An intramolecular quadruplex of (GGA)4 triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction
Identifieur interne : 002629 ( Istex/Corpus ); précédent : 002628; suivant : 002630An intramolecular quadruplex of (GGA)4 triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction
Auteurs : Akimasa Matsugami ; Kiyoshi Ouhashi ; Mayumi Kanagawa ; Hui Liu ; Sakura Kanagawa ; Seiichi Uesugi ; Masato KatahiraSource :
- Journal of Molecular Biology [ 0022-2836 ] ; 2001.
English descriptors
- KwdEn :
- Teeft :
- Acids symp, Amino, Amino group, Amino protons, Arrowhead motifs, Biol, Chemical shifts, Complementary strand, Conformation, Constraint, Dihedral, Dihedral angle constraints, Dimer, Dimer structure, Distance constraints, Double quantum, Duplex, Endo, H2hh, H5hh, Heptad, Heptad figure, Heptad plane, Heptad planes, Hetcor spectrum, Imino, Imino protons, Interstrand, Intramolecular, Intramolecular quadruplex, Main chain, Monomer, Multimeric form, Noesy, Noesy spectrum, Nucl, Nucleic acids, Parallel quadruplex, Physiological monovalent cation conditions, Planarity constraints, Proton, Purine strand, Quadruplex, Quadruplex structure, Quadruplexes, Representative structure, Residue, Salt conditions, Sheared, Sodium phosphate, Solution structure, Stereo view, Strand stoichiometry, Strong noes, Structural statistics, Tetrad, Torsion angles, Trinucleotide, Trinucleotide loop, Triplet, Upper monomer.
Abstract
Abstract: The structure of d(GGAGGAGGAGGA) containing four tandem repeats of a GGA triplet sequence has been determined under physiological K+ conditions. d(GGAGGAGGAGGA) folds into an intramolecular quadruplex composed of a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad. Four G-G segments of d(GGAGGAGGAGGA) are aligned parallel with each other due to six successive turns of the main chain at each of the GGA and GAGG segments. Two quadruplexes form a dimer stabilized through a stacking interaction between the heptads of the two quadruplexes. Comparison of the structure of d(GGAGGAGGAGGA) with the reported structure of d(GGAGGAN) (N=G or T) containing two tandem repeats of the GGA triplet revealed that although the two structures resemble each other to some extent, the extension of the repeats of the GGA triplet leads to distinct structural differences: intramolecular quadruplex for 12-mer versus intermolecular quadruplex for 7-mer; heptad versus hexad in the quadruplex; and three sheared G:A base-pairs versus two sheared G:A base-pairs plus one A:A base-pair per quadruplex. It was also suggested that d(GGAGGAGGAGGA) forms a similar quadruplex under low salt concentration conditions. This is in contrast to the case of d(GGAGGAN) (N=G or T), which forms a duplex under low salt concentration conditions. On the basis of these results, the structure of naturally occurring GGA triplet repeat DNA is discussed.
Url:
DOI: 10.1006/jmbi.2001.5047
Links to Exploration step
ISTEX:F24D09F5DF59A6A147DE49A15DCBF4FD8C82F86FLe document en format XML
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interaction</title><author><name sortKey="Matsugami, Akimasa" sort="Matsugami, Akimasa" uniqKey="Matsugami A" first="Akimasa" last="Matsugami">Akimasa Matsugami</name><affiliation><mods:affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</mods:affiliation></affiliation></author><author><name sortKey="Ouhashi, Kiyoshi" sort="Ouhashi, Kiyoshi" uniqKey="Ouhashi K" first="Kiyoshi" last="Ouhashi">Kiyoshi Ouhashi</name><affiliation><mods:affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</mods:affiliation></affiliation></author><author><name sortKey="Kanagawa, Mayumi" sort="Kanagawa, Mayumi" uniqKey="Kanagawa M" first="Mayumi" last="Kanagawa">Mayumi Kanagawa</name><affiliation><mods:affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</mods:affiliation></affiliation></author><author><name sortKey="Liu, Hui" sort="Liu, Hui" uniqKey="Liu H" first="Hui" last="Liu">Hui Liu</name><affiliation><mods:affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</mods:affiliation></affiliation></author><author><name sortKey="Kanagawa, Sakura" sort="Kanagawa, Sakura" uniqKey="Kanagawa S" first="Sakura" last="Kanagawa">Sakura Kanagawa</name><affiliation><mods:affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</mods:affiliation></affiliation></author><author><name sortKey="Uesugi, Seiichi" sort="Uesugi, Seiichi" uniqKey="Uesugi S" first="Seiichi" last="Uesugi">Seiichi Uesugi</name><affiliation><mods:affiliation>E-mail: siuesugi@ynu.ac.jp</mods:affiliation></affiliation><affiliation><mods:affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</mods:affiliation></affiliation></author><author><name sortKey="Katahira, Masato" sort="Katahira, Masato" uniqKey="Katahira M" first="Masato" last="Katahira">Masato Katahira</name><affiliation><mods:affiliation>E-mail: siuesugi@ynu.ac.jp</mods:affiliation></affiliation><affiliation><mods:affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Journal of Molecular Biology</title><title level="j" type="abbrev">YJMBI</title><idno type="ISSN">0022-2836</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="2001">2001</date><biblScope unit="volume">313</biblScope><biblScope unit="issue">2</biblScope><biblScope unit="page" from="255">255</biblScope><biblScope unit="page" to="269">269</biblScope></imprint><idno type="ISSN">0022-2836</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0022-2836</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DQF-COSY</term><term>DSS</term><term>HSQC</term><term>NMR</term><term>NOESY</term><term>TOCSY</term><term>d(GGA)</term><term>ppm</term><term>quadruplex</term><term>rmsd</term><term>structure</term><term>triplet repeat</term></keywords><keywords scheme="Teeft" xml:lang="en"><term>Acids symp</term><term>Amino</term><term>Amino group</term><term>Amino protons</term><term>Arrowhead motifs</term><term>Biol</term><term>Chemical shifts</term><term>Complementary strand</term><term>Conformation</term><term>Constraint</term><term>Dihedral</term><term>Dihedral