The importance of coulombic end effects: experimental characterization of the effects of oligonucleotide flanking charges on the strength and salt dependence of oligocation (L8+) binding to single-stranded DNA oligomers.
Identifieur interne : 003778 ( Main/Exploration ); précédent : 003777; suivant : 003779The importance of coulombic end effects: experimental characterization of the effects of oligonucleotide flanking charges on the strength and salt dependence of oligocation (L8+) binding to single-stranded DNA oligomers.
Auteurs : W. Zhang [États-Unis] ; H. Ni ; M W Capp ; C F Anderson ; T M Lohman ; M T RecordSource :
- Biophysical journal [ 0006-3495 ] ; 1999.
Descripteurs français
- KwdFr :
- MESH :
- métabolisme : Anions, Cations, Oligopeptides, Poly T.
- pharmacologie : Sels.
- ADN simple brin, Fluorescence, Oligopeptides, Sites de fixation, Thermodynamique, Électricité statique.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, Single-Stranded, Oligopeptides.
- chemical , metabolism : Anions, Cations, Oligopeptides, Poly T.
- chemical , pharmacology : Salts.
- Binding Sites, Fluorescence, Static Electricity, Thermodynamics.
Abstract
Binding constants Kobs, expressed per site and evaluated in the limit of zero binding density, are quantified as functions of salt (sodium acetate) concentration for the interactions of the oligopeptide ligand KWK6NH2 (designated L8+, with ZL = 8 charges) with three single-stranded DNA oligomers (ss dT-mers, with |ZD| = 15, 39, and 69 charges). These results provide the first systematic experimental information about the effect of changing |ZD| on the strength and salt dependence of oligocation-oligonucleotide binding interactions. In a comparative study of L8+ binding to poly dT and to a short dT oligomer (|ZD| = 10),. Proc. Natl. Acad. Sci. USA. 93:2511-2516) demonstrated the profound thermodynamic effects of phosphate charges that flank isolated nonspecific L8+ binding sites on DNA. Here we find that both Kobs and the magnitude of its power dependence on salt activity (|SaKobs|) increase monotonically with increasing |ZD|. The dependences of Kobs and SaKobs on |ZD| are interpreted by introducing a simple two-state thermodynamic model for Coulombic end effects, which accounts for our finding that when L8+ binds to sufficiently long dT-mers, both DeltaGobso = -RT ln Kobs and SaKobs approach the values characteristic of binding to poly-dT as linear functions of the reciprocal of the number of potential oligocation binding sites on the DNA lattice. Analysis of our L8+-dT-mer binding data in terms of this model indicates that the axial range of the Coulombic end effect for ss DNA extends over approximately 10 phosphate charges. We conclude that Coulombic interactions cause an oligocation (with ZL < |ZD|) to bind preferentially to interior rather than terminal binding sites on oligoanionic or polyanionic DNA, and we quantify the strong increase of this preference with decreasing salt concentration. Coulombic end effects must be considered when oligonucleotides are used as models for polyanionic DNA in thermodynamic studies of the binding of charged ligands, including proteins.
DOI: 10.1016/S0006-3495(99)77265-6
PubMed: 9916032
Affiliations:
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Ni</name></author><author><name sortKey="Capp, M W" sort="Capp, M W" uniqKey="Capp M" first="M W" last="Capp">M W Capp</name></author><author><name sortKey="Anderson, C F" sort="Anderson, C F" uniqKey="Anderson C" first="C F" last="Anderson">C F Anderson</name></author><author><name sortKey="Lohman, T M" sort="Lohman, T M" uniqKey="Lohman T" first="T M" last="Lohman">T M Lohman</name></author><author><name sortKey="Record, M T" sort="Record, M T" uniqKey="Record M" first="M T" last="Record">M T Record</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="1999">1999</date><idno type="RBID">pubmed:9916032</idno><idno type="pmid">9916032</idno><idno type="doi">10.1016/S0006-3495(99)77265-6</idno><idno type="wicri:Area/PubMed/Corpus">002650</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002650</idno><idno type="wicri:Area/PubMed/Curation">002650</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002650</idno><idno type="wicri:Area/PubMed/Checkpoint">002463</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002463</idno><idno type="wicri:Area/Ncbi/Merge">002B55</idno><idno type="wicri:Area/Ncbi/Curation">002B55</idno><idno type="wicri:Area/Ncbi/Checkpoint">002B55</idno><idno type="wicri:doubleKey">0006-3495:1999:Zhang W:the:importance:of</idno><idno type="wicri:Area/Main/Merge">003822</idno><idno type="wicri:Area/Main/Curation">003778</idno><idno type="wicri:Area/Main/Exploration">003778</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">The importance of coulombic end effects: experimental characterization of the effects of oligonucleotide flanking charges on the strength and salt dependence of oligocation (L8+) binding to single-stranded DNA oligomers.</title><author><name sortKey="Zhang, W" sort="Zhang, W" uniqKey="Zhang W" first="W" last="Zhang">W. Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706</wicri:regionArea><wicri:noRegion>Wisconsin 53706</wicri:noRegion></affiliation></author><author><name sortKey="Ni, H" sort="Ni, H" uniqKey="Ni H" first="H" last="Ni">H. Ni</name></author><author><name sortKey="Capp, M W" sort="Capp, M W" uniqKey="Capp M" first="M W" last="Capp">M W Capp</name></author><author><name sortKey="Anderson, C F" sort="Anderson, C F" uniqKey="Anderson C" first="C F" last="Anderson">C F Anderson</name></author><author><name sortKey="Lohman, T M" sort="Lohman, T M" uniqKey="Lohman T" first="T M" last="Lohman">T M Lohman</name></author><author><name sortKey="Record, M T" sort="Record, M T" uniqKey="Record M" first="M T" last="Record">M T Record</name></author></analytic><series><title level="j">Biophysical journal</title><idno type="ISSN">0006-3495</idno><imprint><date when="1999" type="published">1999</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Anions (metabolism)</term><term>Binding Sites</term><term>Cations (metabolism)</term><term>DNA, Single-Stranded (chemistry)</term><term>Fluorescence</term><term>Oligopeptides (chemistry)</term><term>Oligopeptides (metabolism)</term><term>Poly T (metabolism)</term><term>Salts (pharmacology)</term><term>Static Electricity</term><term>Thermodynamics</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN simple brin ()</term><term>Anions (métabolisme)</term><term>Cations (métabolisme)</term><term>Fluorescence</term><term>Oligopeptides ()</term><term>Oligopeptides (métabolisme)</term><term>Poly T (métabolisme)</term><term>Sels (pharmacologie)</term><term>Sites de fixation</term><term>Thermodynamique</term><term>Électricité statique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA, Single-Stranded</term><term>Oligopeptides</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Anions</term><term>Cations</term><term>Oligopeptides</term><term>Poly T</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Salts</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Anions</term><term>Cations</term><term>Oligopeptides</term><term>Poly T</term></keywords><keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Sels</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Fluorescence</term><term>Static Electricity</term><term>Thermodynamics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN simple brin</term><term>Fluorescence</term><term>Oligopeptides</term><term>Sites de fixation</term><term>Thermodynamique</term><term>Électricité statique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Binding constants Kobs, expressed per site and evaluated in the limit of zero binding density, are quantified as functions of salt (sodium acetate) concentration for the interactions of the oligopeptide ligand KWK6NH2 (designated L8+, with ZL = 8 charges) with three single-stranded DNA oligomers (ss dT-mers, with |ZD| = 15, 39, and 69 charges). These results provide the first systematic experimental information about the effect of changing |ZD| on the strength and salt dependence of oligocation-oligonucleotide binding interactions. In a comparative study of L8+ binding to poly dT and to a short dT oligomer (|ZD| = 10),. Proc. Natl. Acad. Sci. USA. 93:2511-2516) demonstrated the profound thermodynamic effects of phosphate charges that flank isolated nonspecific L8+ binding sites on DNA. Here we find that both Kobs and the magnitude of its power dependence on salt activity (|SaKobs|) increase monotonically with increasing |ZD|. The dependences of Kobs and SaKobs on |ZD| are interpreted by introducing a simple two-state thermodynamic model for Coulombic end effects, which accounts for our finding that when L8+ binds to sufficiently long dT-mers, both DeltaGobso = -RT ln Kobs and SaKobs approach the values characteristic of binding to poly-dT as linear functions of the reciprocal of the number of potential oligocation binding sites on the DNA lattice. Analysis of our L8+-dT-mer binding data in terms of this model indicates that the axial range of the Coulombic end effect for ss DNA extends over approximately 10 phosphate charges. We conclude that Coulombic interactions cause an oligocation (with ZL < |ZD|) to bind preferentially to interior rather than terminal binding sites on oligoanionic or polyanionic DNA, and we quantify the strong increase of this preference with decreasing salt concentration. Coulombic end effects must be considered when oligonucleotides are used as models for polyanionic DNA in thermodynamic studies of the binding of charged ligands, including proteins.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Anderson, C F" sort="Anderson, C F" uniqKey="Anderson C" first="C F" last="Anderson">C F Anderson</name><name sortKey="Capp, M W" sort="Capp, M W" uniqKey="Capp M" first="M W" last="Capp">M W Capp</name><name sortKey="Lohman, T M" sort="Lohman, T M" uniqKey="Lohman T" first="T M" last="Lohman">T M Lohman</name><name sortKey="Ni, H" sort="Ni, H" uniqKey="Ni H" first="H" last="Ni">H. Ni</name><name sortKey="Record, M T" sort="Record, M T" uniqKey="Record M" first="M T" last="Record">M T Record</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Zhang, W" sort="Zhang, W" uniqKey="Zhang W" first="W" last="Zhang">W. 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