Direct measurements of memory effects in single-molecule kinetics

2002 ◽  
Vol 117 (24) ◽  
pp. 10996-11009 ◽  
Author(s):  
Shilong Yang ◽  
Jianshu Cao
Keyword(s):  
Single Molecule ◽  
Memory Effects ◽  
Direct Measurements

Memory effects in single-molecule force spectroscopy measurements of biomolecular folding

2019 ◽  
Vol 21 (44) ◽  
pp. 24527-24534 ◽  
Author(s):  
Andrew G. T. Pyo ◽  
Michael T. Woodside
Keyword(s):  
Autocorrelation Function ◽  
Single Molecule ◽  
Force Spectroscopy ◽  
Memory Effects ◽  
Single Molecule Force Spectroscopy ◽  
Force Probes

The force probes used in force spectroscopy measurements of folding induce memory, which can be quantified from the autocorrelation function.

scholarly journals Bacterial RNA polymerase can retain σ70 throughout transcription

2016 ◽  
Vol 113 (3) ◽  
pp. 602-607 ◽  
Author(s):  
Timothy T. Harden ◽  
Christopher D. Wells ◽  
Larry J. Friedman ◽  
Robert Landick ◽  
Ann Hochschild ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Single Molecule ◽  
Transcription Initiation ◽  
Messenger Rna ◽  
Initiation Factors ◽  
Bacterial Rna ◽  
Direct Measurements ◽  
Promoter Recognition ◽  
Σ Factor ◽  
Transcript Elongation

Production of a messenger RNA proceeds through sequential stages of transcription initiation and transcript elongation and termination. During each of these stages, RNA polymerase (RNAP) function is regulated by RNAP-associated protein factors. In bacteria, RNAP-associated σ factors are strictly required for promoter recognition and have historically been regarded as dedicated initiation factors. However, the primary σ factor in Escherichia coli, σ70, can remain associated with RNAP during the transition from initiation to elongation, influencing events that occur after initiation. Quantitative studies on the extent of σ70 retention have been limited to complexes halted during early elongation. Here, we used multiwavelength single-molecule fluorescence-colocalization microscopy to observe the σ70–RNAP complex during initiation from the λ PR′ promoter and throughout the elongation of a long (>2,000-nt) transcript. Our results provide direct measurements of the fraction of actively transcribing complexes with bound σ70 and the kinetics of σ70 release from actively transcribing complexes. σ70 release from mature elongation complexes was slow (0.0038 s−1); a substantial subpopulation of elongation complexes retained σ70 throughout transcript elongation, and this fraction depended on the sequence of the initially transcribed region. We also show that elongation complexes containing σ70 manifest enhanced recognition of a promoter-like pause element positioned hundreds of nucleotides downstream of the promoter. Together, the results provide a quantitative framework for understanding the postinitiation roles of σ70 during transcription.

Verification of Single-Molecule Imaging and Single-Molecule Measurements

2010 ◽  
Vol 22 (5) ◽  
pp. 568-578
Author(s):  
Akihiko Ishijima ◽  
◽  
Hajime Fukuoka ◽  
Yuichi Inoue
Keyword(s):  
Single Molecule ◽  
Research Method ◽  
Life Science ◽  
Science Research ◽  
Past Research ◽  
Single Molecule Imaging ◽  
Research Outcomes ◽  
Direct Measurements ◽  
Mechanical Methods ◽  
Statistical Mechanical

Single-molecule imaging and single-molecule measurements constitute an integral part of life science researches. The research method, which allows direct measurements of individual motions and events of biomolecules, has contributed much to the development of life science research by providing us with numerous findings. It is left up to the judgment of researchers, however, whether the measurements really represent single-molecule events, which make it harder for more researchers to enter into this field. This paper deals with how single-molecule measurements were presented in past research outcomes and illustrates statistical-mechanical methods as well.

scholarly journals Direct measurements of mRNA translation kinetics in living cells

2020 ◽  
Author(s):  
Mikhail Metelev ◽  
Ivan L. Volkov ◽  
Erik Lundin ◽  
Arvid H. Gynnå ◽  
Johan Elf ◽  
...  
Keyword(s):  
Single Molecule ◽  
Mrna Translation ◽  
Living Cells ◽  
Single Molecule Tracking ◽  
Ribosomal Subunits ◽  
Reading Frame ◽  
Direct Measurements ◽  
Translation Start ◽  
Labeling Method ◽  
Correct Translation

ABSTRACTRibosome mediated mRNA translation is central to life as we know it. The cycle of translation has, however, not been characterized in a living cell. Here we have developed a live-cell ribosome-labeling method, which allows us to characterize the whole processes of finding an mRNA and translating it, using single-molecule tracking techniques. We find that more than 90% of both bacterial ribosomal subunits are engaged in elongation at any particular time, and that neither of the subunits, in general, continues translation from one open reading frame to the next on a poly-cistronic mRNA. Furthermore, we find that a variety of previously published orthogonal ribosomes, with altered anti-Shine-Dalgarno sequences, show significant binding to endogenous mRNAs, with the rate of translation initiation only modestly affected. Hence, our results suggest that other mRNA elements than the SD sequence play major roles in directing the ribosome to the correct translation start sites.

scholarly journals Structural Memory Effects in Gold–4,4′-Bipyridine–Gold Single-Molecule Nanowires

2021 ◽  
Vol 12 (7) ◽  
pp. 1759-1764
Author(s):  
A. Magyarkuti ◽  
Z. Balogh ◽  
G. Mezei ◽  
A. Halbritter
Keyword(s):  
Single Molecule ◽  
Memory Effects ◽  
Structural Memory

scholarly journals Tetra-gel enables superior accuracy in combined super-resolution imaging and expansion microscopy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hsuan Lee ◽  
Chih-Chieh Yu ◽  
Edward S. Boyden ◽  
Xiaowei Zhuang ◽  
Pallav Kosuri
Keyword(s):  
Standard Deviation ◽  
Single Molecule ◽  
Super Resolution ◽  
Structural Features ◽  
Chain Growth ◽  
Radical Chain ◽  
Stochastic Optical Reconstruction Microscopy ◽  
Direct Measurements ◽  
Optical Reconstruction ◽  
Structural Preservation

AbstractThe accuracy of expansion microscopy (ExM) depends on the structural preservation of samples embedded in a hydrogel. However, it has been unknown to what extent gel embedding alters the molecular positions of individual labeled sites. Here, we quantified the accuracy of gel embedding by using stochastic optical reconstruction microscopy (STORM) to image DNA origami with well-defined structures. We found that embedding in hydrogels based on polyacrylamide, the most widely used chemistry in ExM, resulted in random displacements of labeled sites with a standard deviation of ~ 16 nm. In contrast, we found that embedding in tetra-gel, a hydrogel that does not depend on free-radical chain-growth polymerization, preserved labeled sites with a standard deviation of less than 5 nm. By combining tetra-gel ExM with STORM, we were able to resolve 11-nm structural features without the loss in accuracy seen with polyacrylamide gels. Our study thus provides direct measurements of the single-molecule distortions resulting from hydrogel embedding, and presents a way to improve super-resolution microscopy through combination with tetra-gel ExM.

scholarly journals Memory effects and oscillations in single-molecule kinetics

2002 ◽  
Vol 99 (20) ◽  
pp. 12548-12555 ◽  
Author(s):  
M. O. Vlad ◽  
F. Moran ◽  
F. W. Schneider ◽  
J. Ross
Keyword(s):  
Single Molecule ◽  
Memory Effects
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