Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs
Identifieur interne : 000E80 ( Istex/Corpus ); précédent : 000E79; suivant : 000E81Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs
Auteurs : Shan-Ho Chou ; Ko-Hsin ChinSource :
- Journal of Molecular Biology [ 0022-2836 ] ; 2001.
English descriptors
- KwdEn :
- Teeft :
- Abundant noes, Academic press, Adenosine bases, Backbone, Backbone torsion angles, Backbone torsional angles, Biochemistry, Biol, Capital letters, Characteristic noes, Chemical shift, Chemical shifts, Chou, Complex points, Consecutive figure, Consecutive mismatches, Consecutive table, Constraint, Crossstrand, Crystal structure, Curve program, Dihedral angles, Distance bounds, Distance constraints, Distance geometry, Double helix, Duplex, Duplex structure, Easier sample preparation, Exchangeable protons, Hairpin, Hairpin ribozyme, Helical, Helical axis, Helix, Heteronuclear correlation, High resolution, Human centromeres, Human signal recognition particle, Imino, Imino proton, Imino protons, Important genomic regions, Initial structures, Internal loop, Internal loop region, Internal loop sequence, Internal loops, Limited repertoire, Lower case letters, Mismatch, Molecular dynamics, Molecular dynamics calculations, National science council, Natl acad, Nature struct, Noesy, Noesy data, Noesy experiments, Nuclear overhauser effect, Nucleic acid structure, Oligomer, Oligomers, Phosphate group, Phosphorous atoms, Present study, Proton, Proton pairs, Proton resonances, Relaxation delay, Residue numbers, Salt buffer condition, Sheared, Sheared pair, Sheared pairing, Sheared type, Solution structure, Spectral width, Strong noes, Struct, Structural studies, Such noes, Such sequences, Supplementary material, Tandem, Temperature controller, Terminal residue, Torsion angles, Torsional, Torsional angle, Torsional angle constraints, Torsional angles, Tppi mode, Trans domain, Unusual motif, Unusual structures.
Abstract
Abstract: A series of DNA 21-mers containing a variety of the 4 × 4 internal loop sequence 5′-CAAG-3′/3′-ACGT-5′ were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers exhibit excellent resolution in the NMR spectra and reveal many unusual NOEs (nuclear Overhauser effect) that allow for the detailed characterization of a DNA hairpin incorporating a track of four different non-Watson-Crick base-pairs in the stem. These include a wobble C·A base-pair, a sheared A·C base-pair, a sheared A·G base-pair, and a wobble G·T base-pair. Significantly different twisting angles were observed between the base-pairs in internal loop that results with excellent intra-strand and inter-strand base stacking within the four consecutive mismatches and the surrounding canonical base-pairs. This explains why it melts at 52°C even though five out of ten base-pairs in the stem adopt non-Watson-Crick pairs. However, the 4 × 4 internal loop still fits into a B-DNA double helix very well without significant change in the backbone torsion angles; only ζ torsion angles between the tandem sheared base-pairs are changed to a great extent from the gauche− domain to the trans domain to accommodate the cross-strand base stacking in the internal loop. The observation that several consecutive non-canonical base-pairs can stably co-exist with Watson-Crick base-pairs greatly increases the limited repertoire of irregular DNA folds and reveals the possibility for unusual structural formation in the functionally important genomic regions that have potential to become single-stranded.
