scholarly journals Combining single-molecule manipulation and peptide nucleic acid binding studies for unraveling how RNA structures regulate ribosomal frameshifting and alternative splicing

2019 ◽  
Author(s):  
Lixia Yang
Keyword(s):  
Alternative Splicing ◽  
Nucleic Acid ◽  
Single Molecule ◽  
Peptide Nucleic Acid ◽  
Nucleic Acid Binding ◽  
Rna Structures ◽  
Binding Studies ◽  
Ribosomal Frameshifting ◽  
Single Molecule Manipulation

scholarly journals DNA skybridge: 3D structure producing a light sheet for high-throughput single-molecule imaging

2019 ◽  
Vol 47 (18) ◽  
pp. e107-e107 ◽  
Author(s):  
Daehyung Kim ◽  
Fahad Rashid ◽  
Yeonmo Cho ◽  
Manal S Zaher ◽  
I I Hwan Cho ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
High Throughput ◽  
Single Molecule ◽  
Surface Condition ◽  
3D Structure ◽  
Light Sheet ◽  
Bottom Surface ◽  
Nucleic Acid Binding ◽  
Nucleic Acid Binding Proteins ◽  
Real Time Visualization

Abstract Real-time visualization of single-proteins or -complexes on nucleic acid substrates is an essential tool for characterizing nucleic acid binding proteins. Here, we present a novel surface-condition independent and high-throughput single-molecule optical imaging platform called ‘DNA skybridge’. The DNA skybridge is constructed in a 3D structure with 4 μm-high thin quartz barriers in a quartz slide. Each DNA end is attached to the top of the adjacent barrier, resulting in the extension and immobilization of DNA. In this 3D structure, the bottom surface is out-of-focus when the target molecules on the DNA are imaged. Moreover, the DNA skybridge itself creates a thin Gaussian light sheet beam parallel to the immobilized DNA. This dual property allows for imaging a single probe-tagged molecule moving on DNA while effectively suppressing interference with the surface and background signals from the surface.

scholarly journals Deaminase-independent inhibition of HIV-1 reverse transcription by APOBEC3G

2007 ◽  
Vol 35 (21) ◽  
pp. 7096-7108 ◽  
Author(s):  
Yasumasa Iwatani ◽  
Denise S.B. Chan ◽  
F. Wang ◽  
Kristen Stewart-Maynard ◽  
Wataru Sugiura ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Single Molecule ◽  
Reverse Transcription ◽  
Cytidine Deaminase ◽  
Rnase H ◽  
Host Protein ◽  
Nucleic Acid Binding ◽  
Nucleic Acid Chaperone ◽  
Kinetics Of ◽  
Hiv 1

Abstract APOBEC3G (A3G), a host protein that inhibits HIV-1 reverse transcription and replication in the absence of Vif, displays cytidine deaminase and single-stranded (ss) nucleic acid binding activities. HIV-1 nucleocapsid protein (NC) also binds nucleic acids and has a unique property, nucleic acid chaperone activity, which is crucial for efficient reverse transcription. Here we report the interplay between A3G, NC and reverse transcriptase (RT) and the effect of highly purified A3G on individual reactions that occur during reverse transcription. We find that A3G did not affect the kinetics of NC-mediated annealing reactions, nor did it inhibit RNase H cleavage. In sharp contrast, A3G significantly inhibited all RT-catalyzed DNA elongation reactions with or without NC. In the case of ( − ) strong-stop DNA synthesis, the inhibition was independent of A3G's catalytic activity. Fluorescence anisotropy and single molecule DNA stretching analyses indicated that NC has a higher nucleic acid binding affinity than A3G, but more importantly, displays faster association/disassociation kinetics. RT binds to ssDNA with a much lower affinity than either NC or A3G. These data support a novel mechanism for deaminase-independent inhibition of reverse transcription that is determined by critical differences in the nucleic acid binding properties of A3G, NC and RT.

scholarly journals Nucleic Acid Binding Kinetics of HIV-1 Nucleocapsid Proteins from Single Molecule DNA Stretching

2013 ◽  
Vol 104 (2) ◽  
pp. 254a
Author(s):  
Jialin Li ◽  
Robert J. Gorelick ◽  
Ioulia Rouzina ◽  
Mark C. Williams
Keyword(s):  
Nucleic Acid ◽  
Single Molecule ◽  
Binding Kinetics ◽  
Nucleic Acid Binding ◽  
Dna Stretching ◽  
Nucleocapsid Proteins ◽  
Kinetics Of ◽  
Hiv 1

Insight into why pyrrolidinyl peptide nucleic acid binding to DNA is more stable than the DNA·DNA duplex

2008 ◽  
Vol 372 (4) ◽  
pp. 765-771 ◽  
Author(s):  
Khatcharin Siriwong ◽  
Parawan Chuichay ◽  
Suwipa Saen-oon ◽  
Chaturong Suparpprom ◽  
Tirayut Vilaivan ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Nucleic Acid Binding ◽  
Insight Into

Quinoxaline Antibiotics Enhance Peptide Nucleic Acid Binding to Double-Stranded DNA†

Biochemistry ◽  
2000 ◽  
Vol 39 (31) ◽  
pp. 9502-9507 ◽  
Author(s):  
Niels Erik Møllegaard ◽  
Christian Bailly ◽  
Michael J. Waring ◽  
Peter E. Nielsen
Keyword(s):  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Nucleic Acid Binding ◽  
Double Stranded Dna
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