, Reno</wicri:cityArea>
</affiliation>
<affiliation wicri:level="1">
<mods:affiliation>Correspondence address: Department of Biochemistry, University of Nevada Reno, Reno, NV 89557, USA===</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>Correspondence address: Department of Biochemistry, University of Nevada Reno, Reno, NV 89557</wicri:regionArea>
</affiliation>
</author>
</analytic>
<monogr></monogr>
<series>
<title level="j" type="main">ELECTROPHORESIS</title>
<title level="j" type="alt">ELECTROPHORESIS</title>
<idno type="ISSN">0173-0835</idno>
<idno type="eISSN">1522-2683</idno>
<imprint>
<biblScope unit="vol">14</biblScope>
<biblScope unit="issue">1</biblScope>
<biblScope unit="page" from="732">732</biblScope>
<biblScope unit="page" to="746">746</biblScope>
<biblScope unit="page-count">15</biblScope>
<publisher>Wiley Subscription Services, Inc., A Wiley Company</publisher>
<pubPlace>Hoboken</pubPlace>
<date type="published" when="1993">1993</date>
</imprint>
<idno type="ISSN">0173-0835</idno>
</series>
</biblStruct>
</sourceDesc>
<seriesStmt>
<idno type="ISSN">0173-0835</idno>
</seriesStmt>
</fileDesc>
<profileDesc>
<textClass>
<keywords scheme="Teeft" xml:lang="en">
<term>Acad</term>
<term>Alternative structure</term>
<term>Anisotropic</term>
<term>Anisotropic flexibility</term>
<term>Assay</term>
<term>Association processes</term>
<term>Bimolecular association</term>
<term>Binding domain</term>
<term>Binding site</term>
<term>Binding sites</term>
<term>Biochem</term>
<term>Biochemistry</term>
<term>Biol</term>
<term>Biopolymers</term>
<term>Chem</term>
<term>Chloroquine phosphate</term>
<term>Circle concentrations</term>
<term>Circle sizes</term>
<term>Circular species</term>
<term>Cohesive ends</term>
<term>Complementary strand</term>
<term>Complementary strands</term>
<term>Computer modeling</term>
<term>Consensus sequence</term>
<term>Correct sequence design</term>
<term>Cpgms</term>
<term>Cpgms method</term>
<term>Crothers</term>
<term>Crystallographic studies</term>
<term>Curvature</term>
<term>Curvature adenine press</term>
<term>Cyclic</term>
<term>Cyclic permutation</term>
<term>Cyclization</term>
<term>Cyclization kinetics</term>
<term>Cyclization pathways</term>
<term>Cyclization probabilities</term>
<term>Cyclization probability</term>
<term>Cyclization properties</term>
<term>Cyclization studies</term>
<term>Dinucleotide</term>
<term>Dinucleotide elements</term>
<term>Direct determination</term>
<term>Double helical</term>
<term>Double helix</term>
<term>Electron microscopy</term>
<term>Electrooptical methods</term>
<term>Electrophoresis</term>
<term>Electrophoresis methods</term>
<term>Electrophoresis technique</term>
<term>Electrophoretic methods</term>
<term>Excellent agreement</term>
<term>Experimental conditions</term>
<term>Experimental error</term>
<term>Favorable cases</term>
<term>First dimension</term>
<term>Flexible elements</term>
<term>Fragment</term>
<term>Fragment size</term>
<term>Groove</term>
<term>Hagerman</term>
<term>Helical</term>
<term>Helical axis</term>
<term>Helical periodicity</term>
<term>Helical phase</term>
<term>Helical spacing</term>
<term>Helical twist</term>
<term>Higher temperatures</term>
<term>Hydrogen bonds</term>
<term>Integral helical</term>
<term>Junction model</term>
<term>Kinetic experiments</term>
<term>Kinetics</term>
<term>Kink</term>
<term>Kinking</term>
<term>Large degree</term>
<term>Levene</term>
<term>Ligase</term>
<term>Ligation</term>
<term>Ligation experiments</term>
<term>Ligation method</term>
<term>Ligation methods</term>
<term>Ligation mixture</term>
<term>Ligation process</term>
<term>Ligation products</term>
<term>Ligation reactions</term>
<term>Linear species</term>
<term>Linear substrates</term>
<term>Locus</term>
<term>Lyubchenko</term>
<term>Major groove</term>
<term>Minor groove</term>
<term>Misalignment</term>
<term>Mismatch</term>