angle constraints</term><term>Dimer</term><term>Dimer structure</term><term>Distance constraints</term><term>Double quantum</term><term>Duplex</term><term>Endo</term><term>H2hh</term><term>H5hh</term><term>Heptad</term><term>Heptad figure</term><term>Heptad plane</term><term>Heptad planes</term><term>Hetcor spectrum</term><term>Imino</term><term>Imino protons</term><term>Interstrand</term><term>Intramolecular</term><term>Intramolecular quadruplex</term><term>Main chain</term><term>Monomer</term><term>Multimeric form</term><term>Noesy</term><term>Noesy spectrum</term><term>Nucl</term><term>Nucleic acids</term><term>Parallel quadruplex</term><term>Physiological monovalent cation conditions</term><term>Planarity constraints</term><term>Proton</term><term>Purine strand</term><term>Quadruplex</term><term>Quadruplex structure</term><term>Quadruplexes</term><term>Representative structure</term><term>Residue</term><term>Salt conditions</term><term>Sheared</term><term>Sodium phosphate</term><term>Solution structure</term><term>Stereo view</term><term>Strand stoichiometry</term><term>Strong noes</term><term>Structural statistics</term><term>Tetrad</term><term>Torsion angles</term><term>Trinucleotide</term><term>Trinucleotide loop</term><term>Triplet</term><term>Upper monomer</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract: The structure of d(GGAGGAGGAGGA) containing four tandem repeats of a GGA triplet sequence has been determined under physiological K+ conditions. d(GGAGGAGGAGGA) folds into an intramolecular quadruplex composed of a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad. Four G-G segments of d(GGAGGAGGAGGA) are aligned parallel with each other due to six successive turns of the main chain at each of the GGA and GAGG segments. Two quadruplexes form a dimer stabilized through a stacking interaction between the heptads of the two quadruplexes. Comparison of the structure of d(GGAGGAGGAGGA) with the reported structure of d(GGAGGAN) (N=G or T) containing two tandem repeats of the GGA triplet revealed that although the two structures resemble each other to some extent, the extension of the repeats of the GGA triplet leads to distinct structural differences: intramolecular quadruplex for 12-mer versus intermolecular quadruplex for 7-mer; heptad versus hexad in the quadruplex; and three sheared G:A base-pairs versus two sheared G:A base-pairs plus one A:A base-pair per quadruplex. It was also suggested that d(GGAGGAGGAGGA) forms a similar quadruplex under low salt concentration conditions. This is in contrast to the case of d(GGAGGAN) (N=G or T), which forms a duplex under low salt concentration conditions. On the basis of these results, the structure of naturally occurring GGA triplet repeat DNA is discussed.</div></front></TEI><istex><corpusName>elsevier</corpusName><keywords><teeft><json:string>quadruplex</json:string><json:string>heptad</json:string><json:string>tetrad</json:string><json:string>imino</json:string><json:string>dihedral</json:string><json:string>interstrand</json:string><json:string>dimer</json:string><json:string>sheared</json:string><json:string>trinucleotide</json:string><json:string>endo</json:string><json:string>biol</json:string><json:string>nucl</json:string><json:string>trinucleotide loop</json:string><json:string>triplet</json:string><json:string>constraint</json:string><json:string>dihedral angle constraints</json:string><json:string>noesy</json:string><json:string>quadruplexes</json:string><json:string>intramolecular</json:string><json:string>imino protons</json:string><json:string>salt conditions</json:string><json:string>h5hh</json:string><json:string>amino protons</json:string><json:string>h2hh</json:string><json:string>proton</json:string><json:string>amino</json:string><json:string>duplex</json:string><json:string>heptad planes</json:string><json:string>intramolecular quadruplex</json:string><json:string>heptad plane</json:string><json:string>representative structure</json:string><json:string>heptad figure</json:string><json:string>quadruplex structure</json:string><json:string>chemical shifts</json:string><json:string>noesy spectrum</json:string><json:string>arrowhead motifs</json:string><json:string>conformation</json:string><json:string>residue</json:string><json:string>solution structure</json:string><json:string>hetcor spectrum</json:string><json:string>multimeric form</json:string><json:string>sodium phosphate</json:string><json:string>distance constraints</json:string><json:string>monomer</json:string><json:string>dimer structure</json:string><json:string>strand stoichiometry</json:string><json:string>physiological monovalent cation conditions</json:string><json:string>planarity constraints</json:string><json:string>strong noes</json:string><json:string>stereo view</json:string><json:string>double quantum</json:string><json:string>amino group</json:string><json:string>complementary strand</json:string><json:string>upper monomer</json:string><json:string>purine strand</json:string><json:string>parallel quadruplex</json:string><json:string>torsion angles</json:string><json:string>main chain</json:string><json:string>acids symp</json:string><json:string>nucleic acids</json:string><json:string>structural statistics</json:string></teeft></keywords><author><json:item><name>Akimasa Matsugami</name><affiliations><json:string>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</json:string></affiliations></json:item><json:item><name>Kiyoshi Ouhashi</name><affiliations><json:string>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</json:string></affiliations></json:item><json:item><name>Mayumi Kanagawa</name><affiliations><json:string>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</json:string></affiliations></json:item><json:item><name>Hui Liu</name><affiliations><json:string>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</json:string></affiliations></json:item><json:item><name>Sakura