Url:
DOI: 10.1006/jmbi.2001.4964
Links to Exploration step
ISTEX:1E01838D487FC7263CFC8D111E6313D9381F3337Le document en format XML
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ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract: A series of DNA 21-mers containing a variety of the 4 × 4 internal loop sequence 5′-CAAG-3′/3′-ACGT-5′ were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers exhibit excellent resolution in the NMR spectra and reveal many unusual NOEs (nuclear Overhauser effect) that allow for the detailed characterization of a DNA hairpin incorporating a track of four different non-Watson-Crick base-pairs in the stem. These include a wobble C·A base-pair, a sheared A·C base-pair, a sheared A·G base-pair, and a wobble G·T base-pair. Significantly different twisting angles were observed between the base-pairs in internal loop that results with excellent intra-strand and inter-strand base stacking within the four consecutive mismatches and the surrounding canonical base-pairs. This explains why it melts at 52°C even though five out of ten base-pairs in the stem adopt non-Watson-Crick pairs. However, the 4 × 4 internal loop still fits into a B-DNA double helix very well without significant change in the backbone torsion angles; only ζ torsion angles between the tandem sheared base-pairs are changed to a great extent from the gauche− domain to the trans domain to accommodate the cross-strand base stacking in the internal loop. The observation that several consecutive non-canonical base-pairs can stably co-exist with Watson-Crick base-pairs greatly increases the limited repertoire of irregular DNA folds and reveals the possibility for unusual structural formation in the functionally important genomic regions that have potential to become single-stranded.</div></front></TEI><istex><corpusName>elsevier</corpusName><keywords><teeft><json:string>sheared</json:string><json:string>mismatch</json:string><json:string>internal loop</json:string><json:string>biol</json:string><json:string>noesy</json:string><json:string>torsional</json:string><json:string>hairpin</json:string><json:string>oligomer</json:string><json:string>imino</json:string><json:string>tandem</json:string><json:string>duplex</json:string><json:string>helix</json:string><json:string>oligomers</json:string><json:string>biochemistry</json:string><json:string>internal loop 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domain</json:string><json:string>distance geometry</json:string><json:string>torsional angles</json:string><json:string>phosphorous atoms</json:string><json:string>backbone torsion angles</json:string><json:string>present study</json:string><json:string>dihedral angles</json:string><json:string>hairpin ribozyme</json:string><json:string>unusual structures</json:string><json:string>torsional angle</json:string><json:string>academic press</json:string><json:string>high resolution</json:string><json:string>strong noes</json:string><json:string>sheared type</json:string><json:string>abundant noes</json:string><json:string>proton pairs</json:string><json:string>such sequences</json:string><json:string>important genomic regions</json:string><json:string>salt buffer condition</json:string><json:string>such noes</json:string><json:string>adenosine bases</json:string><json:string>characteristic noes</json:string><json:string>limited repertoire</json:string><json:string>imino 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mode</json:string><json:string>molecular dynamics calculations</json:string><json:string>torsional angle constraints</json:string><json:string>distance constraints</json:string><json:string>initial structures</json:string><json:string>national science council</json:string><json:string>human centromeres</json:string><json:string>internal loop sequence</json:string><json:string>structural studies</json:string><json:string>sheared pairing</json:string><json:string>heteronuclear correlation</json:string><json:string>constraint</json:string><json:string>backbone</json:string></teeft></keywords><author><json:item><name>Shan-Ho Chou</name><affiliations><json:string>E-mail: shchou@dragon.nchu.edu.tw</json:string><json:string>Institute of Biochemistry, National Chung-Hsing University, Taichung, 40227 Taiwan</json:string></affiliations></json:item><json:item><name>Ko-Hsin Chin</name><affiliations><json:string>Institute of Biochemistry, National Chung-Hsing University, Taichung, 40227 Taiwan</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>sheared