scholarly journals Towards characterization of DNA structure under physiological conditions in vivo at the single-molecule level using single-pair FRET

2012 ◽  
Vol 40 (16) ◽  
pp. e121-e121 ◽  
Author(s):  
Tomáš Fessl ◽  
František Adamec ◽  
Tomáš Polívka ◽  
Silvie Foldynová-Trantírková ◽  
František Vácha ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Structure ◽  
Single Pair ◽  
Single Molecule Level ◽  
Physiological Conditions

Supramolecular Enhancement of Aminoxyl ORCA Contrast Agents

2019 ◽  
Author(s):  
Hamilton Lee ◽  
Jenica Lumata ◽  
Michael A. Luzuriaga ◽  
Candace Benjamin ◽  
Olivia Brohlin ◽  
...  
Keyword(s):  
Magnetic Resonance Imaging ◽  
Side Effects ◽  
Magnetic Resonance ◽  
Tobacco Mosaic Virus ◽  
Contrast Agents ◽  
Single Molecule ◽  
Organic Radical ◽  
Resonance Imaging ◽  
Physiological Conditions

<div><div><div><p>Many contrast agents for magnetic resonance imaging are based on gadolinium, however side effects limit their use in some patients. Organic radical contrast agents (ORCAs) are potential alternatives, but are reduced rapidly in physiological conditions and have low relaxivities as single molecule contrast agents. Herein, we use a supramolecular strategy where cucurbit[8]uril binds with nanomolar affinities to ORCAs and protects them against biological reductants to create a stable radical in vivo. We further over came the weak contrast by conjugating this complex on the surface of a self-assembled biomacromolecule derived from the tobacco mosaic virus.</p></div></div></div>

scholarly journals Characterization of Fluorescent Base Analogs to Study DNA Base Flipping at the Single Molecule Level

2013 ◽  
Vol 104 (2) ◽  
pp. 346a
Author(s):  
Xochitl A. Sosa-Vazquez ◽  
Matthew Vander-Schuur ◽  
Liza Valencia ◽  
Elvin A. Aleman
Keyword(s):  
Single Molecule ◽  
Base Flipping ◽  
Single Molecule Level ◽  
Dna Base

scholarly journals In vivo assembly and single-molecule characterization of the transcription machinery from Shewanella oneidensis MR-1

2009 ◽  
Vol 65 (1) ◽  
pp. 66-76 ◽  
Author(s):  
Natalie R. Gassman ◽  
Sam On Ho ◽  
You Korlann ◽  
Janet Chiang ◽  
Yim Wu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Shewanella Oneidensis ◽  
Transcription Machinery

Characterization of Pteridines: a New Approach by Fluorescence Correlation Spectroscopy and Analysis of Assay Sensitivity

Pteridines ◽  
2001 ◽  
Vol 12 (4) ◽  
pp. 147-153 ◽  
Author(s):  
U. Demel ◽  
Z. Foldes-Papp ◽  
D. Fuchs ◽  
G. P. Tilz
Keyword(s):  
Single Molecule ◽  
Fluorescence Correlation Spectroscopy ◽  
Correlation Spectroscopy ◽  
Cell Mediated Immunity ◽  
Distribution Analysis ◽  
Assay Sensitivity ◽  
New Approach ◽  
Single Molecule Level ◽  
Fluorescence Correlation

Abstract In the present investigation, fluorescence con-elation spectroscopy (FCS) was used to measure the molecular motion of the pteridine derivative neopterin. However, technical limitations in the present optical setup precluded the identification of ,single neopterin molecules. FCS measurements with a fluorophore were also can-ied out for comparison. Exemplified by rhodamine green, we have introduced a concept that allows the detection, identification and analysis of assays in solution at the single-molecule level in tenns of bulk concentration. This concept is based on FCS and Poisson distribution analysis of assay sensitivity. The molecules had not to be quantified in a more concentrated fonn, or in flow and trapping experiments. The study demonstrated an ultrasensitive, reliable, rapid and direct tool for analytics and diagnostics in solution. We discuss a possible application of our new concept in activation control of cell-mediated immunity via neopterin determination.

scholarly journals Kinetic Characterization of Nonmuscle Myosin IIB at the Single Molecule Level

2013 ◽  
Vol 104 (2) ◽  
pp. 642a
Author(s):  
Attila Nagy ◽  
Yasuharu Takagi ◽  
Neil Billington ◽  
Earl Homsher ◽  
James R. Sellers
Keyword(s):  
Single Molecule ◽  
Kinetic Characterization ◽  
Nonmuscle Myosin ◽  
Single Molecule Level

scholarly journals Watching cellular machinery in action, one molecule at a time

2016 ◽  
Vol 216 (1) ◽  
pp. 41-51 ◽  
Author(s):  
Enrico Monachino ◽  
Lisanne M. Spenkelink ◽  
Antoine M. van Oijen
Keyword(s):  
Dynamic Behavior ◽  
Single Molecule ◽  
Protein Complexes ◽  
Imaging Techniques ◽  
Ensemble Averaging ◽  
Cellular Processes ◽  
Cellular Machinery

