Structural properties of DNA oligomers containing (GACX)(n) and (GAXC)(n) tandem repeats.
Identifieur interne : 000888 ( Ncbi/Merge ); précédent : 000887; suivant : 000889Structural properties of DNA oligomers containing (GACX)(n) and (GAXC)(n) tandem repeats.
Auteurs : Indrani Dasgupta [États-Unis] ; Xiaolian Gao ; George E. FoxSource :
- Biopolymers [ 0006-3525 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
- antagonistes et inhibiteurs : microARN.
- Animaux, Conformation d'acide nucléique, Oligodésoxyribonucléotides antisens, Souris, Séquences répétées en tandem.
English descriptors
- KwdEn :
- MESH :
- chemical , antagonists & inhibitors : MicroRNAs.
- chemical , chemistry : Oligodeoxyribonucleotides, Antisense.
- Animals, Mice, Nucleic Acid Conformation, Tandem Repeat Sequences.
Abstract
The antisense DNA sequence of mature mouse micro RNA, miR341, includes three repeats of the tetranucleotide (GACC). The -GAC- repeat is known to form a parallel duplex, in acidic environments. The thermal melting profile of miR341 DNA, at pH 4, 5, and 6 indicates the formation of a very stable structure, which loses its stability when pH is increased. Thus, the addition of a cytosine at the 3' end of the (GAC) motif preserves the molecule's potential to fold into an unusual structure at low pH. The effect of modifying the nucleotide composition of the GACC sequence on the secondary structures formed by oligomers containing seven tandem repeats of the altered motifs was examined here. UV melting profiles were determined, as a function of pH, for 28-mers of the two series (GAXC)(7) and (GACX)(7) (X= A/C/T/G)(.) The sequence (GACC)(7) was found to be extremely sensitive to pH variations, with a stable structure formed at pH 5 (T(m) ≥ 60°C). NMR spectroscopy established that the low pH structure is not B-DNA. (GACA)(7) and (GACT)(7) also formed stable structures at low pH but the addition of guanine at the 3'end, as seen in the (GACG) series resulted in the loss of this property. Introducing a break in the 5'-GAC-3' motif, explored in the (GAXC) series, also inhibits formation of stable structures under acidic conditions.
DOI: 10.1002/bip.21719
PubMed: 21953019
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Fox</name></author></analytic><series><title level="j">Biopolymers</title><idno type="ISSN">0006-3525</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Mice</term><term>MicroRNAs (antagonists & inhibitors)</term><term>Nucleic Acid Conformation</term><term>Oligodeoxyribonucleotides, Antisense (chemistry)</term><term>Tandem Repeat Sequences</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Conformation d'acide nucléique</term><term>Oligodésoxyribonucléotides antisens ()</term><term>Souris</term><term>Séquences répétées en tandem</term><term>microARN (antagonistes et inhibiteurs)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="antagonists & inhibitors" xml:lang="en"><term>MicroRNAs</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Oligodeoxyribonucleotides, Antisense</term></keywords><keywords scheme="MESH" qualifier="antagonistes et inhibiteurs" xml:lang="fr"><term>microARN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Mice</term><term>Nucleic Acid Conformation</term><term>Tandem Repeat Sequences</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Conformation d'acide nucléique</term><term>Oligodésoxyribonucléotides antisens</term><term>Souris</term><term>Séquences répétées en tandem</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The antisense DNA sequence of mature mouse micro RNA, miR341, includes three repeats of the tetranucleotide (GACC). The -GAC- repeat is known to form a parallel duplex, in acidic environments. The thermal melting profile of miR341 DNA, at pH 4, 5, and 6 indicates the formation of a very stable structure, which loses its stability when pH is increased. Thus, the addition of a cytosine at the 3' end of the (GAC) motif preserves the molecule's potential to fold into an unusual structure at low pH. The effect of modifying the nucleotide composition of the GACC sequence on the secondary structures formed by oligomers containing seven tandem repeats of the altered motifs was examined here. UV melting profiles were determined, as a function of pH, for 28-mers of the two series (GAXC)(7) and (GACX)(7) (X= A/C/T/G)(.) The sequence (GACC)(7) was found to be extremely sensitive to pH variations, with a stable structure formed at pH 5 (T(m) ≥ 60°C). NMR spectroscopy established that the low pH structure is not B-DNA. (GACA)(7) and (GACT)(7) also formed stable structures at low pH but the addition of guanine at the 3'end, as seen in the (GACG) series resulted in the loss of this property. Introducing a break in the 5'-GAC-3' motif, explored in the (GAXC) series, also inhibits formation of stable structures under acidic conditions.