scholarly journals Single Molecule Studies of Physiologically Relevant Telomeric Tails Reveal POT1 Mechanism for Promoting G-quadruplex Unfolding

2010 ◽  
Vol 286 (9) ◽  
pp. 7479-7489 ◽  
Author(s):  
Hong Wang ◽  
Gerald J. Nora ◽  
Harshad Ghodke ◽  
Patricia L. Opresko
Keyword(s):  
Single Molecule ◽  
G Quadruplex ◽  
Single Molecule Studies

scholarly journals Impact of Small Molecules on Intermolecular G-Quadruplex Formation

Molecules ◽  
2019 ◽  
Vol 24 (8) ◽  
pp. 1570 ◽  
Author(s):  
Prabesh Gyawali ◽  
Keshav GC ◽  
Yue Ma ◽  
Sanjaya Abeysirigunawardena ◽  
Kazuo Nagasawa ◽  
...  
Keyword(s):  
Small Molecules ◽  
Single Molecule ◽  
The Other ◽  
Single Molecule Level ◽  
G Quadruplex ◽  
Dna Strands ◽  
Order Of Magnitude ◽  
Single Molecule Studies ◽  
Quadruplex Formation ◽  
The Impact

We performed single molecule studies to investigate the impact of several prominent small molecules (the oxazole telomestatin derivative L2H2-6OTD, pyridostatin, and Phen-DC3) on intermolecular G-quadruplex (i-GQ) formation between two guanine-rich DNA strands that had 3-GGG repeats in one strand and 1-GGG repeat in the other (3+1 GGG), or 2-GGG repeats in each strand (2+2 GGG). Such structures are not only physiologically significant but have recently found use in various biotechnology applications, ranging from DNA-based wires to chemical sensors. Understanding the extent of stability imparted by small molecules on i-GQ structures, has implications for these applications. The small molecules resulted in different levels of enhancement in i-GQ formation, depending on the small molecule and arrangement of GGG repeats. The largest enhancement we observed was in the 3+1 GGG arrangement, where i-GQ formation increased by an order of magnitude, in the presence of L2H2-6OTD. On the other hand, the enhancement was limited to three-fold with Pyridostatin (PDS) or less for the other small molecules in the 2+2 GGG repeat case. By demonstrating detection of i-GQ formation at the single molecule level, our studies illustrate the feasibility to develop more sensitive sensors that could operate with limited quantities of materials.

scholarly journals Single Molecule Studies on G-Quadruplex, Protein, and Small Molecule Interactions

2017 ◽  
Vol 112 (3) ◽  
pp. 170a
Author(s):  
Hamza Balci ◽  
Sujay Ray ◽  
Jagat Budhathoki ◽  
Parastoo Maleki
Keyword(s):  
Small Molecule ◽  
Single Molecule ◽  
G Quadruplex ◽  
Single Molecule Studies ◽  
Molecule Interactions

scholarly journals Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription

2021 ◽  
Vol 22 (5) ◽  
pp. 2398
Author(s):  
Wooyoung Kang ◽  
Seungha Hwang ◽  
Jin Young Kang ◽  
Changwon Kang ◽  
Sungchul Hohng
Keyword(s):  
Single Molecule ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Facilitated Diffusion ◽  
One Dimensional ◽  
Bacterial Transcription ◽  
Fluorescence Measurements ◽  
Dimensional Diffusion ◽  
Single Molecule Studies ◽  
Hopping Diffusion

Two different molecular mechanisms, sliding and hopping, are employed by DNA-binding proteins for their one-dimensional facilitated diffusion on nonspecific DNA regions until reaching their specific target sequences. While it has been controversial whether RNA polymerases (RNAPs) use one-dimensional diffusion in targeting their promoters for transcription initiation, two recent single-molecule studies discovered that post-terminational RNAPs use one-dimensional diffusion for their reinitiation on the same DNA molecules. Escherichia coli RNAP, after synthesizing and releasing product RNA at intrinsic termination, mostly remains bound on DNA and diffuses in both forward and backward directions for recycling, which facilitates reinitiation on nearby promoters. However, it has remained unsolved which mechanism of one-dimensional diffusion is employed by recycling RNAP between termination and reinitiation. Single-molecule fluorescence measurements in this study reveal that post-terminational RNAPs undergo hopping diffusion during recycling on DNA, as their one-dimensional diffusion coefficients increase with rising salt concentrations. We additionally find that reinitiation can occur on promoters positioned in sense and antisense orientations with comparable efficiencies, so reinitiation efficiency depends primarily on distance rather than direction of recycling diffusion. This additional finding confirms that orientation change or flipping of RNAP with respect to DNA efficiently occurs as expected from hopping diffusion.

Breaking Down the Supramolecular Ensemble: Single-Molecule Studies of the Concentration Dependence of Main-Chain Supramolecular Polymer Molecular Weight Distributions on Surfaces

2010 ◽  
Vol 63 (4) ◽  
pp. 624
Author(s):  
Michael J. Serpe ◽  
Jason R. Whitehead ◽  
Stephen L. Craig
Keyword(s):  
Molecular Weight ◽  
Single Molecule ◽  
Monomer Concentration ◽  
Supramolecular Polymer ◽  
Force Microscopy ◽  
Molecular Weight Distributions ◽  
Atomic Force ◽  
Multi Stage ◽  
Single Molecule Studies ◽  
Supramolecular Ensemble

Single molecule atomic force microscopy (AFM) studies of oligonucleotide-based supramolecular polymers on surfaces are used to examine the molecular weight distribution of the polymers formed between a functionalized surface and an AFM tip as a function of monomer concentration. For the concentrations examined here, excellent agreement with a multi-stage open association model of polymerization is obtained, without the need to invoke additional contributions from secondary steric interactions at the surface.

scholarly journals Single-Molecule Studies of the Na+/K+-ATPase

2011 ◽  
Vol 100 (3) ◽  
pp. 464a
Author(s):  
Promod R. Pratap ◽  
Gregor Heiss ◽  
Martin Sikor ◽  
Don C. Lamb ◽  
Max Burnett
Keyword(s):  
Single Molecule ◽  
Single Molecule Studies

scholarly journals Single Molecule Studies of DNA-Binding Proteins: Development of New Covalent DNA Anchoring Techniques for the Study of Rupture Forces of Replication Blocks

2014 ◽  
Vol 106 (2) ◽  
pp. 394a
Author(s):  
Richard Janissen ◽  
Bojk A. Berghuis ◽  
Orkide Ordu ◽  
Max M. Wink ◽  
David Dulin ◽  
...  
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Single Molecule Studies
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