Single-molecule experiments in biological physics: methods and applications

Ritort, Fèlix

doi:10.1088/0953-8984/18/32/r01

Cited by 389 publications

(479 citation statements)

References 461 publications

(587 reference statements)

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“…Double-stranded DNA elongates abruptly at a force of about 65 pN if it is pulled along its axis [1,2]. The resulting 'overstretched' form of the molecule is approximately 1.7 times longer than helical B-DNA.…”

Section: Introductionmentioning

confidence: 99%

Stretching chimeric DNA: A test for the putative S-form

Whitelam

Pronk

Geissler

2008

The Journal of Chemical Physics

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Double-stranded DNA 'overstretches' at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and technological application. Overstretching is thought by some to be a force-induced denaturation, and by others to consist of a transition to an elongated, hybridized state called S-DNA. Within a statistical mechanical model we consider the effect upon overstretching of extreme sequence heterogeneity. 'Chimeric' sequences possessing halves of markedly different AT composition elongate under fixed external conditions via distinct, spatially segregated transitions. The corresponding force-extension data display two plateaux at forces whose difference varies with pulling rate in a manner that depends qualitatively upon whether the hybridized S-form is accessible. This observation implies a test for S-DNA that could be performed in experiment. Our results suggest that qualitatively different, spatially segregated conformational transitions can occur at a single thermodynamic state within single molecules of DNA.

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Section: Introductionmentioning

confidence: 99%

Stretching chimeric DNA: A test for the putative S-form

Whitelam

Pronk

Geissler

2008

The Journal of Chemical Physics

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“…Mathematically one can model the replication as the force applied on an end of the DNA chain [33]. Physics of opening of chain due to thermal fluctuation and mechanical forces is completely different [34][35][36]. Thus, the study on the mismatch in the sequence and its role in the replication process is an interesting way to look into the physics of a complex mechanism.…”

Section: Force Induced Transitionsmentioning

confidence: 99%

Pulling short DNA molecules having defects on different locations

Singh

2015

Phys. Rev. E

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We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects that occurs anywhere in the molecule. For the investigation, we consider four different kinds of chains. Not only the ratio of AT to GC different in these molecules but also the distributions of AT and GC along the molecule are different. With suitable modifications in the statistical model to show the defect in a pair, we investigate the denaturation of short DNA molecules in thermal as well as constant force ensemble. In the force ensemble, we pulled the DNA molecule from each end (keeping other end free) and observed some interesting features of opening of the molecule in the presence of defects in the molecule. We calculate the probability of opening of the DNA molecule in the constant force ensemble to explain the opening of base pairs and hence the denaturation of molecules in the presence of defects.

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“…Other forms of loading include optical traps, and excellent reviews of this work are given by Bustamante et al (2003) and Ritort (2006).…”

Section: Introductionmentioning

confidence: 99%

Single-molecule magnetic tweezer tests on DNA: bounds on topoisomerase relaxation

Thompson

2008

Proc. R. Soc. A.

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Biomedical researchers regularly stretch and twist single DNA molecules in magnetic tweezer experiments. By making the molecule writhe into a plectoneme (ply) and plotting its load-extension curves, key DNA parameters, such as effective radius, can be estimated. Adding untangling enzymes (topoisomerases) to the DNA's environment, their individual cuts are detected as jumps in extension.Sufficient information is now known about the topoisomerases for us to make good idealizations about their kinematics and mechanics. The novelty of this paper is to study their actions in the context of accurate ply solutions from the theory of elastic rods. To do this, we define an extended rod-plus-tension system that allows us to determine the stored energies from areas in the conventional link versus writhe plane.After a cut, the molecule relaxes dynamically to a new equilibrium state, and often there will be two or more alternative stable configurations onto which it might settle. Knowing the energy levels allows us to identify which states can and cannot be reached over the unstable mountain passes, and which of the accessible states offer the greatest energy relaxation. Strict energy bounds on behaviour are established.This knowledge has medical value because topoisomerase inhibitors, lethal for cells, are used as antibiotics and in chemotherapy for cancer.

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Single-molecule experiments in biological physics: methods and applications

Cited by 389 publications

References 461 publications

Stretching chimeric DNA: A test for the putative S-form

Stretching chimeric DNA: A test for the putative S-form

Pulling short DNA molecules having defects on different locations

Single-molecule magnetic tweezer tests on DNA: bounds on topoisomerase relaxation

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