Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 One- and two-dimensional NMR studies on the conformation of DNA containing the oligo(dA)oligo(dT) tract.

Literature DB >> 3419927

One- and two-dimensional NMR studies on the conformation of DNA containing the oligo(dA)oligo(dT) tract.

M Katahira¹, H Sugeta, Y Kyogoku, S Fujii, R Fujisawa, K Tomita.

Abstract

The resonances of the imino protons and all of the non-exchangeable protons (except for H5'/H5'') of d(CGCAAAAAAGCG)d(CGCTTTTTTGCG) have been assigned by means of one- and two-dimensional NMR spectroscopies. Qualitative analyses showed that the overall structure is of the B-form, but local conformational deviations exist. The NOEs between the imino protons of thymines and H2 of adenines suggest that the A-T base pairs are propeller-twisted to almost the same degree as in crystals. A remarkable chemical shift of H1' was observed for the residue located just before the oligo(dA)oligo(dT) tract, suggesting the presence of conformational discontinuity at the junctions between the oligo(dA)oligo(dT) tract and the other portions. Analyses of cross peaks in NOESY spectra between H2 of adenines and H1' of the 3'-neighbouring residues on the complementary strand revealed that the minor groove of the oligo(dA)oligo(dT) tract is narrow and compressed gradually, from 5' to 3', along the tract.

Entities: Chemical

Mesh：

Substances：

Year: 1988 PMID： 3419927 PMCID： PMC338580 DOI： 10.1093/nar/16.17.8619

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

35 in total

1. Ring current shielding effects in nucleic acid double helices.

Authors: D B Arter; P G Schmidt
Journal: Nucleic Acids Res Date: 1976-06 Impact factor: 16.971

2. Optimised parameters for A-DNA and B-DNA.

Authors: S Arnott; D W Hukins
Journal: Biochem Biophys Res Commun Date: 1972-06-28 Impact factor: 3.575

3. Two-dimensional 1H NMR study of the lambda operator site OL1: a sequential assignment strategy and its application.

Authors: M A Weiss; D J Patel; R T Sauer; M Karplus
Journal: Proc Natl Acad Sci U S A Date: 1984-01 Impact factor: 11.205

4. Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional nuclear magnetic resonance methods.

Authors: D R Hare; D E Wemmer; S H Chou; G Drobny; B R Reid
Journal: J Mol Biol Date: 1983-12-15 Impact factor: 5.469

5. Kinematic model for B-DNA.

Authors: R E Dickerson; H R Drew
Journal: Proc Natl Acad Sci U S A Date: 1981-12 Impact factor: 11.205

6. Crystal structure analysis of a complete turn of B-DNA.

Authors: R Wing; H Drew; T Takano; C Broka; S Tanaka; K Itakura; R E Dickerson
Journal: Nature Date: 1980-10-23 Impact factor: 49.962

7. Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG.

Authors: A V Fratini; M L Kopka; H R Drew; R E Dickerson
Journal: J Biol Chem Date: 1982-12-25 Impact factor: 5.157

8. Proton nuclear magnetic resonance investigation of the conformation and dynamics in the synthetic deoxyribonucleic acid decamers d(ATATCGATAT) and d(ATATGCATAT).

Authors: J Feigon; W A Denny; W Leupin; D R Kearns
Journal: Biochemistry Date: 1983-12-06 Impact factor: 3.162

9. Proton nuclear Overhauser effect study of the structure of a deoxyoligonucleotide duplex in aqueous solution.

Authors: D G Reid; S A Salisbury; S Bellard; Z Shakked; D H Williams
Journal: Biochemistry Date: 1983-04-12 Impact factor: 3.162

10. Heteronomous DNA.

Authors: S Arnott; R Chandrasekaran; I H Hall; L C Puigjaner
Journal: Nucleic Acids Res Date: 1983-06-25 Impact factor: 16.971

15 in total

1. Sequence-dependent variation in DNA minor groove width dictates orientational preference of Hoechst 33258 in A-tract recognition: solution NMR structure of the 2:1 complex with d(CTTTTGCAAAAG)(2).

Authors: E Gavathiotis; G J Sharman; M S Searle
Journal: Nucleic Acids Res Date: 2000-02-01 Impact factor: 16.971

10. Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations.

Authors: Evgenia N Nikolova; Gavin D Bascom; Ioan Andricioaei; Hashim M Al-Hashimi
Journal: Biochemistry Date: 2012-10-18 Impact factor: 3.162

One- and two-dimensional NMR studies on the conformation of DNA containing the oligo(dA)oligo(dT) tract.

1. Ring current shielding effects in nucleic acid double helices.

2. Optimised parameters for A-DNA and B-DNA.

3. Two-dimensional 1H NMR study of the lambda operator site OL1: a sequential assignment strategy and its application.

4. Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional nuclear magnetic resonance methods.

5. Kinematic model for B-DNA.

6. Crystal structure analysis of a complete turn of B-DNA.

7. Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG.

8. Proton nuclear magnetic resonance investigation of the conformation and dynamics in the synthetic deoxyribonucleic acid decamers d(ATATCGATAT) and d(ATATGCATAT).

9. Proton nuclear Overhauser effect study of the structure of a deoxyoligonucleotide duplex in aqueous solution.

10. Heteronomous DNA.

1. Sequence-dependent variation in DNA minor groove width dictates orientational preference of Hoechst 33258 in A-tract recognition: solution NMR structure of the 2:1 complex with d(CTTTTGCAAAAG)(2).

2. Structural analysis of the binding modes of minor groove ligands comprised of disubstituted benzenes.

3. Distinct patterns in the dinucleotide nearest neighbors to G/C and A/T oligomers in eukaryotic sequences.

4. Sequence effects on local DNA topology.

5. A new model for the bending of DNAs containing the oligo(dA) tracts based on NMR observations.

6. Formation of sheared G:A base pairs in an RNA duplex modelled after ribozymes, as revealed by NMR.

7. Molecular modelling of (A4T4NN)n and (T4A4NN)n: sequence elements responsible for curvature.

8. Sequence-dependent dynamics of TATA-Box binding sites.

9. Structural basis for DNA bending.

10. Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations.