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Literature DB >> 11139620

Solution structure and dynamics of GCN4 cognate DNA: NMR investigations.

P Khandelwal¹, S C Panchal, P K Radha, R V Hosur.

Abstract

A 12 bp long GCN4-binding, self-complementary duplex DNA d(CATGACGTCATG)(2) has been investigated by NMR spectroscopy to study the structure and dynamics of the molecule in aqueous solution. The NMR structure of the DNA obtained using simulated annealing and iterative relaxation matrix calculations compares quite closely with the X-ray structure of ATF/CREB DNA in complex with GCN4 protein (DNA-binding domain). The DNA is also seen to be curved in the free state and this has a significant bearing on recognition by the protein. The dynamic characteristics of the molecule have been studied by (13)C relaxation measurements at natural abundance. A correlation has been observed between sequence-dependent dynamics and recognition by GCN4 protein.

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Year: 2001 PMID： 11139620 PMCID： PMC29655 DOI： 10.1093/nar/29.2.499

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

21 in total

1. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex.

Authors: T E Ellenberger; C J Brandl; K Struhl; S C Harrison
Journal: Cell Date: 1992-12-24 Impact factor: 41.582

Review 2. RNA structure and NMR spectroscopy.

Authors: G Varani; I Tinoco
Journal: Q Rev Biophys Date: 1991-11 Impact factor: 5.318

3. Selectively 13C-enriched DNA: evidence from 13C1' relaxation rate measurements of an internal dynamics sequence effect in the lac operator.

Authors: F Paquet; F Gaudin; G Lancelot
Journal: J Biomol NMR Date: 1996-10 Impact factor: 2.835

4. A test of the model-free formulas. Effects of anisotropic rotational diffusion and dimerization.

Authors: J M Schurr; H P Babcock; B S Fujimoto
Journal: J Magn Reson B Date: 1994-11

5. Dynamics in psoralen-damaged DNA by 1H-detected natural abundance 13C NMR spectroscopy.

Authors: H P Spielmann
Journal: Biochemistry Date: 1998-04-21 Impact factor: 3.162

6. Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition.

Authors: W Keller; P König; T J Richmond
Journal: J Mol Biol Date: 1995-12-08 Impact factor: 5.469

7. Polymer support oligonucleotide synthesis XVIII: use of beta-cyanoethyl-N,N-dialkylamino-/N-morpholino phosphoramidite of deoxynucleosides for the synthesis of DNA fragments simplifying deprotection and isolation of the final product.

Authors: N D Sinha; J Biernat; J McManus; H Köster
Journal: Nucleic Acids Res Date: 1984-06-11 Impact factor: 16.971

Solution structure and dynamics of GCN4 cognate DNA: NMR investigations.

1. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex.

Review 2. RNA structure and NMR spectroscopy.

3. Selectively 13C-enriched DNA: evidence from 13C1' relaxation rate measurements of an internal dynamics sequence effect in the lac operator.

4. A test of the model-free formulas. Effects of anisotropic rotational diffusion and dimerization.

5. Dynamics in psoralen-damaged DNA by 1H-detected natural abundance 13C NMR spectroscopy.

6. Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition.

7. Polymer support oligonucleotide synthesis XVIII: use of beta-cyanoethyl-N,N-dialkylamino-/N-morpholino phosphoramidite of deoxynucleosides for the synthesis of DNA fragments simplifying deprotection and isolation of the final product.

8. Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation.

9. Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme.

10. Selectively 13C-enriched DNA: dynamics of the C1'-H1' vector in d(CGCAAATTTGCG)2.

1. DNA-binding domain of GCN4 induces bending of both the ATF/CREB and AP-1 binding sites of DNA.

2. Role of microscopic flexibility in tightly curved DNA.

3. Alkaloid Escholidine and Its Interaction with DNA Structures.