<term>Mobility effects</term>
<term>Mobility shift</term>
<term>Molecular biology</term>
<term>Multisubunit nucleoprotein complexes</term>
<term>Mutation</term>
<term>Natl</term>
<term>Nevada reno</term>
<term>Nucleic</term>
<term>Nucleic acids</term>
<term>Nucleoprotein</term>
<term>Nucleoprotein complexes</term>
<term>Ordinary temperatures</term>
<term>Other studies</term>
<term>Other techniques</term>
<term>Overhang</term>
<term>Permutation</term>
<term>Persistence length</term>
<term>Phage</term>
<term>Polyacrylamide</term>
<term>Polyethylene glycol</term>
<term>Precursor</term>
<term>Precursor concentration</term>
<term>Precursor fragments</term>
<term>Precursor sequence</term>
<term>Present time</term>
<term>Proc</term>
<term>Protein binding</term>
<term>Putative</term>
<term>Recognition region</term>
<term>Recognition sequence</term>
<term>Recognition site</term>
<term>Reference sequences</term>
<term>Repressor</term>
<term>Resolution cocrystal structure</term>
<term>Restriction fragments</term>
<term>Same reaction vessel</term>
<term>Same sequence</term>
<term>Same time</term>
<term>Sarma</term>
<term>Second dimension</term>
<term>Sequence element</term>
<term>Sequence elements</term>
<term>Short fragments</term>
<term>Single base mutations</term>
<term>Size product</term>
<term>Small rings</term>
<term>Static curvature</term>
<term>Stereochemical kinking</term>
<term>Steric</term>
<term>Steric factors</term>
<term>Sticky ends</term>
<term>Structural polymorphism</term>
<term>Such kinking</term>
<term>Temperature dependence</term>
<term>Torsional flexibility</term>
<term>Trifonov</term>
<term>True cyclization probability</term>
<term>Twist misalignment</term>
<term>Ulanovsky</term>
<term>Various methods</term>
<term>Wedge model</term>
<term>Zhurkin</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front>
<div type="abstract" xml:lang="en">Gel electrophoretic methods have become established as primary tools in the study and elucidation of sequence‐directed curvature both in free DNA and in the operator DNA of several site‐specific nucleoprotein complexes. Results using them have been generally consistent with physical methods sensitive to DNA structure and conformation in those instances where direct comparisons can be made, and in a number of cases, gel methods have provided unique information not presently available from other techniques. Two basic strategies have been used: one based upon anomalous gel mobility effects; and a second based upon cyclization properties of curved DNA. Within each of these categories, various approaches have been used, some of which can lead, in favorable cases, to quantitative estimation of bending angles. In this review, the various gel‐based methods that have been used to date are critically discussed and the qualitative and quantitative information that can be obtained from them is evaluated. A number of possible structural models for DNA curvature are described and a distinction is drawn between static or fixed bending and bending due to anisotropic flexibility at specific sequence loci. The importance and roles of gel electrophoretic methods in providing experimental approaches to this question are discussed. It is suggested that both static curvature and anisotropic flexibility in operator DNA may provide much of the basis for indirect readout of sequence information by specific sitebinding regulatory proteins.</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 001433 | SxmlIndent | more

Ou

HfdSelect -h $EXPLOR_AREA/Data/Istex/Curation/biblio.hfd -nk 001433 | 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:211EDCC834B6D81056614084E93A2E7095B8CE57
   |texte=   Studies of DNA bending and flexibility using gel electrophoresis
}}

Wicri

This area was generated with Dilib version V0.6.33.
Data generation: Mon Apr 20 23:26:43 2020. Site generation: Sat Mar 27 09:06:09 2021