Hairpin Loops Consisting of Single Adenine Residues Closed by Sheared A·A and G·G Pairs Formed by the DNA Triplets AAA and GAG: Solution Structure of the d(GTAC AAA GTAC) Hairpin
Identifieur interne : 003F68 ( Main/Exploration ); précédent : 003F67; suivant : 003F69Hairpin Loops Consisting of Single Adenine Residues Closed by Sheared A·A and G·G Pairs Formed by the DNA Triplets AAA and GAG: Solution Structure of the d(GTAC AAA GTAC) Hairpin
Auteurs : Shan-Ho Chou [États-Unis] ; Leiming Zhu [États-Unis] ; Zeming Gao [États-Unis] ; Jya-Wei Cheng [États-Unis] ; Brian R. Reid [États-Unis]Source :
- Journal of Molecular Biology [ 0022-2836 ] ; 1996.
Descripteurs français
- KwdFr :
- ADN (), ADN (génétique), Adénine (), Composition en bases nucléiques, Conformation d'acide nucléique, Modèles moléculaires, Oligodésoxyribonucléotides (), Oligodésoxyribonucléotides (génétique), Protons, Solutions, Spectroscopie par résonance magnétique, Structure moléculaire, Séquence nucléotidique.
- MESH :
English descriptors
- KwdEn :
- AAA loop, Adenine (chemistry), Base Composition, Base Sequence, DNA (chemistry), DNA (genetics), GAG loop, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Structure, NMR structure, Nucleic Acid Conformation, Oligodeoxyribonucleotides (chemistry), Oligodeoxyribonucleotides (genetics), Protons, Solutions, hairpin, sheared Pu·Pu pair.
- MESH :
- chemical , chemistry : Adenine, DNA, Oligodeoxyribonucleotides.
- chemical , genetics : DNA, Oligodeoxyribonucleotides.
- Teeft :
- Aanti, Aanti pairing, Adenine, Adenine base, Altona, Backbone, Backbone torsion angles, Backbone trace, Base Composition, Base Sequence, Biochemistry, Biol, Blommers, Case letters, Chemical shift, Chemical shifts, Cheng, Chiral, Chiral protons, Chou, Complex points, Conformation, Connectivity, Constraint, Continuous lines, Crosspeaks, Dihedral, Dihedral angle constraints, Distance geometry, Duplex, Energy minimization, Experimental data, Ganti, Gauche, Groove, Hairpin, Hairpin loop, Hairpin loops, Hairpin structure, Hairpin structures, Helix, Helix axis, Heteronuclear, Heteronuclear correlation spectrum, Imino, Loop, Loop residue, Loop residues, Magnetic Resonance Spectroscopy, Major groove, Minimization, Minor groove, Mismatch, Mismatch pairs, Models, Molecular, Molecular Structure, Natl acad, Nature struct, Noesy, Noesy spectra, Noesy spectrum, Nucleic Acid Conformation, Pairing, Phosphate group, Proton, Protons, Purine, Relaxation delay, Residue, Residue numbers, Sequential, Sharp backbone, Sheared, Sheared aanti, Sheared ganti, Sheared pair, Sheared pairing, Sheared pairs, Single adenine residues, Single adenine residues figure, Solution structure, Solutions, Spectral width, Stacks, Sugar conformation, Sugar protons, Sugar stacks, Torsion, Torsion angle, Torsion angles, Trans, Trans conformation, Trans domain, Triplet.
Abstract
Abstract: The DNA undecamers GTACAAAGTAC (AAA 11-mer) and GTAC-GAGGTAC (GAG 11-mer) have been studied in solution by high-resol ution NMR spectroscopy. Both duplexes form stable hairpins containing single deoxyadenosine loops and stems containing five base-pairs that are closed at the loop end by sheared A·A and G·C pairs, respectively. These molecules thus contain new AAA and GAG loop turn motifs. All protons, including the chiral H5′/H5″ protons of the loop residues, were assigned using NOESY, DQF-COSY and heteronuclear1H-31P COSY experiments. The backbone torsion angles were constrained using experimental data from NOE crosspeaks, three-bond1H-1H coupling constants and four-bond1H-31P coupling constants and four-bond1H-31P coupling constants. The AAA and GAG 11-mers form similar structures in solution. The detailed structure of the AAA 11-mer was determined by the combined use of NMR, distance geometry and energy minimization methods. This structure exhibits good stacking of the loop adenosine base on the closing 5A·7A sheared pair, with the 6A base stacking on the 5A base and the 6A deoxyribose stacking with the 7A base. All sugars in the AAA 11-mer hairpin adopt the typical DNA C2′-endoconformation and a sharp backbone turn occurs between residues 6A and 7A. This loop turn is brought about mainly by a change in the backbone phosphate torsion angles from ζ(g−) α(g−) to ζ(g) α(g) at the turn. The γ torsion angle of residue 7A in the closing sheared pair also changes fromgauchetotrans. In Pu1NPu2loop turns of the GCA, AAA and GAG types, the chemical shift of the H4′ proton of the loop deoxyribose depends on the nature of Pu2; this reflects the stacking of the loop sugar on the Pu2base and the different ring current effects of A or G in this position.
