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.

Effect of YOYO-1 on the mechanical properties of DNA

Soft Matter ◽  
2014 ◽  
Vol 10 (48) ◽  
pp. 9721-9728 ◽  
Author(s):  
Binu Kundukad ◽  
Jie Yan ◽  
Patrick S. Doyle
Keyword(s):  
Mechanical Properties ◽  
Atomic Force Microscopy ◽  
Persistence Length ◽  
Contour Length ◽  
Force Microscopy ◽  
Atomic Force

Atomic force microscopy studies show that binding of YOYO-1 to DNA increases the contour length of DNA without affecting the persistence length due to the underwinding of DNA.

scholarly journals Atomic Force Microscopy Investigation of the Interactions between the MCM Helicase and DNA

Materials ◽  
2021 ◽  
Vol 14 (3) ◽  
pp. 687
Author(s):  
Amna Abdalla Mohammed Khalid ◽  
Pietro Parisse ◽  
Barbara Medagli ◽  
Silvia Onesti ◽  
Loredana Casalis
Keyword(s):  
Atomic Force Microscopy ◽  
Nucleic Acid ◽  
Single Molecule ◽  
Protein Complex ◽  
The Other ◽  
Contour Length ◽  
Force Microscopy ◽  
Atomic Force ◽  
Mcm Complex ◽  
Dna Double Helix

The MCM (minichromosome maintenance) protein complex forms an hexameric ring and has a key role in the replication machinery of Eukaryotes and Archaea, where it functions as the replicative helicase opening up the DNA double helix ahead of the polymerases. Here, we present a study of the interaction between DNA and the archaeal MCM complex from Methanothermobacter thermautotrophicus by means of atomic force microscopy (AFM) single molecule imaging. We first optimized the protocol (surface treatment and buffer conditions) to obtain AFM images of surface-equilibrated DNA molecules before and after the interaction with the protein complex. We discriminated between two modes of interaction, one in which the protein induces a sharp bend in the DNA, and one where there is no bending. We found that the presence of the MCM complex also affects the DNA contour length. A possible interpretation of the observed behavior is that in one case the hexameric ring encircles the dsDNA, while in the other the nucleic acid wraps on the outside of the ring, undergoing a change of direction. We confirmed this topographical assignment by testing two mutants, one affecting the N-terminal β-hairpins projecting towards the central channel, and thus preventing DNA loading, the other lacking an external subdomain and thus preventing wrapping. The statistical analysis of the distribution of the protein complexes between the two modes, together with the dissection of the changes of DNA contour length and binding angle upon interaction, for the wild type and the two mutants, is consistent with the hypothesis. We discuss the results in view of the various modes of nucleic acid interactions that have been proposed for both archaeal and eukaryotic MCM complexes.

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 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.

Towards monitoring transport of single cargos across individual nuclear pore complexes by time-lapse atomic force microscopy

2010 ◽  
Vol 171 (2) ◽  
pp. 154-162 ◽  
Author(s):  
Ning-Ping Huang ◽  
Mike Stubenrauch ◽  
Joachim Köser ◽  
Nicole Taschner ◽  
Ueli Aebi ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Time Lapse ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Force Microscopy ◽  
Atomic Force ◽  
Pore Complexes
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