G·A pair</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>sheared A·C pair</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>wobble A·C pair</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>wobble G·T pair</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>consecutive mismatches</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>DG : distance geometry</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>MD : molecular dynamics</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>NOE : nuclear Overhauser effect</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>NOESY : NOE spectroscopy</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>DQ-COSY : double-quantum correlated spectroscopy</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>ppm : parts per million</value></json:item></subject><arkIstex>ark:/67375/6H6-ZGL5GFNJ-N</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>Full-length article</json:string></originalGenre><abstract>Abstract: A series of DNA 21-mers containing a variety of the 4 × 4 internal loop sequence 5′-CAAG-3′/3′-ACGT-5′ were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers exhibit excellent resolution in the NMR spectra and reveal many unusual NOEs (nuclear Overhauser effect) that allow for the detailed characterization of a DNA hairpin incorporating a track of four different non-Watson-Crick base-pairs in the stem. These include a wobble C·A base-pair, a sheared A·C base-pair, a sheared A·G base-pair, and a wobble G·T base-pair. Significantly different twisting angles were observed between the base-pairs in internal loop that results with excellent intra-strand and inter-strand base stacking within the four consecutive mismatches and the surrounding canonical base-pairs. This explains why it melts at 52°C even though five out of ten base-pairs in the stem adopt non-Watson-Crick pairs. However, the 4 × 4 internal loop still fits into a B-DNA double helix very well without significant change in the backbone torsion angles; only ζ torsion angles between the tandem sheared base-pairs are changed to a great extent from the gauche− domain to the trans domain to accommodate the cross-strand base stacking in the internal loop. The observation that several consecutive non-canonical base-pairs can stably co-exist with Watson-Crick base-pairs greatly increases the limited repertoire of irregular DNA folds and reveals the possibility for unusual structural formation in the functionally important genomic regions that have potential to become single-stranded.</abstract><qualityIndicators><score>9.88</score><pdfWordCount>7176</pdfWordCount><pdfCharCount>42186</pdfCharCount><pdfVersion>1.3</pdfVersion><pdfPageCount>13</pdfPageCount><pdfPageSize>595 x 842 pts (A4)</pdfPageSize><refBibsNative>true</refBibsNative><abstractWordCount>240</abstractWordCount><abstractCharCount>1655</abstractCharCount><keywordCount>12</keywordCount></qualityIndicators><title>Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs</title><pmid><json:string>11575931</json:string></pmid><pii><json:string>S0022-2836(01)94964-2</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)X0243-4</json:string></pii><volume>312</volume><issue>4</issue><pages><first>769</first><last>781</last></pages><genre><json:string>journal</json:string></genre></host><namedEntities><unitex><date><json:string>2001</json:string><json:string>1000</json:string><json:string>5300</json:string></date><geogName></geogName><orgName><json:string>National Science Council, Taiwan</json:string><json:string>National Science Council</json:string><json:string>Chung-Zhen Agricultural Foundation Society of Taiwan, ROC</json:string><json:string>Outstanding Research Award</json:string><json:string>MSI, Inc.</json:string><json:string>MSI Inc.</json:string><json:string>NSC</json:string></orgName><orgName_funder><json:string>NSC</json:string></orgName_funder><orgName_provider></orgName_provider><persName><json:string>Material</json:string><json:string>Lavery</json:string></persName><placeName></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-ZGL5GFNJ-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.2001.4964</json:string></doi><id>1E01838D487FC7263CFC8D111E6313D9381F3337</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-ZGL5GFNJ-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-ZGL5GFNJ-N/bundle.zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/ark:/67375/6H6-ZGL5GFNJ-N/fulltext.tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main" xml:lang="en">Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs</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 