Single-molecule force spectroscopy has emerged as a powerful tool to investigate the forces and motions associated with biological molecules and enzymatic activity. The most common force spectroscopy techniques are optical tweezers, magnetic tweezers and atomic force microscopy. Here we describe these techniques and illustrate them with examples highlighting current capabilities and limitations.

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

Dynamic atomic force microscopy methods

The 'toxic Aβ oligomer' hypothesis has attracted considerable attention among Alzheimer's disease researchers as a way of resolving the lack of correlation between deposited amyloid-β (Aβ) in amyloid plaques-in terms of both amount and location-and cognitive impairment or neurodegeneration. However, the lack of a common, agreed-upon experimental description of the toxic Aβ oligomer makes interpretation and direct comparison of data between different research groups impossible. Here we critically review the evidence supporting toxic Aβ oligomers as drivers of neurodegeneration and make some suggestions that might facilitate progress in this complex field.

The toxic Aβ oligomer and Alzheimer's disease: an emperor in need of clothes

Long noncoding RNAs (lncRNAs) have gained widespread attention in recent years as a potentially new and crucial layer of biological regulation. lncRNAs of all kinds have been implicated in a range of developmental processes and diseases, but knowledge of the mechanisms by which they act is still surprisingly limited, and claims that almost the entirety of the mammalian genome is transcribed into functional noncoding transcripts remain controversial. At the same time, a small number of well-studied lncRNAs have given us important clues about the biology of these molecules, and a few key functional and mechanistic themes have begun to emerge, although the robustness of these models and classification schemes remains to be seen. Here, we review the current state of knowledge of the lncRNA field, discussing what is known about the genomic contexts, biological functions, and mechanisms of action of lncRNAs. We also reflect on how the recent interest in lncRNAs is deeply rooted in biology’s longstanding concern with the evolution and function of genomes.

https://www.genetics.org/content/genetics/193/3/651.full.pdf

Long noncoding RNAs: past, present, and future.

https://www.ccbb.pitt.edu/Faculty/bahar/publications/143.pdf

Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model

http://users.df.uba.ar/catalina/TBM/Rivetti_1996.pdf

Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis.

Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility

https://users.wfu.edu/~shapiro/Biophysics14/papers/Guthold%20et%20al%20Biophys%20J_77_2284-2294.pdf

Direct Observation of One-Dimensional Diffusion and Transcription by Escherichia coli RNA Polymerase

Visualizing Protein-Nucleic Acid Interactions on a Large Scale with the Scanning Force Microscope

High-resolution atomic force microscopy (AFM) and biochemical methods were used to analyze the structure of Escherichia coli RNA polymerase.sigma(70) (RNAP) open promoter complex (RP(o)). A detailed analysis of a large number of molecules shows that the DNA contour length of RP(o) is reduced by approximately 30 nm (approximately 90 bp) relative to the free DNA. The DNA bend angle measured with different methods varied from 55 to 88 degrees. The contour length reduction and the DNA bend angle were much less in inactive RNAP-DNA complexes. These results, together with previously published observations, strongly support the notion that during transcription initiation, the promoter DNA wraps nearly 300 degrees around the polymerase. This amount of DNA bending requires an energy of 60 kJ/mol. The structural analysis of the open promoter complexes revealed that two-thirds of the DNA wrapped around the RNAP is part of a region upstream of the transcription start site, whereas the remaining one-third is part of the downstream region. Based on these data, a model of the sigma(70).RP(o) conformation is proposed.

http://www.phys.ens.fr/~vincent/courdea/PDF/rivetti.pdf

Claudio Rivetti

Papers

Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis.

Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility

Direct Observation of One-Dimensional Diffusion and Transcription by Escherichia coli RNA Polymerase

Visualizing Protein-Nucleic Acid Interactions on a Large Scale with the Scanning Force Microscope

Wrapping of DNA around the E.coli RNA polymerase open promoter complex.