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21953019</PMID><DateCompleted><Year>2012</Year><Month>03</Month><Day>06</Day></DateCompleted><DateRevised><Year>2011</Year><Month>12</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0006-3525</ISSN><JournalIssue CitedMedium="Print"><Volume>97</Volume><Issue>3</Issue><PubDate><Year>2012</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Biopolymers</Title><ISOAbbreviation>Biopolymers</ISOAbbreviation></Journal><ArticleTitle>Structural properties of DNA oligomers containing (GACX)(n) and (GAXC)(n) tandem repeats.</ArticleTitle><Pagination><MedlinePgn>155-64</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/bip.21719</ELocationID><Abstract><AbstractText>The antisense DNA sequence of mature mouse micro RNA, miR341, includes three repeats of the tetranucleotide (GACC). The -GAC- repeat is known to form a parallel duplex, in acidic environments. The thermal melting profile of miR341 DNA, at pH 4, 5, and 6 indicates the formation of a very stable structure, which loses its stability when pH is increased. Thus, the addition of a cytosine at the 3' end of the (GAC) motif preserves the molecule's potential to fold into an unusual structure at low pH. The effect of modifying the nucleotide composition of the GACC sequence on the secondary structures formed by oligomers containing seven tandem repeats of the altered motifs was examined here. UV melting profiles were determined, as a function of pH, for 28-mers of the two series (GAXC)(7) and (GACX)(7) (X= A/C/T/G)(.) The sequence (GACC)(7) was found to be extremely sensitive to pH variations, with a stable structure formed at pH 5 (T(m) ≥ 60°C). NMR spectroscopy established that the low pH structure is not B-DNA. (GACA)(7) and (GACT)(7) also formed stable structures at low pH but the addition of guanine at the 3'end, as seen in the (GACG) series resulted in the loss of this property. Introducing a break in the 5'-GAC-3' motif, explored in the (GAXC) series, also inhibits formation of stable structures under acidic conditions.</AbstractText><CopyrightInformation>Copyright © 2011 Wiley Periodicals, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Dasgupta</LastName><ForeName>Indrani</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>Xiaolian</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Fox</LastName><ForeName>George E</ForeName><Initials>GE</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2011</Year><Month>09</Month><Day>22</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Biopolymers</MedlineTA><NlmUniqueID>0372525</NlmUniqueID><ISSNLinking>0006-3525</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D035683">MicroRNAs</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020319">Oligodeoxyribonucleotides, Antisense</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D051379" MajorTopicYN="N">Mice</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D035683" MajorTopicYN="N">MicroRNAs</DescriptorName><QualifierName UI="Q000037" MajorTopicYN="N">antagonists & inhibitors</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009690" MajorTopicYN="N">Nucleic Acid Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020319" MajorTopicYN="N">Oligodeoxyribonucleotides, Antisense</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020080" MajorTopicYN="Y">Tandem Repeat Sequences</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2011</Year><Month>07</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2011</Year><Month>09</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2011</Year><Month>09</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2011</Year><Month>9</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2011</Year><Month>9</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2012</Year><Month>3</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">21953019</ArticleId><ArticleId IdType="doi">10.1002/bip.21719</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Texas</li></region></list><tree><noCountry><name sortKey="Fox, George E" sort="Fox, George E" uniqKey="Fox G" first="George E" last="Fox">George E. Fox</name><name sortKey="Gao, Xiaolian" sort="Gao, Xiaolian" uniqKey="Gao X" first="Xiaolian" last="Gao">Xiaolian Gao</name></noCountry><country name="États-Unis"><region name="Texas"><name sortKey="Dasgupta, Indrani" sort="Dasgupta, Indrani" uniqKey="Dasgupta I" first="Indrani" last="Dasgupta">Indrani Dasgupta</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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