Url:
DOI: 10.1006/jmbi.1996.0691
Affiliations:
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Le document en format XML
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>AAA loop</term>
<term>Adenine (chemistry)</term>
<term>Base Composition</term>
<term>Base Sequence</term>
<term>DNA (chemistry)</term>
<term>DNA (genetics)</term>
<term>GAG loop</term>
<term>Magnetic Resonance Spectroscopy</term>
<term>Models, Molecular</term>
<term>Molecular Structure</term>
<term>NMR structure</term>
<term>Nucleic Acid Conformation</term>
<term>Oligodeoxyribonucleotides (chemistry)</term>
<term>Oligodeoxyribonucleotides (genetics)</term>
<term>Protons</term>
<term>Solutions</term>
<term>hairpin</term>
<term>sheared Pu·Pu pair</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term>
<term>ADN (génétique)</term>
<term>Adénine ()</term>
<term>Composition en bases nucléiques</term>
<term>Conformation d'acide nucléique</term>
<term>Modèles moléculaires</term>
<term>Oligodésoxyribonucléotides ()</term>
<term>Oligodésoxyribonucléotides (génétique)</term>
<term>Protons</term>
<term>Solutions</term>
<term>Spectroscopie par résonance magnétique</term>
<term>Structure moléculaire</term>
<term>Séquence nucléotidique</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Adenine</term>
<term>DNA</term>
<term>Oligodeoxyribonucleotides</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA</term>
<term>Oligodeoxyribonucleotides</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN</term>
<term>Oligodésoxyribonucléotides</term>
</keywords>
<keywords scheme="Teeft" xml:lang="en"><term>Aanti</term>
<term>Aanti pairing</term>
<term>Adenine</term>
<term>Adenine base</term>
<term>Altona</term>
<term>Backbone</term>
<term>Backbone torsion angles</term>
<term>Backbone trace</term>
<term>Base Composition</term>
<term>Base Sequence</term>
<term>Biochemistry</term>
<term>Biol</term>
<term>Blommers</term>
<term>Case letters</term>
<term>Chemical shift</term>
<term>Chemical shifts</term>
<term>Cheng</term>
<term>Chiral</term>
<term>Chiral protons</term>
<term>Chou</term>
<term>Complex points</term>
<term>Conformation</term>
<term>Connectivity</term>
<term>Constraint</term>
<term>Continuous lines</term>
<term>Crosspeaks</term>
<term>Dihedral</term>
<term>Dihedral angle constraints</term>
<term>Distance geometry</term>
<term>Duplex</term>
<term>Energy minimization</term>
<term>Experimental data</term>
<term>Ganti</term>
<term>Gauche</term>
<term>Groove</term>
<term>Hairpin</term>
<term>Hairpin loop</term>
<term>Hairpin loops</term>
<term>Hairpin structure</term>
<term>Hairpin structures</term>
<term>Helix</term>
<term>Helix axis</term>
<term>Heteronuclear</term>
<term>Heteronuclear correlation spectrum</term>
<term>Imino</term>
<term>Loop</term>
<term>Loop residue</term>
<term>Loop residues</term>
<term>Magnetic Resonance Spectroscopy</term>
<term>Major groove</term>
<term>Minimization</term>
<term>Minor groove</term>
<term>Mismatch</term>
<term>Mismatch pairs</term>
<term>Models, Molecular</term>
<term>Molecular Structure</term>
<term>Natl acad</term>
<term>Nature struct</term>
<term>Noesy</term>
<term>Noesy spectra</term>
<term>Noesy spectrum</term>
<term>Nucleic Acid Conformation</term>
<term>Pairing</term>
<term>Phosphate group</term>
<term>Proton</term>
<term>Protons</term>
<term>Purine</term>
<term>Relaxation delay</term>
<term>Residue</term>
<term>Residue numbers</term>
<term>Sequential</term>
<term>Sharp backbone</term>
<term>Sheared</term>
<term>Sheared aanti</term>
<term>Sheared ganti</term>
<term>Sheared pair</term>
<term>Sheared pairing</term>
<term>Sheared pairs</term>
