scholarly journals Denaturation transition of stretched DNA

2013 ◽  
Vol 41 (2) ◽  
pp. 639-645 ◽  
Author(s):  
Andreas Hanke

In the last two decades, single-molecule force measurements using optical and magnetic tweezers and atomic force spectroscopy have dramatically expanded our knowledge of nucleic acids and proteins. These techniques characterize the force on a biomolecule required to produce a given molecular extension. When stretching long DNA molecules, the observed force–extension relationship exhibits a characteristic plateau at approximately 65 pN where the DNA may be extended to almost twice its B-DNA length with almost no increase in force. In the present review, I describe this transition in terms of the Poland–Scheraga model and summarize recent related studies.

2004 ◽  
Vol 18 (2) ◽  
pp. 203-211 ◽  
Author(s):  
Mark C. Williams ◽  
Kiran Pant ◽  
Ioulia Rouzina ◽  
Richard L. Karpel

Single molecule force spectroscopy is an emerging technique that can be used to measure the biophysical properties of single macromolecules such as nucleic acids and proteins. In particular, single DNA molecule stretching experiments are used to measure the elastic properties of these molecules and to induce structural transitions. We have demonstrated that double‒stranded DNA molecules undergo a force‒induced melting transition at high forces. Force–extension measurements of single DNA molecules using optical tweezers allow us to measure the stability of DNA under a variety of solution conditions and in the presence of DNA binding proteins. Here we review the evidence of DNA melting in these experiments and discuss the example of DNA force‒induced melting in the presence of the single‒stranded DNA binding protein T4 gene 32. We show that this force spectroscopy technique is a useful probe of DNA–protein interactions, which allows us to obtain binding rates and binding free energies for these interactions.


Author(s):  
Frank W. S. Stetter ◽  
Sandra Kienle ◽  
Stefanie Krysiak ◽  
Thorsten Hugel

2010 ◽  
Vol 98 (3) ◽  
pp. 593a-594a
Author(s):  
Minkyu Kim ◽  
Khadar Abdi ◽  
Gwangrog Lee ◽  
Mahir Rabbi ◽  
Whasil Lee ◽  
...  

2014 ◽  
Vol 54 ◽  
pp. 492-498 ◽  
Author(s):  
Francis T. Hane ◽  
Brenda Y. Lee ◽  
Anahit Petoyan ◽  
Arvi Rauk ◽  
Zoya Leonenko

Nanomaterials ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2424
Author(s):  
Lyan M. van der Sleen ◽  
Katarzyna M. Tych

The mechanical properties of proteins can be studied with single molecule force spectroscopy (SMFS) using optical tweezers, atomic force microscopy and magnetic tweezers. It is common to utilize a flexible linker between the protein and trapped probe to exclude short-range interactions in SMFS experiments. One of the most prevalent linkers is DNA due to its well-defined properties, although attachment strategies between the DNA linker and protein or probe may vary. We will therefore provide a general overview of the currently existing non-covalent and covalent bioconjugation strategies to site-specifically conjugate DNA-linkers to the protein of interest. In the search for a standardized conjugation strategy, considerations include their mechanical properties in the context of SMFS, feasibility of site-directed labeling, labeling efficiency, and costs.


2018 ◽  
Author(s):  
Carolina Pimenta-Lopes ◽  
Carmen Suay-Corredera ◽  
Diana Velázquez-Carreras ◽  
David Sánchez-Ortiz ◽  
Jorge Alegre-Cebollada

ABSTRACTForce-spectroscopy by Atomic Force Microscopy (AFM) is the technique of choice to measure mechanical properties of molecules, cells, tissues and materials at the nano and micro scales. However, unavoidable calibration errors of AFM probes make it cumbersome to quantify modulation of mechanics. Here, we show that concurrent AFM force measurements enable relative mechanical characterization with an accuracy that is independent of calibration uncertainty, even when averaging data from multiple, independent experiments. Compared to traditional AFM, we estimate that concurrent strategies can measure differences in protein mechanical unfolding forces with a 6-fold improvement in accuracy and a 30-fold increase in throughput. Prompted by our results, we demonstrate widely applicable orthogonal fingerprinting strategies for concurrent single-molecule nanomechanical profiling of proteins.


2008 ◽  
Vol 377 (3) ◽  
pp. 706-714 ◽  
Author(s):  
Wenke Zhang ◽  
Cristina Machón ◽  
Alberto Orta ◽  
Nicola Phillips ◽  
Clive J. Roberts ◽  
...  

Author(s):  
Chandrayee Mukherjee ◽  
Manindra Bera ◽  
Sri Rama Koti Ainavarapu ◽  
Kaushik Sengupta

The fundamental unit of the human body comprises of the cells which remain embedded in a fibrillar network of extracellular matrix proteins which in turn provides necessary anchorage the cells. Tissue repair, regeneration and reprogramming predominantly involve a traction force mediated signalling originating in the ECM and travelling deep into the cell including the nucleus via circuitry of spring-like filamentous proteins like microfilaments or actin, intermediate filaments and microtubules to elicit a response in the form of mechanical movement as well as biochemical changes. The ‘springiness’ of these proteins is highlighted in their extension–contraction behaviour which is manifested as an effect of differential traction force. Atomic force microscope (AFM) provides the magic eye to visualize and quantify such force-extension/indentation events in these filamentous proteins as well as in whole cells. In this review, we have presented a summary of the current understanding and advancement of such measurements by AFM based single-molecule force spectroscopy in the context of cytoskeletal and nucleoskeletal proteins which act in tandem to facilitate mechanotransduction.


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