Intermediate species possessing bent DNA are present along the pathway to formation of a final TBP-TATA complex 1 1Edited by R. Ebright

Parkhurst, Kay M.; Richards, Robyn M.; Brenowitz, Michael; Parkhurst, Lawrence J.

doi:10.1006/jmbi.1999.2835

Cited by 80 publications

(229 citation statements)

References 30 publications

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“…The unlabeled complementary strand was also obtained from TriLink. These same probes have been fully characterized and used extensively in previous studies of yeast TBP-DNA binding (4,(7)(8)(9)(10)(11).…”

Section: Methodsmentioning

confidence: 99%

“…1 and references therein and Refs. [2][3][4][5][6][7][8][9][10][11]. The extent of the DNA TATA bending is TATA sequence-dependent in solution (8,9,12,13).…”

mentioning

confidence: 99%

“…The recognition mechanisms of TBP for promoter DNA and the solution structures of TBP-DNA complexes have been primary research interests in our laboratory for several years (4,(7)(8)(9)(10)(11). Our focus has been 2-fold: 1) identifying and comparing detailed kinetic models for TBP binding to consensus (TATAa/ tAa/tN) and variant promoter TATA sequences, and 2) evaluating the solution structure of the TBP-DNA TATA complex.…”

mentioning

confidence: 99%

“…Function studies conducted using three TATA sequences have shown multistep interaction mechanisms overall with concurrent binding and DNA bending (7,10,11). The associated structure studies have revealed TATA sequence-dependent DNA bend angles for yTBP-DNA complexes in solution, with bends varying from ϳ30 to ϳ80°for the seven sequences examined.…”

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confidence: 99%

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Native Human TATA-binding Protein Simultaneously Binds and Bends Promoter DNA without a Slow Isomerization Step or TFIIB Requirement

Masters

Parkhurst

Daugherty

et al. 2003

Journal of Biological Chemistry

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The association of TATA-binding protein (TBP) with promoter DNA is central to the initiation and regulation of eukaryotic protein synthesis. Our laboratory has previously conducted detailed investigations of this interaction using yeast TBP and seven consensus and variant TATA sequences. We have now investigated this key interaction using human TBP and the TATA sequence from the adenovirus major late promoter (AdMLP). Recombinant native human protein was used together with fluorescently labeled DNA, allowing real time data acquisition in solution. We find that the wild-type hTBP-DNA AdMLP reaction is characterized by high affinity (K d ‫؍‬ 5 nM), simultaneous binding and DNA bending, and rapid formation of a stable human TBP-DNA complex having DNA bent ϳ100°. These data allow, for the first time, a direct comparison of the reactions of the full-length, native human and yeast TBPs with a consensus promoter, studied under identical conditions. The general reaction characteristics are similar for the human and yeast proteins, although the details differ and the hTBP wt -induced bend is more severe. This directly measured hTBP wt -DNA AdMLP interaction differs fundamentally from a recently published hTBP wt -DNA AdMLP model characterized by low affinity ( M) binding and an unstable complex requiring either a 30-min isomerization or TFIIB to achieve DNA bending. Possible sources of these significant differences are discussed.The recognition and binding of promoter TATA sequences (DNA TATA ) 1 by the TATA-binding protein (TBP) is central to the initiation and regulation of gene transcription in eukaryotes. The importance of the TBP-DNA TATA interaction has prompted extensive biochemical and biophysical investigations, which have revealed complex binding mechanisms and dramatic TBP-induced helical distortion, including DNA TATA bending and unwinding (see Ref. 1 and references therein and Refs. 2-11). The extent of the DNA TATA bending is TATA sequence-dependent in solution (8,9,12,13). Because these collective results have been obtained using different TBPs, full-length and truncated proteins, and diverse experimental conditions, key issues relating to the behavior and structure of TBP-promoter complexes remain unresolved.The 180-residue C-terminal DNA binding domains (CTD) of the TBPs from yeast (yTBP), human (hTBP), and Arabidopsis thaliana (aTBP) are highly conserved, with greater than 80% homology and with generally conservative substitutions in the remainder. The pseudo-symmetric TBP CTD contacts the duplex along the distorted minor groove via interactions that are largely non-polar and hydrophobic. The amino acid residues involved in these DNA contacts are nearly 100% conserved, with only a single variation in which Arg-204 in hTBP changes to Lys-110 in yTBP and Lys-68 in aTBP (2). The N-terminal domain is, in contrast, heterogenous between the yeast (60 amino acids (14)) and human (159 amino acids (15)) proteins and severely truncated in the A. thaliana protein (18 amino acids (16)).How these similarities and di...

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Section: Methodsmentioning

confidence: 99%

“…1 and references therein and Refs. [2][3][4][5][6][7][8][9][10][11]. The extent of the DNA TATA bending is TATA sequence-dependent in solution (8,9,12,13).…”

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Native Human TATA-binding Protein Simultaneously Binds and Bends Promoter DNA without a Slow Isomerization Step or TFIIB Requirement

Masters

Parkhurst

Daugherty

et al. 2003

Journal of Biological Chemistry

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show abstract

“…Using this approach, we confirmed earlier results, which showed that human TBP bends the TATA DNA by 102°when evaluated with the twokink bend model. 18 It is interesting to note that yeast TBP bends TATA DNA by 80°, 41 which is significantly less than that for human TBP, indicating that human TBP and yeast TBP have different properties in binding and bending TATA DNA.…”

Section: Tbp Binding and Bending Of Tata Dna As Measured By Quantitatmentioning

confidence: 99%

TFIIA Changes the Conformation of the DNA in TBP/TATA Complexes and Increases their Kinetic Stability

Hieb

Halsey

Betterton

et al. 2007

Journal of Molecular Biology

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Photophysical Probes of DNA Sequence‐Directed Structure and Dynamics

Murphy

2001

Advances in Photochemistry

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Intermediate species possessing bent DNA are present along the pathway to formation of a final TBP-TATA complex 1 1Edited by R. Ebright

Cited by 80 publications

References 30 publications

Native Human TATA-binding Protein Simultaneously Binds and Bends Promoter DNA without a Slow Isomerization Step or TFIIB Requirement

Native Human TATA-binding Protein Simultaneously Binds and Bends Promoter DNA without a Slow Isomerization Step or TFIIB Requirement

TFIIA Changes the Conformation of the DNA in TBP/TATA Complexes and Increases their Kinetic Stability

Photophysical Probes of DNA Sequence‐Directed Structure and Dynamics

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