Fluorescence Intensity Fluctuations of Individual Labeled DNA Fragments and a DNA Binding Protein in Solution at the Single Molecule Level:  A Comparison of Photobleaching, Diffusion, and Binding Dynamics

2000 ◽  
Vol 104 (6) ◽  
pp. 1382-1390 ◽  
Author(s):  
Douglas C. Daniel ◽  
Martin Thompson ◽  
Neal W. Woodbury
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Fluorescence Intensity ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Dna Fragments ◽  
Single Molecule Level ◽  
Intensity Fluctuations

scholarly journals Single-molecule DREEM imaging reveals DNA wrapping around human mitochondrial single-stranded DNA binding protein

2018 ◽  
Vol 46 (21) ◽  
pp. 11287-11302 ◽  
Author(s):  
Parminder Kaur ◽  
Matthew J Longley ◽  
Hai Pan ◽  
Hong Wang ◽  
William C Copeland
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Single Stranded Dna ◽  
Dna Wrapping

scholarly journals Switch-like control of helicase processivity by single-stranded DNA binding protein

2020 ◽  
Author(s):  
Barbara Stekas ◽  
Masayoshi Honda ◽  
Maria Spies ◽  
Yann R. Chemla
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Molecular Mechanisms ◽  
Binding Protein ◽  
Optical Trap ◽  
Dna Binding Protein ◽  
Single Stranded Dna ◽  
Associated Proteins ◽  
Underlying Mechanisms ◽  
Xpd Helicase

Helicases utilize the energy of NTP hydrolysis to translocate along single-stranded nucleic acids (NA) and unwind the duplex. In the cell, helicases function in the context of other NA-associated proteins which regulate helicase function. For example, single-stranded DNA binding proteins are known to enhance helicase activity, although the underlying mechanisms remain largely unknown. F. acidarmanus XPD helicase serves as a model for understanding the molecular mechanisms of Superfamily 2B helicases, and previous work has shown that its activity is enhanced by the cognate single-stranded DNA binding protein RPA2. Here, single-molecule optical trap measurements of the unwinding activity of a single XPD helicase in the presence of RPA2 reveal a mechanism in which XPD interconverts between two states with different processivities and transient RPA2 interactions stabilize the more processive state, activating a latent “processivity switch” in XPD. These findings provide new insights on mechanisms of helicase regulation by accessory proteins.

Using Single-Molecule Approaches To Study Archaeal DNA-Binding Protein Alba1

Biochemistry ◽  
2013 ◽  
Vol 52 (44) ◽  
pp. 7714-7722 ◽  
Author(s):  
Yen-Wen Lu ◽  
Tao Huang ◽  
Cheng-Ting Tsai ◽  
Yu-Yung Chang ◽  
Hung-Wen Li ◽  
...  
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Approaches To Study

scholarly journals Single-molecule level structural dynamics of DNA unwinding by human mitochondrial Twinkle helicase

2020 ◽  
Vol 295 (17) ◽  
pp. 5564-5576 ◽  
Author(s):  
Parminder Kaur ◽  
Matthew J. Longley ◽  
Hai Pan ◽  
Wendy Wang ◽  
Preston Countryman ◽  
...  
Keyword(s):  
Dna Binding ◽  
Mitochondrial Genome ◽  
Single Molecule ◽  
Molecular Mechanisms ◽  
Binding Protein ◽  
Dna Unwinding ◽  
Microscopy Imaging ◽  
Single Molecule Level ◽  
Closed Ring ◽  
Mtdna Replication

Knowledge of the molecular events in mitochondrial DNA (mtDNA) replication is crucial to understanding the origins of human disorders arising from mitochondrial dysfunction. Twinkle helicase is an essential component of mtDNA replication. Here, we employed atomic force microscopy imaging in air and liquids to visualize ring assembly, DNA binding, and unwinding activity of individual Twinkle hexamers at the single-molecule level. We observed that the Twinkle subunits self-assemble into hexamers and higher-order complexes that can switch between open and closed-ring configurations in the absence of DNA. Our analyses helped visualize Twinkle loading onto and unloading from DNA in an open-ringed configuration. They also revealed that closed-ring conformers bind and unwind several hundred base pairs of duplex DNA at an average rate of ∼240 bp/min. We found that the addition of mitochondrial single-stranded (ss) DNA–binding protein both influences the ways Twinkle loads onto defined DNA substrates and stabilizes the unwound ssDNA product, resulting in a ∼5-fold stimulation of the apparent DNA-unwinding rate. Mitochondrial ssDNA-binding protein also increased the estimated translocation processivity from 1750 to >9000 bp before helicase disassociation, suggesting that more than half of the mitochondrial genome could be unwound by Twinkle during a single DNA-binding event. The strategies used in this work provide a new platform to examine Twinkle disease variants and the core mtDNA replication machinery. They also offer an enhanced framework to investigate molecular mechanisms underlying deletion and depletion of the mitochondrial genome as observed in mitochondrial diseases.

The DNA-binding protein YB-1 is a direct MYCN target and influences repair and resistance in neuroblastoma cell lines

2010 ◽  
Vol 222 (03) ◽  
Author(s):  
S Degen ◽  
S Kuhfittig-Kulle ◽  
JH Schulte ◽  
F Westermann ◽  
A Schramm ◽  
...  
Keyword(s):  
Dna Binding ◽  
Cell Lines ◽  
Binding Protein ◽  
Neuroblastoma Cell ◽  
Dna Binding Protein ◽  
Neuroblastoma Cell Lines
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