Kanagawa</name><affiliations><json:string>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</json:string></affiliations></json:item><json:item><name>Seiichi Uesugi</name><affiliations><json:string>E-mail: siuesugi@ynu.ac.jp</json:string><json:string>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</json:string></affiliations></json:item><json:item><name>Masato Katahira</name><affiliations><json:string>E-mail: siuesugi@ynu.ac.jp</json:string><json:string>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>Regular article</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>quadruplex</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>triplet repeat</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>NMR</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>structure</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>d(GGA)</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>NMR : nuclear magnetic resonance</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>NOESY : two-dimensional nuclear Overhauser effect spectroscopy</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>TOCSY : total correlation spectroscopy</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>DQF-COSY : double quantum filtered correlation spectroscopy</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>HSQC : heteronuclear single quantum coherence spectroscopy</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>DSS : sodium 2,2-dimethyl-2-silapentane-5-sulfonate</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>ppm : parts per million</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>rmsd : root-mean-square deviation</value></json:item></subject><arkIstex>ark:/67375/6H6-PXCHX5P0-N</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>Full-length article</json:string></originalGenre><abstract>Abstract: The structure of d(GGAGGAGGAGGA) containing four tandem repeats of a GGA triplet sequence has been determined under physiological K+ conditions. d(GGAGGAGGAGGA) folds into an intramolecular quadruplex composed of a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad. Four G-G segments of d(GGAGGAGGAGGA) are aligned parallel with each other due to six successive turns of the main chain at each of the GGA and GAGG segments. Two quadruplexes form a dimer stabilized through a stacking interaction between the heptads of the two quadruplexes. Comparison of the structure of d(GGAGGAGGAGGA) with the reported structure of d(GGAGGAN) (N=G or T) containing two tandem repeats of the GGA triplet revealed that although the two structures resemble each other to some extent, the extension of the repeats of the GGA triplet leads to distinct structural differences: intramolecular quadruplex for 12-mer versus intermolecular quadruplex for 7-mer; heptad versus hexad in the quadruplex; and three sheared G:A base-pairs versus two sheared G:A base-pairs plus one A:A base-pair per quadruplex. It was also suggested that d(GGAGGAGGAGGA) forms a similar quadruplex under low salt concentration conditions. This is in contrast to the case of d(GGAGGAN) (N=G or T), which forms a duplex under low salt concentration conditions. On the basis of these results, the structure of naturally occurring GGA triplet repeat DNA is discussed.</abstract><qualityIndicators><score>9.568</score><pdfWordCount>7636</pdfWordCount><pdfCharCount>44885</pdfCharCount><pdfVersion>1.3</pdfVersion><pdfPageCount>15</pdfPageCount><pdfPageSize>595 x 842 pts (A4)</pdfPageSize><refBibsNative>true</refBibsNative><abstractWordCount>214</abstractWordCount><abstractCharCount>1427</abstractCharCount><keywordCount>14</keywordCount></qualityIndicators><title>An intramolecular quadruplex of (GGA)4 triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction</title><pmid><json:string>11800555</json:string></pmid><pii><json:string>S0022-2836(01)95047-8</json:string></pii><genre><json:string>research-article</json:string></genre><host><title>Journal of Molecular Biology</title><language><json:string>unknown</json:string></language><publicationDate>2001</publicationDate><issn><json:string>0022-2836</json:string></issn><pii><json:string>S0022-2836(00)X0256-2</json:string></pii><volume>313</volume><issue>2</issue><pages><first>255</first><last>269</last></pages><genre><json:string>journal</json:string></genre></host><namedEntities><unitex><date><json:string>2001</json:string></date><geogName></geogName><orgName><json:string>Yokohama National University</json:string><json:string>Ministry of Education, Science, Sports and Culture of Japan</json:string></orgName><orgName_funder></orgName_funder><orgName_provider></orgName_provider><persName><json:string>Patel</json:string><json:string>Mayumi Kanagawa</json:string><json:string>An Intramolecular</json:string><json:string>Sakura Kanagawa</json:string></persName><placeName><json:string>Japan</json:string></placeName><ref_url><json:string>http://www.idealibrary.com</json:string></ref_url><ref_bibl></ref_bibl><bibl></bibl></unitex></namedEntities><ark><json:string>ark:/67375/6H6-PXCHX5P0-N</json:string></ark><categories><wos><json:string>1 - science</json:string><json:string>2 - biochemistry & molecular biology</json:string></wos><scienceMetrix><json:string>1 - health sciences</json:string><json:string>2 - biomedical research</json:string><json:string>3 - biochemistry & molecular biology</json:string></scienceMetrix><scopus><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Molecular Biology</json:string></scopus><inist><json:string>1 - sciences appliquees, technologies et medecines</json:string><json:string>2 - sciences biologiques et medicales</json:string><json:string>3 - sciences biologiques fondamentales et