Intrinsic hTRF1 fluorescence quenching reveals details of telomere DNA binding activity: Impact of DNA length, structure and position of telomeric repeats

Tahmaseb, Kambiz; Turchi, John J.

doi:10.1016/j.abb.2009.10.015

Archives of Biochemistry and Biophysics

2010

DOI: 10.1016/j.abb.2009.10.015

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Intrinsic hTRF1 fluorescence quenching reveals details of telomere DNA binding activity: Impact of DNA length, structure and position of telomeric repeats

Kambiz Tahmaseb¹,

John J. Turchi²

Abstract: The myb-DNA binding domain is characterized by a 3-alpha helical bundle and three repeats of this domain drive sequence specific DNA-binding of the c-myb transcription factor. Human TRF1 contains a single myb-related domain and as a homodimer, enables the sequence specific binding of telomeric DNA. In this report we provide a kinetic assessment of hTRF1 DNA binding activity. Using intrinsic fluorescence quenching we present evidence that hTRF1 binds to both telomeric and non-telomeric DNA with kinetic discrimi… Show more

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Cited by 3 publications

References 31 publications

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Biochemical analysis of the interaction between Arabidopsis thaliana AtMYB30 transcription factor and its DNA specific target site

Tavares

Terenzi

2015

J. Plant Biochem. Biotechnol.

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AtMYB30 is well known as a transcription factor involved in cell death processes during the hypersensitive response against biotic stress in Arabidopsis thaliana. Despite the relevant function played by R2R3-MYB transcription factors in the regulation of plant gene expression, limited information exists about how these proteins interact with their DNA targets, their specificity, and binding affinity. Our findings confirm the binding of a specific DNA sequence (5′-AAACCAA) to AtMYB30, binding affinities were calculated, and the effect of DNA on AtMYB30 secondary structure was evaluated. Our data shed new light on the interaction between DNA and this important member of a plant-specific transcriptional regulator family.

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Biochemical analysis of the interaction between Arabidopsis thaliana AtMYB30 transcription factor and its DNA specific target site

Tavares

Terenzi

2015

J. Plant Biochem. Biotechnol.

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Dynamic properties of water around a protein–DNA complex from molecular dynamics simulations

Sinha

Bandyopadhyay

2011

The Journal of Chemical Physics

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Formation of protein-DNA complex is an important step in regulation of genes in living organisms. One important issue in this problem is the role played by water in mediating the protein-DNA interactions. In this work, we have carried out atomistic molecular dynamics simulations to explore the heterogeneous dynamics of water molecules present in different regions around a complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. It is demonstrated that such heterogeneous water motions around the complex are correlated with the relaxation time scales of hydrogen bonds formed by those water molecules with the protein and DNA. The calculations reveal the existence of a fraction of extraordinarily restricted water molecules forming a highly rigid thin layer in between the binding motifs of the protein and DNA. It is further proved that higher rigidity of water layers around the complex originates from more frequent reformations of broken water-water hydrogen bonds. Importantly, it is found that the formation of the complex affects the transverse and longitudinal degrees of freedom of surrounding water molecules in a nonuniform manner.

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Conformational fluctuations of a protein–DNA complex and the structure and ordering of water around it

Sinha

Bandyopadhyay

2011

The Journal of Chemical Physics

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Protein-DNA binding is an important process responsible for the regulation of genetic activities in living organisms. The most crucial issue in this problem is how the protein recognizes the DNA and identifies its target base sequences. Water molecules present around the protein and DNA are also expected to play an important role in mediating the recognition process and controlling the structure of the complex. We have performed atomistic molecular dynamics simulations of an aqueous solution of the protein-DNA complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. The conformational fluctuations of the protein and DNA and the microscopic structure and ordering of water around them in the complex have been explored. In agreement with experimental studies, the calculations reveal conformational immobilization of the terminal segments of the protein on complexation. Importantly, it is discovered that both structural adaptations of the protein and DNA, and the subsequent correlation between them to bind, contribute to the net entropy loss associated with the complex formation. Further, it is found that water molecules around the DNA are more structured with significantly higher density and ordering than that around the protein in the complex.

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Intrinsic hTRF1 fluorescence quenching reveals details of telomere DNA binding activity: Impact of DNA length, structure and position of telomeric repeats

Cited by 3 publications

References 31 publications

Biochemical analysis of the interaction between Arabidopsis thaliana AtMYB30 transcription factor and its DNA specific target site

Biochemical analysis of the interaction between Arabidopsis thaliana AtMYB30 transcription factor and its DNA specific target site

Dynamic properties of water around a protein–DNA complex from molecular dynamics simulations

Conformational fluctuations of a protein–DNA complex and the structure and ordering of water around it

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