for this paper comprising one Table and two Figures is available onIDEAL</note><note>Edited by I. Tinoco</note><note type="content">Section title: Regular article</note><note type="content">Figure 1: (a) The series of d(CCCAAGTCCACCGGATGCAGG) hairpin sequences investigated in this study, and their abbreviated designations. The mismatched base-pairs are connected with filled black circles while the canonical base-pairs open circles. b) The one-dimensional imino, amino and aromatic proton NMR spectra of the 4 M_1, 4 M_2, 4 M_3, and 4 M_4 hairpins at 0°C and under a low salt buffer condition (pH 6.8). Assignments of the imino protons were made from the NOESY experiments in 10% 2H2O/90% H2O solution and were marked by capital letters.</note><note type="content">Figure 3: The H-bonding schemes for the four consecutive mismatches of the 4 × 4 internal loop of the 4 M oligomers. The wobble G6·T16 and sheared A5·G17 pairs were bonded through two H-bonds, while the sheared A4·C18 and wobble C3·A19 pairs were bonded only through one H-bond under a neutral pH condition (indicated by dotted lines). The critical NOEs used to identify such non-canonical base-pairs are indicated by curved arrows.</note><note type="content">Figure 2: The exchangeable proton to base/H1′ NOESY in H2O with a mixing time of 120 ms. The G-imino and T-imino to their paired C-NH2 and A-NH2 cross-peaks are bracketed and labeled with C or A residue numbers in the upper left corner. Some important NOE cross-peaks are indicated by lower case letters, i.e. a, T16H3-G6H1; b, T16H3-G17H1; c, T16H3-T7H3; d, G6H1-T7H3; e, G6H1-G6NH2; f, T16H3-A15H2; g, G6H1-A15H2; h, T16H3-A5H2; i, G6H1-A5H2; j, T16H3-G17NH2b; k, G17NH2b-G17NH2n; l, G17H1-G17NH2n; m, G17H1-G17NH2b; n, G17H1-A4H1′; o, G17H1-A4H8; p, G17NH2b-A4H1′; q, G17NH2b-A5H8.</note><note type="content">Figure 4: The expanded base-H1′/H3′ NOESY in 2H2O of the 4 M_1 21-mer hairpin at 20°C and at a mixing time of 600 ms. The (n)CH5-(n)CH6 cross-peaks are drawn in a gray circle and connected to their respective (n)CH5-(n−1)base cross-peaks by continuous horizontal arrows. The H8/H6-H1′ connectivity is traced by continuous dotted lines in the bottom part of the Figure, and those of H8/H6-H3′ in the upper part of the Figure, with the intra-nucleotide base-sugar NOEs labeled with the residue numbers. The chemical shifts of the five AH2 are drawn in vertical dotted lines. Some important NOEs are indicated by lower case letters, namely: a, A15H2-A15H1′; b, A15H2-C8H1′; c, A15H2-T16H1′; d, A19H2-A19H1′; e, A19H2-G20H1′; f, A5H2-A5H1′; g, A5H2-C18H1′; h, A4H2-A4H1′; i, A4H2-G17H1′; j, A4H2-C18H5; k, A4H2-C3H5; l, A10H2-A10H1′; m, A10H2-C12H5; n, A10H2-C9H5. Several absent NOEs are marked by x. The chemical shift of the C9H3′ proton happens to be coincident with the water signal that was saturated during the experiment and the C9H3′ signal is therefore undetectable.</note><note type="content">Figure 5: The scheme of characteristic NOEs for the 5′-(CAAG)/(ACGT)-5′ 4 × 4 internal loop motif in the 4 M_1 oligomer. The cross-strand A4/G17 and C18/A5 stacks are clearly established from the abundant NOEs between the A4-G17 and C18-A5 residues.</note><note type="content">Figure 6: Superimposed picture of the wide-eye stereo view perpendicular to the helical axis of the stem of the 4 M_1 oligomer produced by embedding from and refining against the distance bounds (a) and one of the selected final structures further refined by molecular dynamics (b). The polarized distribution of bases in the 4 M_1 due to the dramatically different base twisting and stacking profile in the internal loop region is shown in (c). The different oval shape of the duplex and the two indents in the backbone tracing due to the different BII backbone phosphate torsional angles adopted within the tandem sheared base-pairs (marked by arrows) are also obvious in this Figure. (d) The stereo picture of the 5′-(C2C3A4A5G6T7)/(G20A19C18G17T16A15)-5′ segment from the view perpendicular to the helical axis. The cross-strand A4/G17 and A5/C18 stacks are clearly revealed in this Figure.