appliquees. psychologie</json:string></inist></categories><publicationDate>2001</publicationDate><copyrightDate>2001</copyrightDate><doi><json:string>10.1006/jmbi.2001.5047</json:string></doi><id>F24D09F5DF59A6A147DE49A15DCBF4FD8C82F86F</id><score>1</score><fulltext><json:item><extension>pdf</extension><original>true</original><mimetype>application/pdf</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-PXCHX5P0-N/fulltext.pdf</uri></json:item><json:item><extension>zip</extension><original>false</original><mimetype>application/zip</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-PXCHX5P0-N/bundle.zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/ark:/67375/6H6-PXCHX5P0-N/fulltext.tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main" xml:lang="en">An intramolecular quadruplex of (GGA)4 triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher scheme="https://scientific-publisher.data.istex.fr">ELSEVIER</publisher><availability><licence><p>©2001 Academic Press</p></licence><p scheme="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-HKKZVM7B-M">elsevier</p></availability><date>2001</date></publicationStmt><notesStmt><note type="research-article" scheme="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</note><note type="journal" scheme="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</note><note>Supplementary Material comprising one Table is available onIDEAL</note><note>Edited by I. Tinoco</note><note type="content">Section title: Regular article</note><note type="content">Figure 1: Imino proton spectra of (a) d(GGAGGAGGAGGA) in the presence of 100 mM KCl, (b) d(GGAGGAGGAGGA) in the absence of KCl, (c) d(GGAGGA) in the presence of 100 mM KCl, and (d) d(GGAGGA) in the absence of KCl in H2O containing 10 mM sodium phosphate (pH 6.7), 10 mM NaCl and 3 mM NaN3 at 1°C.</note><note type="content">Figure 2: CD spectrum of d(GGAGGAGGAGGA) in H2O containing 10 mM sodium phosphate (pH 6.7), 10 mM NaCl and 3 mM NaN3 in the presence of 100 mM KCl (continuous line) and in the absence of KCl (broken line) at 5°C.</note><note type="content">Figure 3: Imino-amino NOESY cross-peaks for each G residue observed for (a) d(GGAGGAGGAGGA), (b) (IGAGGAGGAGGA), (c) d(GGAIGAGGAGGA), (d) d(GGAGGAGGAIGA), and (e) d(GGAGGAGGAGIA) in H2O containing 10 mM sodium phosphate (pH 6.7), 10 mM NaCl, 3 mM NaN3 and 100 mM KCl at 1°C; dark green, G1; brown, G2; red, G4; blue, G5; pink, G7; light green, G8; sky blue, G10; yellow, G11. The initial level of contours is set high in order to show only strong cross-peaks. Asterisks indicate cross-peaks that are not imino-amino cross-peaks. Note that the imino protons of I residues resonate in a low field region at 13.5-14.5 ppm, thus cross-peaks originating from I imino protons appear outside these Figures.</note><note type="content">Figure 4: Expansion of the NOESY spectrum with a mixing time of 200 ms of d(GGAGGAGGAGGA) in 2H2O containing 10 mM sodium phosphate (pH 6.7), 10 mM NaCl, 3 mM NaN3 and 100 mM KCl at 25°C. (a) The H6/H8-H1′ region. The lines show the H1′(i−1)-H6/H8(i)-H1′(i) connectivities, the intraresidue cross-peaks being labeled. Cross-peaks a-e are as follows (see the text for details): a, interstrand A3H2-A9H1′; b, interstrand A9H2-A3H1′; c, interstrand A6H2-A6H1′; d, interstrand G4H8-G7H1′; e, interstrand G7H8-G4H1′. (b) and (c) Expansion of the H6/H8-H1′ region symmetric to that shown in (a) with respect to the diagonal. Cross-peak a in (b) and (c) is interstrand G1H1′-G10H8 and G10H8-G1H1′, respectively. (d) The H2/H8-H2/H8 region. Cross-peaks a-c are as follows: a, A3H8-G4H8; b, A6H8-G7H8; c, A9H8-G10H8.</note><note type="content">Figure 5: (a) The 1H-31P HetCor spectrum of d(GGAGGAGGAGGA). The solution conditions are identical with those described in the legend to Figure 4. 1H and 31P assignments are indicated. (b) and (c) Expansion of the 1H-13C HSQC spectrum confirming the assignments of upfield-shifted G2H1′, and G2H4′, G5H4′ and G8H4′, respectively.</note><note type="content">Figure 6: Expansion of the NOESY spectrum with a mixing time of 200 ms, indicating NOEs originating from (a) imino and amino protons of G residues and (b) amino protons of A residues. The solution conditions are identical with those described in the legend to Figure 3. Cross-peaks a-z and aa-cc in (a) are as follows: a, G1NH-G4H8; b, G4NH-G7H8; c, G7NH-G10H8; d, G10NH-G1H8; e, G2NH-G5H8; f, G5NH-G8H8; g, G8NH-G11H8; h, G11NH-G2H8; i and i′, G1NH2-G4H8; j and j′, G4NH2-G7H8; k and k′, G7NH2-G10H8; l and l′, G10NH2-G1H8; m, G1NH-G4NH; n, G2NH-G11NH; o, G2NH-G5NH; p, G8NH-G11NH; q and q′, G1NH2-A3H8; r and r′, G4NH2-A6H8; s and s′, G7NH2-A9H8; t, t′, t# and t∗, G1NH2-A3NH2; u, u′, u# and u∗, G4NH2-A6NH2; v, v′, v# and v∗, G6NH2-A9NH2; w, G1NH2-G1NH2; x, G4NH2-G4NH2; y, G7NH2-G7NH2; z, G10NH2-G10NH2; aa, G2NH2-G2NH2; bb, G8NH2-G8NH2; cc, G11NH2-G11NH2. Cross peaks a-f in (b) are as follows: a, A3NH2-A3NH2; b, A6NH2-A6NH2; c, A9NH2-A9NH2; d and d′, A3NH2-G1H1′; e and e′, A6NH2-G4H1′; f and f′, A9NH2-G7H1′.</note><note type="content">Figure 7: Schematic representation of (a) tetrad, (b) heptad, and (c) dimer structures. Key NOEs used to construct these structures are shown by continuous lines connecting the corresponding protons (a and b) or by double-headed arrows (c). For spin diffusion through amino protons of G residues, see the text. (d) Schematic representation of one of possible structures of a DNA 24-mer, d(GGA)8.</note><note type="content">Figure 8: A plot of the logarithm of the concentration of the multimeric form of d(GGAGGAGGAGGA) (log[M]) versus the logarithm of the concentration of the single-stranded form of d(GGAGGAGGAGGA) (log[S]).</note><note type="content">Figure 9: (a) A stereo view of the superposition of the 20 final structures of the d(GGAGGAGGAGGA) dimer. The monomers are colored in yellow and green, respectively, O4′ of sugars being colored in red. The A12 residue is labeled. (b) A stereo view of the representative structure with the lowest energy. The sugar-phosphate main chains of each monomer are indicated by yellow and green tubes, respectively.