scholarly journals Supported Lipid Bilayers and DNA Curtains for High-Throughput Single-Molecule Studies

Author(s):  
Ilya J. Finkelstein ◽  
Eric C. Greene
2021 ◽  
Vol 118 (48) ◽  
pp. e2113202118
Author(s):  
Rafael L. Schoch ◽  
Frank L. H. Brown ◽  
Gilad Haran

Lipid membranes are complex quasi–two-dimensional fluids, whose importance in biology and unique physical/materials properties have made them a major target for biophysical research. Recent single-molecule tracking experiments in membranes have caused some controversy, calling the venerable Saffman–Delbrück model into question and suggesting that, perhaps, current understanding of membrane hydrodynamics is imperfect. However, single-molecule tracking is not well suited to resolving the details of hydrodynamic flows; observations involving correlations between multiple molecules are superior for this purpose. Here dual-color molecular tracking with submillisecond time resolution and submicron spatial resolution is employed to reveal correlations in the Brownian motion of pairs of fluorescently labeled lipids in membranes. These correlations extend hundreds of nanometers in freely floating bilayers (black lipid membranes) but are severely suppressed in supported lipid bilayers. The measurements are consistent with hydrodynamic predictions based on an extended Saffman–Delbrück theory that explicitly accounts for the two-leaflet bilayer structure of lipid membranes.


Nano Letters ◽  
2019 ◽  
Vol 19 (9) ◽  
pp. 6182-6191 ◽  
Author(s):  
Damiano Verardo ◽  
Björn Agnarsson ◽  
Vladimir P. Zhdanov ◽  
Fredrik Höök ◽  
Heiner Linke

2009 ◽  
Vol 81 (13) ◽  
pp. 5130-5138 ◽  
Author(s):  
Christopher B. Fox ◽  
Joshua R. Wayment ◽  
Grant A. Myers ◽  
Scott K. Endicott ◽  
Joel M. Harris

2016 ◽  
Vol 113 (46) ◽  
pp. E7185-E7193 ◽  
Author(s):  
Rahul Grover ◽  
Janine Fischer ◽  
Friedrich W. Schwarz ◽  
Wilhelm J. Walter ◽  
Petra Schwille ◽  
...  

In eukaryotic cells, membranous vesicles and organelles are transported by ensembles of motor proteins. These motors, such as kinesin-1, have been well characterized in vitro as single molecules or as ensembles rigidly attached to nonbiological substrates. However, the collective transport by membrane-anchored motors, that is, motors attached to a fluid lipid bilayer, is poorly understood. Here, we investigate the influence of motors’ anchorage to a lipid bilayer on the collective transport characteristics. We reconstituted “membrane-anchored” gliding motility assays using truncated kinesin-1 motors with a streptavidin-binding peptide tag that can attach to streptavidin-loaded, supported lipid bilayers. We found that the diffusing kinesin-1 motors propelled the microtubules in the presence of ATP. Notably, we found the gliding velocity of the microtubules to be strongly dependent on the number of motors and their diffusivity in the lipid bilayer. The microtubule gliding velocity increased with increasing motor density and membrane viscosity, reaching up to the stepping velocity of single motors. This finding is in contrast to conventional gliding motility assays where the density of surface-immobilized kinesin-1 motors does not influence the microtubule velocity over a wide range. We reason that the transport efficiency of membrane-anchored motors is reduced because of their slippage in the lipid bilayer, an effect that we directly observed using single-molecule fluorescence microscopy. Our results illustrate the importance of motor–cargo coupling, which potentially provides cells with an additional means of regulating the efficiency of cargo transport.


2013 ◽  
Vol 104 (2) ◽  
pp. 222a
Author(s):  
Martin Kurylowicz ◽  
Sanjeevan Shivakumar ◽  
Aisha Shamas-Din ◽  
Brian Leber ◽  
David W. Andrews ◽  
...  

2018 ◽  
Author(s):  
Jeffrey M. Schaub ◽  
Hongshan Zhang ◽  
Michael M. Soniat ◽  
Ilya J. Finkelstein

AbstractSingle-stranded DNA (ssDNA) is a critical intermediate in all DNA transactions. As ssDNA is more flexible than double-stranded (ds)DNA, interactions with ssDNA-binding proteins (SSBs) may significantly compact or elongate the ssDNA molecule. Here, we develop and characterize low-complexity ssDNA curtains, a high-throughput single-molecule assay to simultaneously monitor protein binding and correlated ssDNA length changes on supported lipid bilayers. Low-complexity ssDNA is generated via rolling circle replication of short synthetic oligonucleotides, permitting control over the sequence composition and secondary structure-forming propensity. One end of the ssDNA is functionalized with a biotin, while the second is fluorescently labeled to track the overall DNA length. Arrays of ssDNA molecules are organized at microfabricated barriers for high-throughput single-molecule imaging. Using this assay, we demonstrate that E. coli SSB drastically and reversibly compacts ssDNA templates upon changes in NaCl concentration. We also examine the interactions between a phosphomimetic RPA and ssDNA. Our results indicate that RPA-ssDNA interactions are not significantly altered by these modifications. We anticipate low-complexity ssDNA curtains will be broadly useful for single-molecule studies of ssDNA-binding proteins involved in DNA replication, transcription and repair.


2016 ◽  
Vol 113 (44) ◽  
pp. E6749-E6756 ◽  
Author(s):  
P. Benjamin Stranges ◽  
Mirkó Palla ◽  
Sergey Kalachikov ◽  
Jeff Nivala ◽  
Michael Dorwart ◽  
...  

Scalable, high-throughput DNA sequencing is a prerequisite for precision medicine and biomedical research. Recently, we presented a nanopore-based sequencing-by-synthesis (Nanopore-SBS) approach, which used a set of nucleotides with polymer tags that allow discrimination of the nucleotides in a biological nanopore. Here, we designed and covalently coupled a DNA polymerase to an α-hemolysin (αHL) heptamer using the SpyCatcher/SpyTag conjugation approach. These porin–polymerase conjugates were inserted into lipid bilayers on a complementary metal oxide semiconductor (CMOS)-based electrode array for high-throughput electrical recording of DNA synthesis. The designed nanopore construct successfully detected the capture of tagged nucleotides complementary to a DNA base on a provided template. We measured over 200 tagged-nucleotide signals for each of the four bases and developed a classification method to uniquely distinguish them from each other and background signals. The probability of falsely identifying a background event as a true capture event was less than 1.2%. In the presence of all four tagged nucleotides, we observed sequential additions in real time during polymerase-catalyzed DNA synthesis. Single-polymerase coupling to a nanopore, in combination with the Nanopore-SBS approach, can provide the foundation for a low-cost, single-molecule, electronic DNA-sequencing platform.


2012 ◽  
Vol 6 (3) ◽  
pp. 036502 ◽  
Author(s):  
Jeroen A. van Kan ◽  
Ce Zhang ◽  
Piravi Perumal Malar ◽  
Johan R. C. van der Maarel

Sign in / Sign up

Export Citation Format

Share Document