</note><note type="content">Figure 7: Projections down the helical axis of the nearest-neighbor stacking in the 4 × 4 internal loop region. The upper base-pairs toward the viewer are drawn in light blue while the bottom base-pairs away from the viewer in deep blue. The H-bonds are drawn in dotted lines. Top panel shows the intra-strand stacking of the sheared A4·C18 base-pair upon wobble C3·A19 base-pair; middle panel shows the cross-strand stacking of the sheared A5·G17 pair upon sheared A4·C18 pair; and the bottom panel shows the intra-strand stacking of the wobble G6·T16 pair upon the sheared A5·G17 pair. Note the almost perfect stacking of the six-membered rings on top of each other in the Figure.</note><note type="content">Table 1: Structural Statistics for the 5′-d(CCCAAGTCCACCGGATGCAGG)-3′ hairpin</note><note type="content">Table 2: Backbone torsion angles (deg.) in the 5′-d(CCCAAGTCCACCGGATGCAGG)-3′ hairpin</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs</title><author xml:id="author-0000"><persName><forename type="first">Shan-Ho</forename><surname>Chou</surname></persName><email>shchou@dragon.nchu.edu.tw</email><note type="correspondence"><p>Corresponding author</p></note><affiliation>Institute of Biochemistry, National Chung-Hsing University, Taichung, 40227 Taiwan</affiliation></author><author xml:id="author-0001"><persName><forename type="first">Ko-Hsin</forename><surname>Chin</surname></persName><affiliation>Institute of Biochemistry, National Chung-Hsing University, Taichung, 40227 Taiwan</affiliation></author><idno type="istex">1E01838D487FC7263CFC8D111E6313D9381F3337</idno><idno type="ark">ark:/67375/6H6-ZGL5GFNJ-N</idno><idno type="DOI">10.1006/jmbi.2001.4964</idno><idno type="PII">S0022-2836(01)94964-2</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)X0243-4</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="2001"></date><biblScope unit="volume">312</biblScope><biblScope unit="issue">4</biblScope><biblScope unit="page" from="769">769</biblScope><biblScope unit="page" to="781">781</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: A series of DNA 21-mers containing a variety of the 4 × 4 internal loop sequence 5′-CAAG-3′/3′-ACGT-5′ were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers exhibit excellent resolution in the NMR spectra and reveal many unusual NOEs (nuclear Overhauser effect) that allow for the detailed characterization of a DNA hairpin incorporating a track of four different non-Watson-Crick base-pairs in the stem. These include a wobble C·A base-pair, a sheared A·C base-pair, a sheared A·G base-pair, and a wobble G·T base-pair. Significantly different twisting angles were observed between the base-pairs in internal loop that results with excellent intra-strand and inter-strand base stacking within the four consecutive mismatches and the surrounding canonical base-pairs. This explains why it melts at 52°C even though five out of ten base-pairs in the stem adopt non-Watson-Crick pairs. However, the 4 × 4 internal loop still fits into a B-DNA double helix very well without significant change in the backbone torsion angles; only ζ torsion angles between the tandem sheared base-pairs are changed to a great extent from the gauche− domain to the trans domain to accommodate the cross-strand base stacking in the internal loop. The observation that several consecutive non-canonical base-pairs can stably co-exist with Watson-Crick base-pairs greatly increases the limited repertoire of irregular DNA folds and reveals the possibility for unusual structural formation in the functionally important genomic regions that have potential to become single-stranded.</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>sheared G·A pair</term></item><item><term>sheared A·C pair</term></item><item><term>wobble A·C pair</term></item><item><term>wobble G·T pair</term></item><item><term>consecutive mismatches</term></item></list></keywords></textClass><textClass xml:lang="en"><keywords scheme="keyword"><list><head>Abbreviations</head><item><term>DG</term><term>distance geometry</term></item><item><term>MD</term><term>molecular dynamics</term></item><item><term>NOE</term><term>nuclear Overhauser effect</term></item><item><term>NOESY</term><term>NOE spectroscopy</term></item><item><term>DQ-COSY</term><term>double-quantum correlated spectroscopy</term></item><item><term>ppm</term><term>parts per million</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2001-07-25">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-ZGL5GFNJ-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="gr4" NDATA="IMAGE" name="GR4"></istex:entity><istex:entity SYSTEM="gr5" NDATA="IMAGE" name="GR5"></istex:entity><istex:entity SYSTEM="gr6" NDATA="IMAGE" name="GR6"></istex:entity><istex:entity SYSTEM="gr7" NDATA="IMAGE" name="GR7"></istex:entity><istex:entity SYSTEM="mmc1" NDATA="APPLICATION" name="applic1"></istex:entity><istex:entity SYSTEM="mmc2" NDATA="APPLICATION" name="applic2"></istex:entity><istex:entity SYSTEM="mmc3" NDATA="APPLICATION" name="applic3"></istex:entity></istex:docType><istex:document><converted-article version="4.5.2" docsubtype="fla" xml:lang="en"><item-info><jid>YJMBI</jid><aid>94964</aid><ce:pii>S0022-2836(01)94964-2</ce:pii><ce:doi>10.1006/jmbi.2001.4964</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 for this paper comprising one Table and two Figures is available on<ce:inter-ref xlink:href="doi:10.1006/jmbi.2001.4964">IDEAL</ce:inter-ref></ce:note-para></ce:article-footnote><ce:dochead><ce:textfn>Regular article</ce:textfn></ce:dochead><ce:title>Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs<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>Shan-Ho</ce:given-name><ce:surname>Chou</ce:surname><ce:cross-ref refid="COR1">*</ce:cross-ref><ce:cross-ref refid="AFF1"><ce:sup>a</ce:sup></ce:cross-ref><ce:e-address>shchou@dragon.nchu.edu.tw</ce:e-address></ce:author><ce:author><ce:given-name>Ko-Hsin</ce:given-name><ce:surname>Chin</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>a</ce:sup></ce:cross-ref></ce:author><ce:affiliation id="AFF1"><ce:label>a</ce:label><ce:textfn>Institute of Biochemistry, National Chung-Hsing University, Taichung, 40227 Taiwan</ce:textfn></ce:affiliation><ce:correspondence id="COR1"><ce:label>*</ce:label><ce:text>Corresponding author</ce:text></ce:correspondence></ce:author-group><ce:date-received day="10" month="5" year="2001"></ce:date-received><ce:date-revised day="25" month="7" year="2001"></ce:date-revised><ce:date-accepted day="27" month="7" year="2001"></ce:date-accepted><ce:abstract><ce:section-title>Abstract</ce:section-title><ce:abstract-sec><ce:simple-para>A series of DNA 21-mers containing a variety of the 4 × 4 internal loop sequence 5′-CAAG-3′/3′-ACGT-5′ were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers exhibit excellent resolution in the NMR spectra and reveal many unusual NOEs (nuclear Overhauser effect) that allow for the detailed characterization of a DNA hairpin incorporating a track of four different non-Watson-Crick base-pairs in the stem. These include a wobble C·A base-pair, a sheared A·C base-pair, a sheared A·G base-pair, and a wobble G·T base-pair. Significantly different twisting angles were observed between the base-pairs in internal loop that results with excellent intra-strand and inter-strand base stacking within the four consecutive mismatches and the surrounding canonical base-pairs. This explains why it melts at 52°C even though five out of ten base-pairs in the stem adopt non-Watson-Crick pairs. However, the 4 × 4 internal loop still fits into a <ce:italic>B</ce:italic>-DNA double helix very well without significant change in the backbone torsion angles; only ζ torsion angles between the tandem sheared base-pairs are changed to a great extent from the <ce:italic>gauche</ce:italic><ce:sup>−</ce:sup> domain to the <ce:italic>trans</ce:italic> domain to accommodate the cross-strand base stacking in the internal loop. The observation that several consecutive non-canonical base-pairs can stably co-exist with Watson-Crick base-pairs greatly increases the limited repertoire of irregular DNA folds and reveals the possibility for unusual structural formation in the functionally important genomic regions that have potential to become single-stranded.</ce:simple-para></ce:abstract-sec></ce:abstract><ce:keywords><ce:section-title>Keywords</ce:section-title><ce:keyword><ce:text>sheared G·A pair</ce:text></ce:keyword><ce:keyword><ce:text>sheared A·C pair</ce:text></ce:keyword><ce:keyword><ce:text>wobble A·C pair</ce:text></ce:keyword><ce:keyword><ce:text>wobble G·T pair</ce:text></ce:keyword><ce:keyword><ce:text>consecutive mismatches</ce:text></ce:keyword></ce:keywords><ce:keywords class="abr"><ce:section-title>Abbreviations</ce:section-title><ce:keyword><ce:text>DG</ce:text><ce:keyword><ce:text>distance geometry</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>MD</ce:text><ce:keyword><ce:text>molecular dynamics</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>NOE</ce:text><ce:keyword><ce:text>nuclear Overhauser effect</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>NOESY</ce:text><ce:keyword><ce:text>NOE