Footprinting and Missing Nucleoside Analysis of Transcription Factor–DNA Complexes

2011 ◽  
pp. 259-275 ◽  
Author(s):  
Ivana L. Viola ◽  
Daniel H. Gonzalez
Keyword(s):  
Transcription Factor ◽  
Dna Complexes

Inhibition of transcription factor assembly and structural stability on mitoxantrone binding with DNA

2010 ◽  
Vol 30 (5) ◽  
pp. 331-340 ◽  
Author(s):  
Shahper N. Khan ◽  
Mohd Danishuddin ◽  
Asad U. Khan
Keyword(s):  
Transcription Factor ◽  
Binding Mode ◽  
Cd Spectroscopy ◽  
Sequence Specificity ◽  
Mobility Shift ◽  
Dna Complexes ◽  
Naked Dna ◽  
Plasmid Nicking Assay ◽  
Modelling Studies ◽  
Mobility Shift Assay

MTX (mitoxantrone) is perhaps the most promising drug used in the treatment of various malignancies. Comprehensive literature on the therapeutics has indicated it to be the least toxic in its class, although its mechanism of action is still not well defined. In the present study, we have evaluated the associated binding interactions of MTX with naked DNA. The mechanism of MTX binding with DNA was elucidated by steady-state fluorescence and a static-type quenching mechanism is suggested for this interaction. Thermodynamic parameters from van 't Hoff plots showed that the interaction of these drugs with DNA is an entropically driven phenomenon. The binding mode was expounded by attenuance measurements and competitive binding of a known intercalator. Sequence specificity of these drug–DNA complexes was analysed by FTIR (Fourier-transform infrared) spectroscopy and molecular modelling studies. CD spectroscopy and the plasmid nicking assay showed that the binding of this drug with DNA results in structural and conformational perturbations. EMSA (electrophoretic mobility-shift assay) results showed that these drug–DNA complexes prevent the binding of octamer TF (transcription factor) to DNA. In summary, the study implicates MTX-induced conformational instability and transcription inhibition on DNA binding.

scholarly journals 27 Analysis of DNA deformations in transcription factor–DNA complexes

2015 ◽  
Vol 33 (sup1) ◽  
pp. 16-16
Author(s):  
Jared Sagendorf ◽  
Helen M. Berman ◽  
Remo Rohs
Keyword(s):  
Transcription Factor ◽  
Dna Complexes

Inhibiting transcription factor/DNA complexes using fluorescent microgonotropens (FMGTs)

2002 ◽  
Vol 1574 (1) ◽  
pp. 100-108 ◽  
Author(s):  
Christine M White ◽  
Alexander L Satz ◽  
Loretta S Gawron ◽  
Thomas C Bruice ◽  
Terry A Beerman
Keyword(s):  
Transcription Factor ◽  
Dna Complexes

scholarly journals Inhibition of transcription factor-DNA complexes and gene expression by a microgonotropen

2001 ◽  
Vol 98 (19) ◽  
pp. 10590-10595 ◽  
Author(s):  
C. M. White ◽  
A. L. Satz ◽  
T. C. Bruice ◽  
T. A. Beerman
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Dna Complexes

scholarly journals Testing for DNA Tracking by MOT1, a SNF2/SWI2 Protein Family Member

1999 ◽  
Vol 19 (1) ◽  
pp. 412-423 ◽  
Author(s):  
David T. Auble ◽  
Susanne M. Steggerda
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Family Member ◽  
Binding Sites ◽  
Atp Hydrolysis ◽  
Tata Binding Protein ◽  
Protein Family ◽  
Dna Complexes ◽  
Dna Templates ◽  
Dependent Interaction

ABSTRACT Proteins in the SNF2/SWI2 family use ATP hydrolysis to catalyze rearrangements in diverse protein-DNA complexes. How ATP hydrolysis is coupled to these rearrangements is unknown, however. One attractive model is that these ATPases are ATP-dependent DNA-tracking enzymes. This idea was tested for the SNF2/SWI2 protein family member MOT1. MOT1 is an essential Saccharomyces cerevisiae transcription factor that uses ATP to dissociate TATA binding protein (TBP) from DNA. By using a series of DNA templates with one or two TATA boxes in combination with binding sites for heterologous DNA binding “roadblock” proteins, the ability of MOT1 to track along DNA was assayed. The results demonstrate that, following ATP-dependent TBP-DNA dissociation, MOT1 dissociates rapidly from the DNA by a mechanism that does not require a DNA end. Template commitment footprinting experiments support the conclusion that ATP-dependent DNA tracking by MOT1 does not occur. These results support a model in which MOT1 drives TBP-DNA dissociation by a mechanism that involves a transient, ATP-dependent interaction with TBP-DNA which does not involve ATP-dependent DNA tracking.

scholarly journals Domains of the Brf component of RNA polymerase III transcription factor IIIB (TFIIIB): functions in assembly of TFIIIB-DNA complexes and recruitment of RNA polymerase to the promoter.

1997 ◽  
Vol 17 (9) ◽  
pp. 5299-5306 ◽  
Author(s):  
G A Kassavetis ◽  
C Bardeleben ◽  
A Kumar ◽  
E Ramirez ◽  
E P Geiduschek
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase ◽  
Binding Protein ◽  
Rna Polymerase Iii ◽  
Tata Binding Protein ◽  
Terminal Segment ◽  
Dna Complexes ◽  
Polymerase Iii ◽  
Transcription Factor Iiib ◽  
Derivatives Of

Saccharomyces cerevisiae transcription factor IIIB (TFIIIB) is composed of three subunits: the TATA-binding protein, the TFIIB-related protein Brf, and B". TFIIIB, which is brought to RNA polymerase III-transcribed genes indirectly through interaction with DNA-bound TFIIIC or directly through DNA recognition by the TATA-binding protein, in turn recruits RNA polymerase III to the promoter. N-terminally deleted derivatives of Brf have been examined for their ability to interact with DNA-bound TFIIIC and with the other components of TFIIIB and for participation in transcription. Brf(165-596), lacking 164 N-proximal TFIIB-homologous amino acids, is competent to participate in the assembly of TFIIIB-DNA complexes and in TFIIIC-independent transcription. Even deletion of the entire TFIIB-homologous half of the protein, as in Brf(317-596) and Brf(352-596), allows some interaction with DNA-bound TBP and with the B" component of TFIIIB to be retained. The function of Brf(165-596) in transcription has also been examined in the context of B" with small internal deletions. The ability of Brf with this sizable N-terminal segment deleted to function in TFIIIC-independent transcription requires segments of B" that are individually indispensable although required on an either/or basis, in the context of complete Brf. These findings suggest a functional complementarity and reciprocity between the Brf and B" components of TFIIIB.

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