</note><note type="content">Figure 10: The (a) tetrad and (b) heptad planes of the upper monomer of the representative structure shown in Figure 9(b). (c) Stacking between A12 (cyan) and the tetrad plane (white), and (d) between the tetrad (white) and heptad (magenta) planes of the upper monomer of the representative structure, the main chain being colored in yellow. (e) Stacking between the two heptad planes (magenta and orange) of each monomer of the representative structure, the main chains of each monomer being colored in yellow and green, respectively.</note><note type="content">Table 1: NMR constraints and structural statistics for the symmetric d(GGAGGAGGAGGA) dimer</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">An intramolecular quadruplex of (GGA)4 triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction</title><author xml:id="author-0000"><persName><forename type="first">Akimasa</forename><surname>Matsugami</surname></persName><affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</affiliation></author><author xml:id="author-0001"><persName><forename type="first">Kiyoshi</forename><surname>Ouhashi</surname></persName><affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</affiliation></author><author xml:id="author-0002"><persName><forename type="first">Mayumi</forename><surname>Kanagawa</surname></persName><affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</affiliation></author><author xml:id="author-0003"><persName><forename type="first">Hui</forename><surname>Liu</surname></persName><affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</affiliation></author><author xml:id="author-0004"><persName><forename type="first">Sakura</forename><surname>Kanagawa</surname></persName><affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</affiliation></author><author xml:id="author-0005"><persName><forename type="first">Seiichi</forename><surname>Uesugi</surname></persName><email>siuesugi@ynu.ac.jp</email><note type="correspondence"><p>Corresponding authors</p></note><affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</affiliation></author><author xml:id="author-0006"><persName><forename type="first">Masato</forename><surname>Katahira</surname></persName><email>siuesugi@ynu.ac.jp</email><note type="correspondence"><p>Corresponding authors</p></note><affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</affiliation></author><idno type="istex">F24D09F5DF59A6A147DE49A15DCBF4FD8C82F86F</idno><idno type="ark">ark:/67375/6H6-PXCHX5P0-N</idno><idno type="DOI">10.1006/jmbi.2001.5047</idno><idno type="PII">S0022-2836(01)95047-8</idno></analytic><monogr><title level="j">Journal of Molecular Biology</title><title level="j" type="abbrev">YJMBI</title><idno type="pISSN">0022-2836</idno><idno type="PII">S0022-2836(00)X0256-2</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="2001"></date><biblScope unit="volume">313</biblScope><biblScope unit="issue">2</biblScope><biblScope unit="page" from="255">255</biblScope><biblScope unit="page" to="269">269</biblScope></imprint></monogr></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2001</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>Abstract: The structure of d(GGAGGAGGAGGA) containing four tandem repeats of a GGA triplet sequence has been determined under physiological K+ conditions. d(GGAGGAGGAGGA) folds into an intramolecular quadruplex composed of a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad. Four G-G segments of d(GGAGGAGGAGGA) are aligned parallel with each other due to six successive turns of the main chain at each of the GGA and GAGG segments. Two quadruplexes form a dimer stabilized through a stacking interaction between the heptads of the two quadruplexes. Comparison of the structure of d(GGAGGAGGAGGA) with the reported structure of d(GGAGGAN) (N=G or T) containing two tandem repeats of the GGA triplet revealed that although the two structures resemble each other to some extent, the extension of the repeats of the GGA triplet leads to distinct structural differences: intramolecular quadruplex for 12-mer versus intermolecular quadruplex for 7-mer; heptad versus hexad in the quadruplex; and three sheared G:A base-pairs versus two sheared G:A base-pairs plus one A:A base-pair per quadruplex. It was also suggested that d(GGAGGAGGAGGA) forms a similar quadruplex under low salt concentration conditions. This is in contrast to the case of d(GGAGGAN) (N=G or T), which forms a duplex under low salt concentration conditions. On the basis of these results, the structure of naturally occurring GGA triplet repeat DNA is discussed.</p></abstract><textClass><keywords scheme="keyword"><list><head>article-category</head><item><term>Regular article</term></item></list></keywords></textClass><textClass xml:lang="en"><keywords scheme="keyword"><list><head>Keywords</head><item><term>quadruplex</term></item><item><term>triplet repeat</term></item><item><term>NMR</term></item><item><term>structure</term></item><item><term>d(GGA)</term></item></list></keywords></textClass><textClass xml:lang="en"><keywords scheme="keyword"><list><head>Abbreviations</head><item><term>NMR</term><term>nuclear magnetic resonance</term></item><item><term>NOESY</term><term>two-dimensional nuclear Overhauser effect spectroscopy</term></item><item><term>TOCSY</term><term>total correlation spectroscopy</term></item><item><term>DQF-COSY</term><term>double quantum filtered correlation spectroscopy</term></item><item><term>HSQC</term><term>heteronuclear single quantum coherence spectroscopy</term></item><item><term>DSS</term><term>sodium 2,2-dimethyl-2-silapentane-5-sulfonate</term></item><item><term>ppm</term><term>parts per million</term></item><item><term>rmsd</term><term>root-mean-square deviation</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2001-08-27">Modified</change><change when="2001">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-PXCHX5P0-N/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Elsevier, elements deleted: ce:floats; body; tail"><istex:xmlDeclaration>version="1.0" encoding="utf-8"</istex:xmlDeclaration><istex:docType