spectroscopy</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>DQ-COSY</ce:text><ce:keyword><ce:text>double-quantum correlated spectroscopy</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:keywords></head></converted-article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs</title></titleInfo><titleInfo type="alternative" lang="en" contentType="CDATA"><title>Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs</title></titleInfo><name type="personal"><namePart type="given">Shan-Ho</namePart><namePart type="family">Chou</namePart><affiliation>E-mail: shchou@dragon.nchu.edu.tw</affiliation><affiliation>Institute of Biochemistry, National Chung-Hsing University, Taichung, 40227 Taiwan</affiliation><description>Corresponding author</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Ko-Hsin</namePart><namePart type="family">Chin</namePart><affiliation>Institute of Biochemistry, National Chung-Hsing University, Taichung, 40227 Taiwan</affiliation><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">2001-07-25</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: A series of DNA 21-mers containing a variety of the 4 × 4 internal loop sequence 5′-CAAG-3′/3′-ACGT-5′ were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers exhibit excellent resolution in the NMR spectra and reveal many unusual NOEs (nuclear Overhauser effect) that allow for the detailed characterization of a DNA hairpin incorporating a track of four different non-Watson-Crick base-pairs in the stem. These include a wobble C·A base-pair, a sheared A·C base-pair, a sheared A·G base-pair, and a wobble G·T base-pair. Significantly different twisting angles were observed between the base-pairs in internal loop that results with excellent intra-strand and inter-strand base stacking within the four consecutive mismatches and the surrounding canonical base-pairs. This explains why it melts at 52°C even though five out of ten base-pairs in the stem adopt non-Watson-Crick pairs. However, the 4 × 4 internal loop still fits into a B-DNA double helix very well without significant change in the backbone torsion angles; only ζ torsion angles between the tandem sheared base-pairs are changed to a great extent from the gauche− domain to the trans domain to accommodate the cross-strand base stacking in the internal loop. The observation that several consecutive non-canonical base-pairs can stably co-exist with Watson-Crick base-pairs greatly increases the limited repertoire of irregular DNA folds and reveals the possibility for unusual structural formation in the functionally important genomic regions that have potential to become single-stranded.</abstract><note>Supplementary Material for this paper comprising one Table and two Figures 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: (a) The series of d(CCCAAGTCCACCGGATGCAGG) hairpin sequences investigated in this study, and their abbreviated designations. The mismatched base-pairs are connected with filled black circles while the canonical base-pairs open circles. b) The one-dimensional imino, amino and aromatic proton NMR spectra of the 4 M_1, 4 M_2, 4 M_3, and 4 M_4 hairpins at 0°C and under a low salt buffer condition (pH 6.8). Assignments of the imino protons were made from the NOESY experiments in 10% 2H2O/90% H2O solution and were marked by capital letters.</note><note type="content">Figure 3: The H-bonding schemes for the four consecutive mismatches of the 4 × 4 internal loop of the 4 M oligomers. The wobble G6·T16 and sheared A5·G17 pairs were bonded through two H-bonds, while the sheared A4·C18 and wobble C3·A19 pairs were bonded only through one H-bond under a neutral pH condition (indicated by dotted lines). The critical NOEs used to identify such non-canonical base-pairs are indicated by curved arrows.</note><note type="content">Figure 2: The exchangeable proton to base/H1′ NOESY in H2O with a mixing time of 120 ms. The G-imino and T-imino to their paired C-NH2 and A-NH2 cross-peaks are bracketed and labeled with C or A residue numbers in the upper left corner. Some important NOE cross-peaks are indicated by lower case letters, i.e. a, T16H3-G6H1; b, T16H3-G17H1; c, T16H3-T7H3; d, G6H1-T7H3; e, G6H1-G6NH2; f, T16H3-A15H2; g, G6H1-A15H2; h, T16H3-A5H2; i, G6H1-A5H2; j, T16H3-G17NH2b; k, G17NH2b-G17NH2n; l, G17H1-G17NH2n; m, G17H1-G17NH2b; n, G17H1-A4H1′; o, G17H1-A4H8; p, G17NH2b-A4H1′; q, G17NH2b-A5H8.