Conformations of DNA strands containing GAGT, GACA, or GAGC tetranucleotide repeats.
Identifieur interne : 002168 ( PubMed/Corpus ); précédent : 002167; suivant : 002169Conformations of DNA strands containing GAGT, GACA, or GAGC tetranucleotide repeats.
Auteurs : Jaroslav Kypr ; Iva Kejnovská ; Michaela VorlíckováSource :
- Biopolymers [ 0006-3525 ] ; 2007.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, Oligonucleotides.
- Base Sequence, Circular Dichroism, Hydrogen-Ion Concentration, Isomerism, Microsatellite Repeats, Nucleic Acid Conformation.
Abstract
The (GA)(n) microsatellite has been known from previous studies to adopt unusual, ordered, cooperatively melting secondary structures in neutral aqueous solutions containing physiological concentrations of salts, at acid pH values or in aqueous ethanol solutions. To find more about the primary structure specificity of these structures, we performed parallel comparative studies of related tetranucleotide repeats (GAGC)(5), (GAGT)(5), and (GACA)(5). The general conclusion following from these comparative studies is that the primary structure specificity is fairly high, indicating that not only guanines but also adenines play a significant role in the stabilization of these unusual structures. (GAGC)(5) is a hairpin or a duplex depending on DNA concentration. Neither acid pH nor ionic strength or the presence of ethanol changed the secondary structure of (GAGC)(5) in a significant way. (GACA)(5) forms a weakly stable hairpin in neutral aqueous solutions but forms a duplex at acid pH where cytosine is protonated. (GAGT)(5) behaves most similar to (GAGA)(5). Salt induces its hairpin to duplex transition at neutral pH and an isomerization into another, probably parallel stranded, duplex takes place at acid pH. (GAGT)(5) is the only of the three present 20-mers that responds to ethanol like (GAGA)(5).
DOI: 10.1002/bip.20822
PubMed: 17680700
Links to Exploration step
pubmed:17680700Le document en format XML
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<author><name sortKey="Kypr, Jaroslav" sort="Kypr, Jaroslav" uniqKey="Kypr J" first="Jaroslav" last="Kypr">Jaroslav Kypr</name>
<affiliation><nlm:affiliation>Institute of Biophysics, v. v. i., Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.</nlm:affiliation>
</affiliation>
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<author><name sortKey="Kejnovska, Iva" sort="Kejnovska, Iva" uniqKey="Kejnovska I" first="Iva" last="Kejnovská">Iva Kejnovská</name>
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<author><name sortKey="Vorlickova, Michaela" sort="Vorlickova, Michaela" uniqKey="Vorlickova M" first="Michaela" last="Vorlícková">Michaela Vorlícková</name>
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<author><name sortKey="Kejnovska, Iva" sort="Kejnovska, Iva" uniqKey="Kejnovska I" first="Iva" last="Kejnovská">Iva Kejnovská</name>
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<author><name sortKey="Vorlickova, Michaela" sort="Vorlickova, Michaela" uniqKey="Vorlickova M" first="Michaela" last="Vorlícková">Michaela Vorlícková</name>
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<series><title level="j">Biopolymers</title>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term>
<term>Circular Dichroism</term>
<term>DNA (chemistry)</term>
<term>Hydrogen-Ion Concentration</term>
<term>Isomerism</term>
<term>Microsatellite Repeats</term>
<term>Nucleic Acid Conformation</term>
<term>Oligonucleotides (chemistry)</term>
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<term>Circular Dichroism</term>
<term>Hydrogen-Ion Concentration</term>
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<front><div type="abstract" xml:lang="en">The (GA)(n) microsatellite has been known from previous studies to adopt unusual, ordered, cooperatively melting secondary structures in neutral aqueous solutions containing physiological concentrations of salts, at acid pH values or in aqueous ethanol solutions. To find more about the primary structure specificity of these structures, we performed parallel comparative studies of related tetranucleotide repeats (GAGC)(5), (GAGT)(5), and (GACA)(5). The general conclusion following from these comparative studies is that the primary structure specificity is fairly high, indicating that not only guanines but also adenines play a significant role in the stabilization of these unusual structures. (GAGC)(5) is a hairpin or a duplex depending on DNA concentration. Neither acid pH nor ionic strength or the presence of ethanol changed the secondary structure of (GAGC)(5) in a significant way. (GACA)(5) forms a weakly stable hairpin in neutral aqueous solutions but forms a duplex at acid pH where cytosine is protonated. (GAGT)(5) behaves most similar to (GAGA)(5). Salt induces its hairpin to duplex transition at neutral pH and an isomerization into another, probably parallel stranded, duplex takes place at acid pH. (GAGT)(5) is the only of the three present 20-mers that responds to ethanol like (GAGA)(5).</div>
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<Title>Biopolymers</Title>
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<Abstract><AbstractText>The (GA)(n) microsatellite has been known from previous studies to adopt unusual, ordered, cooperatively melting secondary structures in neutral aqueous solutions containing physiological concentrations of salts, at acid pH values or in aqueous ethanol solutions. To find more about the primary structure specificity of these structures, we performed parallel comparative studies of related tetranucleotide repeats (GAGC)(5), (GAGT)(5), and (GACA)(5). The general conclusion following from these comparative studies is that the primary structure specificity is fairly high, indicating that not only guanines but also adenines play a significant role in the stabilization of these unusual structures. (GAGC)(5) is a hairpin or a duplex depending on DNA concentration. Neither acid pH nor ionic strength or the presence of ethanol changed the secondary structure of (GAGC)(5) in a significant way. (GACA)(5) forms a weakly stable hairpin in neutral aqueous solutions but forms a duplex at acid pH where cytosine is protonated. (GAGT)(5) behaves most similar to (GAGA)(5). Salt induces its hairpin to duplex transition at neutral pH and an isomerization into another, probably parallel stranded, duplex takes place at acid pH. (GAGT)(5) is the only of the three present 20-mers that responds to ethanol like (GAGA)(5).</AbstractText>
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<MeshHeading><DescriptorName UI="D018895" MajorTopicYN="Y">Microsatellite Repeats</DescriptorName>
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<MeshHeading><DescriptorName UI="D009690" MajorTopicYN="N">Nucleic Acid Conformation</DescriptorName>
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