PUBLIC="-//ES//DTD journal article DTD version 4.5.2//EN//XML" URI="art452.dtd" name="istex:docType"><istex:entity SYSTEM="gr1" NDATA="IMAGE" name="GR1"></istex:entity><istex:entity SYSTEM="gr2" NDATA="IMAGE" name="GR2"></istex:entity><istex:entity SYSTEM="gr3" NDATA="IMAGE" name="GR3"></istex:entity><istex:entity SYSTEM="gr4a" NDATA="IMAGE" name="GR4a"></istex:entity><istex:entity SYSTEM="gr4b" NDATA="IMAGE" name="GR4b"></istex:entity><istex:entity SYSTEM="gr4c" NDATA="IMAGE" name="GR4c"></istex:entity><istex:entity SYSTEM="gr4d" NDATA="IMAGE" name="GR4d"></istex:entity><istex:entity SYSTEM="gr5" NDATA="IMAGE" name="GR5"></istex:entity><istex:entity SYSTEM="gr6a" NDATA="IMAGE" name="GR6a"></istex:entity><istex:entity SYSTEM="gr6b" NDATA="IMAGE" name="GR6b"></istex:entity><istex:entity SYSTEM="gr7" NDATA="IMAGE" name="GR7"></istex:entity><istex:entity SYSTEM="gr8" NDATA="IMAGE" name="GR8"></istex:entity><istex:entity SYSTEM="gr9" NDATA="IMAGE" name="GR9"></istex:entity><istex:entity SYSTEM="gr10" NDATA="IMAGE" name="GR10"></istex:entity><istex:entity SYSTEM="mmc1" NDATA="APPLICATION" name="applic1"></istex:entity></istex:docType><istex:document><converted-article version="4.5.2" docsubtype="fla" xml:lang="en"><item-info><jid>YJMBI</jid><aid>95047</aid><ce:pii>S0022-2836(01)95047-8</ce:pii><ce:doi>10.1006/jmbi.2001.5047</ce:doi><ce:copyright type="full-transfer" year="2001">Academic Press</ce:copyright><ce:doctopics><ce:doctopic><ce:text>Regular article</ce:text></ce:doctopic></ce:doctopics></item-info><head><ce:article-footnote><ce:label>☆</ce:label><ce:note-para>Supplementary Material comprising one Table is available on<ce:inter-ref xlink:href="doi:10.1006/jmbi.2001.5047">IDEAL</ce:inter-ref></ce:note-para></ce:article-footnote><ce:dochead><ce:textfn>Regular article</ce:textfn></ce:dochead><ce:title>An intramolecular quadruplex of (GGA)<ce:inf>4</ce:inf> triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction <ce:cross-ref refid="FN1"><ce:sup>1</ce:sup></ce:cross-ref><ce:footnote id="FN1"><ce:label>1</ce:label><ce:note-para><ce:bold><ce:italic>Edited by I. Tinoco</ce:italic></ce:bold></ce:note-para></ce:footnote></ce:title><ce:author-group><ce:author><ce:given-name>Akimasa</ce:given-name><ce:surname>Matsugami</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>a</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Kiyoshi</ce:given-name><ce:surname>Ouhashi</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>a</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Mayumi</ce:given-name><ce:surname>Kanagawa</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>a</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Hui</ce:given-name><ce:surname>Liu</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>a</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Sakura</ce:given-name><ce:surname>Kanagawa</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>a</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Seiichi</ce:given-name><ce:surname>Uesugi</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>a</ce:sup></ce:cross-ref><ce:cross-ref refid="COR1">*</ce:cross-ref><ce:e-address>siuesugi@ynu.ac.jp</ce:e-address></ce:author><ce:author><ce:given-name>Masato</ce:given-name><ce:surname>Katahira</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>a</ce:sup></ce:cross-ref><ce:cross-ref refid="COR1">*</ce:cross-ref><ce:e-address>masakata@ynu.ac.jp</ce:e-address></ce:author><ce:affiliation id="AFF1"><ce:label>a</ce:label><ce:textfn>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</ce:textfn></ce:affiliation><ce:correspondence id="COR1"><ce:label>*</ce:label><ce:text>Corresponding authors</ce:text></ce:correspondence></ce:author-group><ce:date-received day="26" month="6" year="2001"></ce:date-received><ce:date-revised day="27" month="8" year="2001"></ce:date-revised><ce:date-accepted day="28" month="8" year="2001"></ce:date-accepted><ce:abstract><ce:section-title>Abstract</ce:section-title><ce:abstract-sec><ce:simple-para>The structure of d(GGAGGAGGAGGA) containing four tandem repeats of a GGA triplet sequence has been determined under physiological K<ce:sup>+</ce:sup> conditions. d(GGAGGAGGAGGA) folds into an intramolecular quadruplex composed of a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad. Four G-G segments of d(GGAGGAGGAGGA) are aligned parallel with each other due to six successive turns of the main chain at each of the GGA and GAGG segments. Two quadruplexes form a dimer stabilized through a stacking interaction between the heptads of the two quadruplexes. Comparison of the structure of d(GGAGGAGGAGGA) with the reported structure of d(GGAGGAN) (N=G or T) containing two tandem repeats of the GGA triplet revealed that although the two structures resemble each other to some extent, the extension of the repeats of the GGA triplet leads to distinct structural differences: intramolecular quadruplex for 12-mer <ce:italic>versus</ce:italic> intermolecular quadruplex for 7-mer; heptad <ce:italic>versus</ce:italic> hexad in the quadruplex; and three sheared G:A base-pairs <ce:italic>versus</ce:italic> two sheared G:A base-pairs plus one A:A base-pair per quadruplex. It was also suggested that d(GGAGGAGGAGGA) forms a similar quadruplex under low salt concentration conditions. This is in contrast to the case of d(GGAGGAN) (N=G or T), which forms a duplex under low salt concentration conditions. On the basis of these results, the structure of naturally occurring GGA triplet repeat DNA is discussed.