scholarly journals Processivity, velocity and universal characteristics of nucleic acid unwinding by helicases

2018 ◽  
Author(s):  
Shaon Chakrabarti ◽  
Christopher Jarzynski ◽  
D. Thirumalai
Keyword(s):  
Quantitative Analysis ◽  
Single Molecule ◽  
Physical Principle ◽  
Single Strand ◽  
Mathematical Framework ◽  
Double Stranded Dna ◽  
Analytic Expressions ◽  
Xpd Helicase ◽  
Partner Proteins ◽  
Magnitude Increase

AbstractHelicases that act as motors and unwind double stranded nucleic acids are broadly classified as either active or passive, depending on whether or not they directly destabilize the double strand. By using this description in a mathematical framework, we derive analytic expressions for the velocity and run-length of a general model of finitely processive helicases. We show that, in contrast to the helicase unwinding velocity, the processivity exhibits a universal increase in response to external force. We use our results to analyze velocity and processivity data from single molecule experiments on the superfamily-4 ring helicase T7, and establish quantitatively that T7 is a weakly active helicase. We predict that compared to single-strand translocation, there is almost a two orders-of-magnitude increase in the back-stepping probability of T7 while unwinding double-stranded DNA. Our quantitative analysis of T7 suggests that the tendency of helicases to take frequent back-steps may be more common than previously anticipated, as was recently shown for the XPD helicase. Finally, our results suggest the intriguing possibility of a single underlying physical principle governing the experimentally observed increase in unwinding efficiencies of helicases in the presence of force, oligomerization or partner proteins like single strand binding proteins. The clear implication is that helicases may have evolved to maximize processivity rather than speed.

scholarly journals Leveraging Surface Siloxide Electronics to Enhance Relaxation Properties of a Single-Molecule Magnet

2020 ◽  
Author(s):  
Maciej Korzynski ◽  
Zachariah Berkson ◽  
Boris Le Guennic ◽  
Olivier Cador ◽  
Christophe Copéret
Keyword(s):  
Single Molecule ◽  
Relaxation Times ◽  
Device Fabrication ◽  
Information Storage ◽  
Commercial Application ◽  
Surface Immobilization ◽  
Single Molecule Magnets ◽  
Magnetization Relaxation ◽  
Surface Deposition ◽  
Magnitude Increase

Single-molecule magnets (SMMs) hold promise for unmatched information storage density as well as applications in quantum computing and spintronics. To date, the most successful SMMs are organometallic lanthanide complexes. However, their surface immobilization, one of the requirements for device fabrication and commercial application, remains challenging due to sensitivity of magnetic properties to small changes in the electronic structure of the parent SMM. Thus, finding controlled approaches to SMM surface deposition is a timely challenge. In this contribution we apply the concept of isolobality to identify siloxides present at the surface of partially dehydroxylated silica as a suitable replacement for archetypal ligand architectures in organometallic SMMs. We demonstrate theoretically and experimentally that isolated siloxide anchorages not only enable successful immobilization, but also lead to two-orders-of-magnitude increase in magnetization relaxation times and provide magnetic site dilution.

scholarly journals Identification and nanomechanical characterization of the fundamental single-strand protofilaments of amyloid α-synuclein fibrils

2018 ◽  
Vol 115 (28) ◽  
pp. 7230-7235 ◽  
Author(s):  
Francesco Simone Ruggeri ◽  
Fabrizio Benedetti ◽  
Tuomas P. J. Knowles ◽  
Hilal A. Lashuel ◽  
Sergey Sekatskii ◽  
...  
Keyword(s):  
Single Molecule ◽  
Self Assembly ◽  
Amyloid Fibrils ◽  
Molecular Assembly ◽  
Single Strand ◽  
Force Microscopy ◽  
Atomic Force ◽  
Presynaptic Protein ◽  
Polypeptide Chains

The formation and spreading of amyloid aggregates from the presynaptic protein α-synuclein in the brain play central roles in the pathogenesis of Parkinson’s disease. Here, we use high-resolution atomic force microscopy to investigate the early oligomerization events of α-synuclein with single monomer angstrom resolution. We identify, visualize, and characterize directly the smallest elementary unit in the hierarchical assembly of amyloid fibrils, termed here single-strand protofilaments. We show that protofilaments form from the direct molecular assembly of unfolded monomeric α-synuclein polypeptide chains. To unravel protofilaments’ internal structure and elastic properties, we manipulated nanomechanically these species by atomic force spectroscopy. The single-molecule scale identification and characterization of the fundamental unit of amyloid assemblies provide insights into early events underlying their formation and shed light on opportunities for therapeutic intervention at the early stages of aberrant protein self-assembly.

scholarly journals Single-molecule visualization of human BLM helicase as it acts upon double- and single-stranded DNA substrates