Single-molecule manipulation and imaging techniques have become important elements of the biologist’s toolkit to gain mechanistic insights into cellular processes. By removing ensemble averaging, single-molecule methods provide unique access to the dynamic behavior of biomolecules. Recently, the use of these approaches has expanded to the study of complex multiprotein systems and has enabled detailed characterization of the behavior of individual molecules inside living cells. In this review, we provide an overview of the various force- and fluorescence-based single-molecule methods with applications both in vitro and in vivo, highlighting these advances by describing their applications in studies on cytoskeletal motors and DNA replication. We also discuss how single-molecule approaches have increased our understanding of the dynamic behavior of complex multiprotein systems. These methods have shown that the behavior of multicomponent protein complexes is highly stochastic and less linear and deterministic than previously thought. Further development of single-molecule tools will help to elucidate the molecular dynamics of these complex systems both inside the cell and in solutions with purified components.

scholarly journals From Starphenes to Non-Benzenoid Linear Conjugated Polymers by Substrate Templating

2020 ◽  
Author(s):  
Mohammed S. G. Mohammed ◽  
James Lawrence ◽  
Fátima García ◽  
Pedro Brandimarte ◽  
Alejandro Berdonces-Layunta ◽  
...  
Keyword(s):  
Conjugated Polymers ◽  
Single Molecule ◽  
Molecular Structures ◽  
Synthetic Methods ◽  
Synthesis And Characterization ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Single Molecule Level ◽  
Templating Effect

Combining on-surface synthetic methods with the power of scanning tunneling microscopy to characterize novel materials at the single molecule level, we show how to steer the reactivity of one anthracene-based precursor towards different product nanostructures. Whereas using a two-dimensional Au(111) surface results in the dominant formation of a starphene derivative, the templating effect of a reconstructed Au(110) surface allows the selective growth of non-benzenoid linear conjugated polymers. We further assess the electronic properties of each of the observed product structures via tunneling spectroscopy and DFT calculations, altogether advancing in the synthesis and characterization of molecular structures of notable scientific interest that have been only scarcely investigated to date, as applied to both starphenes and to non-benzenoid conjugated polymers. <br>

scholarly journals Nuclease dead Cas9 is a programmable roadblock for DNA replication

2018 ◽  
Author(s):  
Kelsey Whinn ◽  
Gurleen Kaur ◽  
Jacob S. Lewis ◽  
Grant Schauer ◽  
Stefan Müller ◽  
...  
Keyword(s):  
Dna Replication ◽  
Single Molecule ◽  
Replication Fork ◽  
Molecular Machines ◽  
Replication Forks ◽  
Chromosomal Dna ◽  
Single Molecule Level ◽  
Replication Fork Arrest

DNA replication occurs on chromosomal DNA while processes such as DNA repair, recombination and transcription continue. However, we have limited experimental tools to study the consequences of collisions between DNA-bound molecular machines. Here, we repurpose a catalytically inactivated Cas9 (dCas9) construct fused to the photo-stable dL5 protein fluoromodule as a novel, targetable protein-DNA roadblock for studying replication fork arrest at the single-molecule level in vitro as well as in vivo. We find that the specifically bound dCas9–guideRNA complex arrests viral, bacterial and eukaryotic replication forks in vitro.

scholarly journals Nanomechanics and co-transcriptional folding of Spinach and Mango

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jaba Mitra ◽  
Taekjip Ha
Keyword(s):  
Single Molecule ◽  
Rna Aptamers ◽  
Biophysical Characterization ◽  
Mechanical Responses ◽  
Discrete Step ◽  
Force Relaxation ◽  
G Quadruplex ◽  
And Function

Abstract Recent advances in fluorogen-binding “light-up” RNA aptamers have enabled protein-free detection of RNA in cells. Detailed biophysical characterization of folding of G-Quadruplex (GQ)-based light-up aptamers such as Spinach, Mango and Corn is still lacking despite the potential implications on their folding and function. In this work we employ single-molecule fluorescence-force spectroscopy to examine mechanical responses of Spinach2, iMangoIII and MangoIV. Spinach2 unfolds in four discrete steps as force is increased to 7 pN and refolds in reciprocal steps upon force relaxation. In contrast, GQ-core unfolding in iMangoIII and MangoIV occurs in one discrete step at forces >10 pN and refolding occurred at lower forces showing hysteresis. Co-transcriptional folding using superhelicases shows reduced misfolding propensity and allowed a folding pathway different from refolding. Under physiologically relevant pico-Newton levels of force, these aptamers may unfold in vivo and subsequently misfold. Understanding of the dynamics of RNA aptamers will aid engineering of improved fluorogenic modules for cellular applications.

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