</ce:simple-para></ce:abstract-sec></ce:abstract><ce:keywords><ce:section-title>Keywords</ce:section-title><ce:keyword><ce:text>quadruplex</ce:text></ce:keyword><ce:keyword><ce:text>triplet repeat</ce:text></ce:keyword><ce:keyword><ce:text>NMR</ce:text></ce:keyword><ce:keyword><ce:text>structure</ce:text></ce:keyword><ce:keyword><ce:text>d(GGA)</ce:text></ce:keyword></ce:keywords><ce:keywords class="abr"><ce:section-title>Abbreviations</ce:section-title><ce:keyword><ce:text>NMR</ce:text><ce:keyword><ce:text>nuclear magnetic resonance</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>NOESY</ce:text><ce:keyword><ce:text>two-dimensional nuclear Overhauser effect spectroscopy</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>TOCSY</ce:text><ce:keyword><ce:text>total correlation spectroscopy</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>DQF-COSY</ce:text><ce:keyword><ce:text>double quantum filtered correlation spectroscopy</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>HSQC</ce:text><ce:keyword><ce:text>heteronuclear single quantum coherence spectroscopy</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>DSS</ce:text><ce:keyword><ce:text>sodium 2,2-dimethyl-2-silapentane-5-sulfonate</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>ppm</ce:text><ce:keyword><ce:text>parts per million</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>rmsd</ce:text><ce:keyword><ce:text>root-mean-square deviation</ce:text></ce:keyword></ce:keyword></ce:keywords></head></converted-article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>An intramolecular quadruplex of (GGA)4 triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction</title></titleInfo><titleInfo type="alternative" lang="en" contentType="CDATA"><title>An intramolecular quadruplex of (GGA)</title></titleInfo><name type="personal"><namePart type="given">Akimasa</namePart><namePart type="family">Matsugami</namePart><affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Kiyoshi</namePart><namePart type="family">Ouhashi</namePart><affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Mayumi</namePart><namePart type="family">Kanagawa</namePart><affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Hui</namePart><namePart type="family">Liu</namePart><affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Sakura</namePart><namePart type="family">Kanagawa</namePart><affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Seiichi</namePart><namePart type="family">Uesugi</namePart><affiliation>E-mail: siuesugi@ynu.ac.jp</affiliation><affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</affiliation><description>Corresponding authors</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Masato</namePart><namePart type="family">Katahira</namePart><affiliation>E-mail: siuesugi@ynu.ac.jp</affiliation><affiliation>Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku Yokohama, 240-8501, Japan</affiliation><description>Corresponding authors</description><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="Full-length article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</genre><originInfo><publisher>ELSEVIER</publisher><dateIssued encoding="w3cdtf">2001</dateIssued><dateModified encoding="w3cdtf">2001-08-27</dateModified><copyrightDate encoding="w3cdtf">2001</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><abstract lang="en">Abstract: The structure of d(GGAGGAGGAGGA) containing four tandem repeats of a GGA triplet sequence has been determined under physiological K+ conditions. d(GGAGGAGGAGGA) folds into an intramolecular quadruplex composed of a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad. Four G-G segments of d(GGAGGAGGAGGA) are aligned parallel with each other due to six successive turns of the main chain at each of the GGA and GAGG segments. Two quadruplexes form a dimer stabilized through a stacking interaction between the heptads of the two quadruplexes. Comparison of the structure of d(GGAGGAGGAGGA) with the reported structure of d(GGAGGAN) (N=G or T) containing two tandem repeats of the GGA triplet revealed that although the two structures resemble each other to some extent, the extension of the repeats of the GGA triplet leads to distinct structural differences: intramolecular quadruplex for 12-mer versus intermolecular quadruplex for 7-mer; heptad versus hexad in the quadruplex; and three sheared G:A base-pairs versus two sheared G:A base-pairs plus one A:A base-pair per quadruplex. It was also suggested that d(GGAGGAGGAGGA) forms a similar quadruplex under low salt concentration conditions. This is in contrast to the case of d(GGAGGAN) (N=G or T), which forms a duplex under low salt concentration conditions. On the basis of these results, the structure of naturally occurring GGA triplet repeat DNA is discussed.</abstract><note>Supplementary Material comprising one Table is available onIDEAL</note><note type="footnote">Edited by I. Tinoco</note><note type="content">Section title: Regular article</note><note type="content">Figure 1: Imino proton spectra of (a) d(GGAGGAGGAGGA) in the presence of 100 mM KCl, (b) d(GGAGGAGGAGGA) in the absence of KCl, (c) d(GGAGGA) in the presence of 100 mM KCl, and (d) d(GGAGGA) in the absence of KCl in H2O containing 10 mM sodium phosphate (pH 6.7), 10 mM NaCl and 3 mM NaN3 at 1°C.</note><note type="content">Figure 2: CD spectrum of d(GGAGGAGGAGGA) in H2O containing 10 mM sodium phosphate (pH 6.7), 10 mM NaCl and 3 mM NaN3 in the presence of 100 mM KCl (continuous line) and in the absence of KCl (broken line) at 5°C.</note><note type="content">Figure 3: Imino-amino NOESY cross-peaks for each G residue observed for (a) d(GGAGGAGGAGGA), (b) (IGAGGAGGAGGA), (c) d(GGAIGAGGAGGA), (d) d(GGAGGAGGAIGA), and (e) d(GGAGGAGGAGIA) in H2O containing 10 mM sodium phosphate (pH 6.7), 10 mM NaCl, 3 mM NaN3 and 100 mM KCl at 1°C; dark green, G1; brown, G2; red, G4; blue, G5; pink, G7; light green, G8; sky blue, G10; yellow, G11. The initial level of contours is set high in order to show only strong cross-peaks. Asterisks indicate cross-peaks that are not imino-amino cross-peaks. Note that the imino protons of I residues resonate in a low field region at 13.5-14.5 ppm, thus cross-peaks originating from I imino protons appear outside these Figures.