2019 ◽  
Vol 47 (21) ◽  
pp. 11225-11237 ◽  
Author(s):  
Chaoyou Xue ◽  
James M Daley ◽  
Xiaoyu Xue ◽  
Justin Steinfeld ◽  
Youngho Kwon ◽  
...  
Keyword(s):  
Single Molecule ◽  
Molecular Mechanisms ◽  
Genetic Disorder ◽  
Protein A ◽  
Base Pairs ◽  
Single Stranded Dna ◽  
Double Stranded Dna ◽  
Blm Helicase ◽  
Dna Replication And Repair ◽  
Regulatory Effects

Abstract Bloom helicase (BLM) and its orthologs are essential for the maintenance of genome integrity. BLM defects represent the underlying cause of Bloom Syndrome, a rare genetic disorder that is marked by strong cancer predisposition. BLM deficient cells accumulate extensive chromosomal aberrations stemming from dysfunctions in homologous recombination (HR). BLM participates in several HR stages and helps dismantle potentially harmful HR intermediates. However, much remains to be learned about the molecular mechanisms of these BLM-mediated regulatory effects. Here, we use DNA curtains to directly visualize the activity of BLM helicase on single molecules of DNA. Our data show that BLM is a robust helicase capable of rapidly (∼70–80 base pairs per second) unwinding extensive tracts (∼8–10 kilobases) of double-stranded DNA (dsDNA). Importantly, we find no evidence for BLM activity on single-stranded DNA (ssDNA) that is bound by replication protein A (RPA). Likewise, our results show that BLM can neither associate with nor translocate on ssDNA that is bound by the recombinase protein RAD51. Moreover, our data reveal that the presence of RAD51 also blocks BLM translocation on dsDNA substrates. We discuss our findings within the context of potential regulator roles for BLM helicase during DNA replication and repair.

scholarly journals Single-molecule visualization of RecQ helicase reveals DNA melting, nucleation, and assembly are required for processive DNA unwinding

2015 ◽  
Vol 112 (50) ◽  
pp. E6852-E6861 ◽  
Author(s):  
Behzad Rad ◽  
Anthony L. Forget ◽  
Ronald J. Baskin ◽  
Stephen C. Kowalczykowski
Keyword(s):  
Single Molecule ◽  
Fluorescent Sensor ◽  
Holliday Junctions ◽  
Dna Unwinding ◽  
Recq Helicase ◽  
Dna Breaks ◽  
Dna Helicases ◽  
Double Stranded Dna ◽  
Functional Forms ◽  
And Migration

DNA helicases are motor proteins that unwind double-stranded DNA (dsDNA) to reveal single-stranded DNA (ssDNA) needed for many biological processes. The RecQ helicase is involved in repairing damage caused by DNA breaks and stalled replication forks via homologous recombination. Here, the helicase activity of RecQ was visualized on single molecules of DNA using a fluorescent sensor that directly detects ssDNA. By monitoring the formation and progression of individual unwinding forks, we observed that both the frequency of initiation and the rate of unwinding are highly dependent on RecQ concentration. We establish that unwinding forks can initiate internally by melting dsDNA and can proceed in both directions at up to 40–60 bp/s. The findings suggest that initiation requires a RecQ dimer, and that continued processive unwinding of several kilobases involves multiple monomers at the DNA unwinding fork. We propose a distinctive model wherein RecQ melts dsDNA internally to initiate unwinding and subsequently assembles at the fork into a distribution of multimeric species, each encompassing a broad distribution of rates, to unwind DNA. These studies define the species that promote resection of DNA, proofreading of homologous pairing, and migration of Holliday junctions, and they suggest that various functional forms of RecQ can be assembled that unwind at rates tailored to the diverse biological functions of RecQ helicase.

Investigation of the binding modes between AIE-active molecules and dsDNA by single molecule force spectroscopy

Nanoscale ◽  
2015 ◽  
Vol 7 (19) ◽  
pp. 8939-8945 ◽  
Author(s):  
Ying Chen ◽  
Ke Ma ◽  
Ting Hu ◽  
Bo Jiang ◽  
Bin Xu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Force Spectroscopy ◽  
Binding Modes ◽  
Single Molecule Force Spectroscopy ◽  
Aggregation Induced Emission ◽  
Double Stranded Dna

The binding modes between double-stranded DNA (dsDNA) and typical AIE (aggregation-induced emission)-active molecules were investigated using AFM-based single molecule force spectroscopy.

scholarly journals Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling

2013 ◽  
Vol 110 (46) ◽  
pp. 18519-18524 ◽  
Author(s):  
X. Nan ◽  
E. A. Collisson ◽  
S. Lewis ◽  
J. Huang ◽  
T. M. Tamguney ◽  
...  
Keyword(s):  
Quantitative Analysis ◽  
Single Molecule ◽  
Superresolution Imaging
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