scholarly journals The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics

2018 ◽  
Vol 140 (2) ◽  
Author(s):  
Kevin D. Dorfman
Keyword(s):  
Genome Mapping ◽  
Persistence Length ◽  
Magnetic Tweezers ◽  
Polymer Physics ◽  
Polymer Dynamics ◽  
Segment Length ◽  
Next Generation ◽  
Bending Energy ◽  
Force Microscopy ◽  
Statistical Segment

The development of bright bisintercalating dyes for deoxyribonucleic acid (DNA) in the 1990s, most notably YOYO-1, revolutionized the field of polymer physics in the ensuing years. These dyes, in conjunction with modern molecular biology techniques, permit the facile observation of polymer dynamics via fluorescence microscopy and thus direct tests of different theories of polymer dynamics. At the same time, they have played a key role in advancing an emerging next-generation method known as genome mapping in nanochannels. The effect of intercalation on the bending energy of DNA as embodied by a change in its statistical segment length (or, alternatively, its persistence length) has been the subject of significant controversy. The precise value of the statistical segment length is critical for the proper interpretation of polymer physics experiments and controls the phenomena underlying the aforementioned genomics technology. In this perspective, we briefly review the model of DNA as a wormlike chain and a trio of methods (light scattering, optical or magnetic tweezers, and atomic force microscopy (AFM)) that have been used to determine the statistical segment length of DNA. We then outline the disagreement in the literature over the role of bisintercalation on the bending energy of DNA, and how a multiscale biomechanical approach could provide an important model for this scientifically and technologically relevant problem.

scholarly journals Scaling Concepts in Serpin Polymer Physics

Materials ◽  
2021 ◽  
Vol 14 (10) ◽  
pp. 2577
Author(s):  
Samuele Raccosta ◽  
Fabio Librizzi ◽  
Alistair M. Jagger ◽  
Rosina Noto ◽  
Vincenzo Martorana ◽  
...  
Keyword(s):  
Persistence Length ◽  
Time Lapse ◽  
Polymer Physics ◽  
Contour Length ◽  
Force Microscopy ◽  
Negative Stain ◽  
Atomic Force ◽  
Linear Chains ◽  
End Distance ◽  
Polymer Size

α1-Antitrypsin is a protease inhibitor belonging to the serpin family. Serpin polymerisation is at the core of a class of genetic conformational diseases called serpinopathies. These polymers are known to be unbranched, flexible, and heterogeneous in size with a beads-on-a-string appearance viewed by negative stain electron microscopy. Here, we use atomic force microscopy and time-lapse dynamic light scattering to measure polymer size and shape for wild-type (M) and Glu342→Lys (Z) α1-antitrypsin, the most common variant that leads to severe pathological deficiency. Our data for small polymers deposited onto mica and in solution reveal a power law relation between the polymer size, namely the end-to-end distance or the hydrodynamic radius, and the polymer mass, proportional to the contour length. We use the scaling concepts of polymer physics to assess that α1-antitrypsin polymers are random linear chains with a low persistence length.

High-resolution and high-coercivity FePtL10 magnetic force microscopy nanoprobes to study next-generation magnetic recording media

2009 ◽  
Vol 105 (7) ◽  
pp. 07D526 ◽  
Author(s):  
Nissim Amos ◽  
Andrey Lavrenov ◽  
Robert Fernandez ◽  
Rabee Ikkawi ◽  
Dmitri Litvinov ◽  
...  
Keyword(s):  
High Resolution ◽  
Magnetic Recording ◽  
Magnetic Force Microscopy ◽  
Magnetic Force ◽  
High Coercivity ◽  
Recording Media ◽  
Next Generation ◽  
Magnetic Recording Media ◽  
Force Microscopy

scholarly journals Intact DNA purified from flow-sorted nuclei unlocks the potential of next-generation genome mapping and assembly in Solanum species

MethodsX ◽  
2018 ◽  
Vol 5 ◽  
pp. 328-336 ◽  
Author(s):  
Paola Gaiero ◽  
Hana Šimková ◽  
Jan Vrána ◽  
Federico F. Santiñaque ◽  
Beatriz López-Carro ◽  
...  
Keyword(s):  
Genome Mapping ◽  
Solanum Species ◽  
Next Generation

scholarly journals Nanochannel-Confined TAMRA-Polypyrrole Stained DNA Stretching by Varying the Ionic Strength from Micromolar to Millimolar Concentrations