</note><note type="content">Figure 4: Expansion of the NOESY spectrum with a mixing time of 200 ms of d(GGAGGAGGAGGA) in 2H2O containing 10 mM sodium phosphate (pH 6.7), 10 mM NaCl, 3 mM NaN3 and 100 mM KCl at 25°C. (a) The H6/H8-H1′ region. The lines show the H1′(i−1)-H6/H8(i)-H1′(i) connectivities, the intraresidue cross-peaks being labeled. Cross-peaks a-e are as follows (see the text for details): a, interstrand A3H2-A9H1′; b, interstrand A9H2-A3H1′; c, interstrand A6H2-A6H1′; d, interstrand G4H8-G7H1′; e, interstrand G7H8-G4H1′. (b) and (c) Expansion of the H6/H8-H1′ region symmetric to that shown in (a) with respect to the diagonal. Cross-peak a in (b) and (c) is interstrand G1H1′-G10H8 and G10H8-G1H1′, respectively. (d) The H2/H8-H2/H8 region. Cross-peaks a-c are as follows: a, A3H8-G4H8; b, A6H8-G7H8; c, A9H8-G10H8.</note><note type="content">Figure 5: (a) The 1H-31P HetCor spectrum of d(GGAGGAGGAGGA). The solution conditions are identical with those described in the legend to Figure 4. 1H and 31P assignments are indicated. (b) and (c) Expansion of the 1H-13C HSQC spectrum confirming the assignments of upfield-shifted G2H1′, and G2H4′, G5H4′ and G8H4′, respectively.</note><note type="content">Figure 6: Expansion of the NOESY spectrum with a mixing time of 200 ms, indicating NOEs originating from (a) imino and amino protons of G residues and (b) amino protons of A residues. The solution conditions are identical with those described in the legend to Figure 3. Cross-peaks a-z and aa-cc in (a) are as follows: a, G1NH-G4H8; b, G4NH-G7H8; c, G7NH-G10H8; d, G10NH-G1H8; e, G2NH-G5H8; f, G5NH-G8H8; g, G8NH-G11H8; h, G11NH-G2H8; i and i′, G1NH2-G4H8; j and j′, G4NH2-G7H8; k and k′, G7NH2-G10H8; l and l′, G10NH2-G1H8; m, G1NH-G4NH; n, G2NH-G11NH; o, G2NH-G5NH; p, G8NH-G11NH; q and q′, G1NH2-A3H8; r and r′, G4NH2-A6H8; s and s′, G7NH2-A9H8; t, t′, t# and t∗, G1NH2-A3NH2; u, u′, u# and u∗, G4NH2-A6NH2; v, v′, v# and v∗, G6NH2-A9NH2; w, G1NH2-G1NH2; x, G4NH2-G4NH2; y, G7NH2-G7NH2; z, G10NH2-G10NH2; aa, G2NH2-G2NH2; bb, G8NH2-G8NH2; cc, G11NH2-G11NH2. Cross peaks a-f in (b) are as follows: a, A3NH2-A3NH2; b, A6NH2-A6NH2; c, A9NH2-A9NH2; d and d′, A3NH2-G1H1′; e and e′, A6NH2-G4H1′; f and f′, A9NH2-G7H1′.</note><note type="content">Figure 7: Schematic representation of (a) tetrad, (b) heptad, and (c) dimer structures. Key NOEs used to construct these structures are shown by continuous lines connecting the corresponding protons (a and b) or by double-headed arrows (c). For spin diffusion through amino protons of G residues, see the text. (d) Schematic representation of one of possible structures of a DNA 24-mer, d(GGA)8.</note><note type="content">Figure 8: A plot of the logarithm of the concentration of the multimeric form of d(GGAGGAGGAGGA) (log[M]) versus the logarithm of the concentration of the single-stranded form of d(GGAGGAGGAGGA) (log[S]).</note><note type="content">Figure 9: (a) A stereo view of the superposition of the 20 final structures of the d(GGAGGAGGAGGA) dimer. The monomers are colored in yellow and green, respectively, O4′ of sugars being colored in red. The A12 residue is labeled. (b) A stereo view of the representative structure with the lowest energy. The sugar-phosphate main chains of each monomer are indicated by yellow and green tubes, respectively.</note><note type="content">Figure 10: The (a) tetrad and (b) heptad planes of the upper monomer of the representative structure shown in Figure 9(b). (c) Stacking between A12 (cyan) and the tetrad plane (white), and (d) between the tetrad (white) and heptad (magenta) planes of the upper monomer of the representative structure, the main chain being colored in yellow. (e) Stacking between the two heptad planes (magenta and orange) of each monomer of the representative structure, the main chains of each monomer being colored in yellow and green, respectively.</note><note type="content">Table 1: NMR constraints and structural statistics for the symmetric d(GGAGGAGGAGGA) dimer</note><subject><genre>article-category</genre><topic>Regular article</topic></subject><subject lang="en"><genre>Keywords</genre><topic>quadruplex</topic><topic>triplet repeat</topic><topic>NMR</topic><topic>structure</topic><topic>d(GGA)</topic></subject><subject lang="en"><genre>Abbreviations</genre><topic>NMR : nuclear magnetic resonance</topic><topic>NOESY : two-dimensional nuclear Overhauser effect spectroscopy</topic><topic>TOCSY : total correlation spectroscopy</topic><topic>DQF-COSY : double quantum filtered correlation spectroscopy</topic><topic>HSQC : heteronuclear single quantum coherence spectroscopy</topic><topic>DSS : sodium 2,2-dimethyl-2-silapentane-5-sulfonate</topic><topic>ppm : parts per million</topic><topic>rmsd : root-mean-square deviation</topic></subject><relatedItem type="host"><titleInfo><title>Journal of Molecular Biology</title></titleInfo><titleInfo type="abbreviated"><title>YJMBI</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><originInfo><publisher>ELSEVIER</publisher><dateIssued encoding="w3cdtf">2001</dateIssued></originInfo><identifier type="ISSN">0022-2836</identifier><identifier type="PII">S0022-2836(00)X0256-2</identifier><part><date>2001</date><detail type="volume"><number>313</number><caption>vol.</caption></detail><detail type="issue"><number>2</number><caption>no.</caption></detail><extent unit="issue-pages"><start>241</start><end>447</end></extent><extent unit="pages"><start>255</start><end>269</end></extent></part></relatedItem><identifier type="istex">F24D09F5DF59A6A147DE49A15DCBF4FD8C82F86F</identifier><identifier type="ark">ark:/67375/6H6-PXCHX5P0-N</identifier><identifier type="DOI">10.1006/jmbi.2001.5047</identifier><identifier type="PII">S0022-2836(01)95047-8</identifier><accessCondition type="use and reproduction" contentType="copyright">©2001 Academic Press</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-HKKZVM7B-M">elsevier</recordContentSource><recordOrigin>Academic Press, ©2001</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-PXCHX5P0-N/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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