</note><note type="content">Figure 4: The expanded base-H1′/H3′ NOESY in 2H2O of the 4 M_1 21-mer hairpin at 20°C and at a mixing time of 600 ms. The (n)CH5-(n)CH6 cross-peaks are drawn in a gray circle and connected to their respective (n)CH5-(n−1)base cross-peaks by continuous horizontal arrows. The H8/H6-H1′ connectivity is traced by continuous dotted lines in the bottom part of the Figure, and those of H8/H6-H3′ in the upper part of the Figure, with the intra-nucleotide base-sugar NOEs labeled with the residue numbers. The chemical shifts of the five AH2 are drawn in vertical dotted lines. Some important NOEs are indicated by lower case letters, namely: a, A15H2-A15H1′; b, A15H2-C8H1′; c, A15H2-T16H1′; d, A19H2-A19H1′; e, A19H2-G20H1′; f, A5H2-A5H1′; g, A5H2-C18H1′; h, A4H2-A4H1′; i, A4H2-G17H1′; j, A4H2-C18H5; k, A4H2-C3H5; l, A10H2-A10H1′; m, A10H2-C12H5; n, A10H2-C9H5. Several absent NOEs are marked by x. The chemical shift of the C9H3′ proton happens to be coincident with the water signal that was saturated during the experiment and the C9H3′ signal is therefore undetectable.</note><note type="content">Figure 5: The scheme of characteristic NOEs for the 5′-(CAAG)/(ACGT)-5′ 4 × 4 internal loop motif in the 4 M_1 oligomer. The cross-strand A4/G17 and C18/A5 stacks are clearly established from the abundant NOEs between the A4-G17 and C18-A5 residues.</note><note type="content">Figure 6: Superimposed picture of the wide-eye stereo view perpendicular to the helical axis of the stem of the 4 M_1 oligomer produced by embedding from and refining against the distance bounds (a) and one of the selected final structures further refined by molecular dynamics (b). The polarized distribution of bases in the 4 M_1 due to the dramatically different base twisting and stacking profile in the internal loop region is shown in (c). The different oval shape of the duplex and the two indents in the backbone tracing due to the different BII backbone phosphate torsional angles adopted within the tandem sheared base-pairs (marked by arrows) are also obvious in this Figure. (d) The stereo picture of the 5′-(C2C3A4A5G6T7)/(G20A19C18G17T16A15)-5′ segment from the view perpendicular to the helical axis. The cross-strand A4/G17 and A5/C18 stacks are clearly revealed in this Figure.</note><note type="content">Figure 7: Projections down the helical axis of the nearest-neighbor stacking in the 4 × 4 internal loop region. The upper base-pairs toward the viewer are drawn in light blue while the bottom base-pairs away from the viewer in deep blue. The H-bonds are drawn in dotted lines. Top panel shows the intra-strand stacking of the sheared A4·C18 base-pair upon wobble C3·A19 base-pair; middle panel shows the cross-strand stacking of the sheared A5·G17 pair upon sheared A4·C18 pair; and the bottom panel shows the intra-strand stacking of the wobble G6·T16 pair upon the sheared A5·G17 pair. Note the almost perfect stacking of the six-membered rings on top of each other in the Figure.</note><note type="content">Table 1: Structural Statistics for the 5′-d(CCCAAGTCCACCGGATGCAGG)-3′ hairpin</note><note type="content">Table 2: Backbone torsion angles (deg.) in the 5′-d(CCCAAGTCCACCGGATGCAGG)-3′ hairpin</note><subject><genre>article-category</genre><topic>Regular article</topic></subject><subject lang="en"><genre>Keywords</genre><topic>sheared G·A pair</topic><topic>sheared A·C pair</topic><topic>wobble A·C pair</topic><topic>wobble G·T pair</topic><topic>consecutive mismatches</topic></subject><subject lang="en"><genre>Abbreviations</genre><topic>DG : distance geometry</topic><topic>MD : molecular dynamics</topic><topic>NOE : nuclear Overhauser effect</topic><topic>NOESY : NOE spectroscopy</topic><topic>DQ-COSY : double-quantum correlated spectroscopy</topic><topic>ppm : parts per million</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)X0243-4</identifier><part><date>2001</date><detail type="volume"><number>312</number><caption>vol.</caption></detail><detail type="issue"><number>4</number><caption>no.</caption></detail><extent unit="issue-pages"><start>583</start><end>896</end></extent><extent unit="pages"><start>769</start><end>781</end></extent></part></relatedItem><identifier type="istex">1E01838D487FC7263CFC8D111E6313D9381F3337</identifier><identifier type="ark">ark:/67375/6H6-ZGL5GFNJ-N</identifier><identifier type="DOI">10.1006/jmbi.2001.4964</identifier><identifier type="PII">S0022-2836(01)94964-2</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-ZGL5GFNJ-N/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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