Polymers ◽  
2018 ◽  
Vol 11 (1) ◽  
pp. 15 ◽  
Author(s):  
Seonghyun Lee ◽  
Yelin Lee ◽  
Yongkyun Kim ◽  
Cong Wang ◽  
Jungyul Park ◽  
...  
Keyword(s):  
Ionic Strength ◽  
Double Helix ◽  
Persistence Length ◽  
Polymer Physics ◽  
Structural Deformation ◽  
Contour Length ◽  
Dna Molecules ◽  
Dna Stretching ◽  
Single Dna Molecules ◽  
Length Changes

Large DNA molecules have been utilized as a model system to investigate polymer physics. However, DNA visualization via intercalating dyes has generated equivocal results due to dye-induced structural deformation, particularly unwanted unwinding of the double helix. Thus, the contour length increases and the persistence length changes so unpredictably that there has been a controversy. In this paper, we used TAMRA-polypyrrole to stain single DNA molecules. Since this staining did not change the contour length of B-form DNA, we utilized TAMRA-polypyrrole stained DNA as a tool to measure the persistence length by changing the ionic strength. Then, we investigated DNA stretching in nanochannels by varying the ionic strength from 0.06 mM to 47 mM to evaluate several polymer physics theories proposed by Odijk, de Gennes and recent papers to deal with these regimes.

scholarly journals Atomic force microscopy of the morphology and mechanical behaviour of barnacle cyprid footprint proteins at the nanoscale

2009 ◽  
Vol 7 (43) ◽  
pp. 285-296 ◽  
Author(s):  
In Yee Phang ◽  
Nick Aldred ◽  
Xing Yi Ling ◽  
Jurriaan Huskens ◽  
Anthony S. Clare ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Sea Water ◽  
Persistence Length ◽  
Force Microscopy ◽  
Bond Model ◽  
Atomic Force ◽  
Extension Force ◽  
Force Curves ◽  
High Elongation ◽  
Glass Surfaces

Barnacles are a major biofouler of man-made underwater structures. Prior to settlement, cypris larvae explore surfaces by reversible attachment effected by a ‘temporary adhesive’. During this exploratory behaviour, cyprids deposit proteinaceous ‘footprints’ of a putatively adhesive material. In this study, footprints deposited by Balanus amphitrite cyprids were probed by atomic force microscopy (AFM) in artificial sea water (ASW) on silane-modified glass surfaces. AFM images obtained in air yielded better resolution than in ASW and revealed the fibrillar nature of the secretion, suggesting that the deposits were composed of single proteinaceous nanofibrils, or bundles of fibrils. The force curves generated in pull-off force experiments in sea water consisted of regions of gradually increasing force, separated by sharp drops in extension force manifesting a characteristic saw-tooth appearance. Following the relaxation of fibrils stretched to high strains, force–distance curves in reverse stretching experiments could be described by the entropic elasticity model of a polymer chain. When subjected to relaxation exceeding 500 ms, extended footprint proteins refolded, and again showed saw-tooth unfolding peaks in subsequent force cycles. Observed rupture and hysteresis behaviour were explained by the ‘sacrificial bond’ model. Longer durations of relaxation (>5 s) allowed more sacrificial bond reformation and contributed to enhanced energy dissipation (higher toughness). The persistence length for the protein chains ( L P ) was obtained. At high elongation, following repeated stretching up to increasing upper strain limits, footprint proteins detached at total stretched length of 10 µm.

Study of Nano-Mechanics of Collagen I Triple-helices by Computerized Processing of AFM Images

2012 ◽  
Vol 1422 ◽  
Author(s):  
Arkady Bitler ◽  
Emanuel Perugia ◽  
Sidney R. Cohen
Keyword(s):  
Mechanical Properties ◽  
Persistence Length ◽  
Collagen Type I ◽  
Segment Length ◽  
Type I ◽  
Ambient Conditions ◽  
Atomic Force ◽  
Collagen Molecules ◽  
High Resolution Images ◽  
Triple Helices

ABSTRACTWe used atomic force microscope (AFM) to acquire high-resolution images of collagen type I triple-helices under ambient conditions in tapping mode. Angles between consecutive fixed-length segments were measured and analyzed to yield persistence length and elastic constant. Changing the segment length allowed exploring the mechanics at various scales. Understanding the mechanical properties of collagen molecules could serve to elucidate mechanisms of complex mechanical properties of interest in nanomedicine and nanotechnology.

Correlation of binary polyolefin phase behavior with statistical segment length asymmetry

1992 ◽  
Vol 25 (20) ◽  
pp. 5547-5550 ◽  
Author(s):  
Frank S. Bates ◽  
Mark F. Schulz ◽  
Jeffrey H. Rosedale ◽  
Kristoffer Almdal
Keyword(s):  
Phase Behavior ◽  
Segment Length ◽  
Statistical Segment
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