<term>Single adenine residues</term>
<term>Single adenine residues figure</term>
<term>Solution structure</term>
<term>Solutions</term>
<term>Spectral width</term>
<term>Stacks</term>
<term>Sugar conformation</term>
<term>Sugar protons</term>
<term>Sugar stacks</term>
<term>Torsion</term>
<term>Torsion angle</term>
<term>Torsion angles</term>
<term>Trans</term>
<term>Trans conformation</term>
<term>Trans domain</term>
<term>Triplet</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>ADN</term>
<term>Adénine</term>
<term>Composition en bases nucléiques</term>
<term>Conformation d'acide nucléique</term>
<term>Modèles moléculaires</term>
<term>Oligodésoxyribonucléotides</term>
<term>Protons</term>
<term>Solutions</term>
<term>Spectroscopie par résonance magnétique</term>
<term>Structure moléculaire</term>
<term>Séquence nucléotidique</term>
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<front><div type="abstract" xml:lang="en">Abstract: The DNA undecamers GTACAAAGTAC (AAA 11-mer) and GTAC-GAGGTAC (GAG 11-mer) have been studied in solution by high-resol ution NMR spectroscopy. Both duplexes form stable hairpins containing single deoxyadenosine loops and stems containing five base-pairs that are closed at the loop end by sheared A·A and G·C pairs, respectively. These molecules thus contain new AAA and GAG loop turn motifs. All protons, including the chiral H5′/H5″ protons of the loop residues, were assigned using NOESY, DQF-COSY and heteronuclear1H-31P COSY experiments. The backbone torsion angles were constrained using experimental data from NOE crosspeaks, three-bond1H-1H coupling constants and four-bond1H-31P coupling constants and four-bond1H-31P coupling constants. The AAA and GAG 11-mers form similar structures in solution. The detailed structure of the AAA 11-mer was determined by the combined use of NMR, distance geometry and energy minimization methods. This structure exhibits good stacking of the loop adenosine base on the closing 5A·7A sheared pair, with the 6A base stacking on the 5A base and the 6A deoxyribose stacking with the 7A base. All sugars in the AAA 11-mer hairpin adopt the typical DNA C2′-endoconformation and a sharp backbone turn occurs between residues 6A and 7A. This loop turn is brought about mainly by a change in the backbone phosphate torsion angles from ζ(g−) α(g−) to ζ(g) α(g) at the turn. The γ torsion angle of residue 7A in the closing sheared pair also changes fromgauchetotrans. In Pu1NPu2loop turns of the GCA, AAA and GAG types, the chemical shift of the H4′ proton of the loop deoxyribose depends on the nature of Pu2; this reflects the stacking of the loop sugar on the Pu2base and the different ring current effects of A or G in this position.</div>
</front>
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<affiliations><list><country><li>États-Unis</li>
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<tree><country name="États-Unis"><region name="Washington (État)"><name sortKey="Chou, Shan Ho" sort="Chou, Shan Ho" uniqKey="Chou S" first="Shan-Ho" last="Chou">Shan-Ho Chou</name>
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<name sortKey="Cheng, Jya Wei" sort="Cheng, Jya Wei" uniqKey="Cheng J" first="Jya-Wei" last="Cheng">Jya-Wei Cheng</name>
<name sortKey="Gao, Zeming" sort="Gao, Zeming" uniqKey="Gao Z" first="Zeming" last="Gao">Zeming Gao</name>
<name sortKey="Reid, Brian R" sort="Reid, Brian R" uniqKey="Reid B" first="Brian R." last="Reid">Brian R. Reid</name>
<name sortKey="Zhu, Leiming" sort="Zhu, Leiming" uniqKey="Zhu L" first="Leiming" last="Zhu">Leiming Zhu</name>
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