scholarly journals Optical tweezer and TIRF microscopy for single molecule manipulation of RNA/DNA nanostructures including their rubbery property and single molecule counting

2021 ◽  
Vol 0 (0) ◽  
pp. 1-26
Author(s):  
Ghimire Chiran ◽  
◽  
Guo Peixuan
Keyword(s):  
Single Molecule ◽  
Optical Tweezer ◽  
Dna Nanostructures ◽  
Tirf Microscopy ◽  
Single Molecule Manipulation

scholarly journals In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics

2014 ◽  
Vol 10 (2) ◽  
pp. e1003456 ◽  
Author(s):  
Pascal Carrivain ◽  
Maria Barbi ◽  
Jean-Marc Victor
Keyword(s):  
Rigid Body ◽  
Single Molecule ◽  
In Silico ◽  
Rigid Body Dynamics ◽  
Body Dynamics ◽  
Single Molecule Manipulation

scholarly journals New Tool for Single Molecule Manipulation: Optical Pushing

2012 ◽  
Vol 102 (3) ◽  
pp. 385a-386a
Author(s):  
Gerrit Sitters ◽  
Niels Laurens ◽  
Emile J. de Rijk ◽  
Erwin J.G. Peterman ◽  
Gijs J.L. Wuite
Keyword(s):  
Single Molecule ◽  
Single Molecule Manipulation

scholarly journals The role of surface corrugation and tip oscillation in single-molecule manipulation with a non-contact atomic force microscope

2014 ◽  
Vol 5 ◽  
pp. 202-209 ◽  
Author(s):  
Christian Wagner ◽  
Norman Fournier ◽  
F Stefan Tautz ◽  
Ruslan Temirov
Keyword(s):  
Frequency Shift ◽  
Single Molecule ◽  
Oscillation Amplitude ◽  
Surface Corrugation ◽  
Atomic Force ◽  
Data Points ◽  
Atomic Surface ◽  
Tetracarboxylic Dianhydride ◽  
Single Molecule Manipulation

Scanning probe microscopy (SPM) plays an important role in the investigation of molecular adsorption. The possibility to probe the molecule–surface interaction while tuning its strength through SPM tip-induced single-molecule manipulation has particularly promising potential to yield new insights. We recently reported experiments, in which 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) molecules were lifted with a qPlus-sensor and analyzed these experiments by using force-field simulations. Irrespective of the good agreement between the experiment and those simulations, systematic inconsistencies remained that we attribute to effects omitted from the initial model. Here we develop a more realistic simulation of single-molecule manipulation by non-contact AFM that includes the atomic surface corrugation, the tip elasticity, and the tip oscillation amplitude. In short, we simulate a full tip oscillation cycle at each step of the manipulation process and calculate the frequency shift by solving the equation of motion of the tip. The new model correctly reproduces previously unexplained key features of the experiment, and facilitates a better understanding of the mechanics of single-molecular junctions. Our simulations reveal that the surface corrugation adds a positive frequency shift to the measurement that generates an apparent repulsive force. Furthermore, we demonstrate that the scatter observed in the experimental data points is related to the sliding of the molecule across the surface.

scholarly journals 3D DNA structural barcode copying and random access

2020 ◽  
Author(s):  
Filip Bošković ◽  
Alexander Ohmann ◽  
Ulrich F. Keyser ◽  
Kaikai Chen
Keyword(s):  
Data Storage ◽  
Single Molecule ◽  
Self Assembly ◽  
Large Scale ◽  
Three Dimensional ◽  
Random Access ◽  
Scale Production ◽  
Digital Information ◽  
Dna Nanostructures ◽  
Large Scale Production

AbstractThree-dimensional (3D) DNA nanostructures built via DNA self-assembly have established recent applications in multiplexed biosensing and storing digital information. However, a key challenge is that 3D DNA structures are not easily copied which is of vital importance for their large-scale production and for access to desired molecules by target-specific amplification. Here, we build 3D DNA structural barcodes and demonstrate the copying and random access of the barcodes from a library of molecules using a modified polymerase chain reaction (PCR). The 3D barcodes were assembled by annealing a single-stranded DNA scaffold with complementary short oligonucleotides containing 3D protrusions at defined locations. DNA nicks in these structures are ligated to facilitate barcode copying using PCR. To randomly access a target from a library of barcodes, we employ a non-complementary end in the DNA construct that serves as a barcode-specific primer template. Readout of the 3D DNA structural barcodes was performed with nanopore measurements. Our study provides a roadmap for convenient production of large quantities of self-assembled 3D DNA nanostructures. In addition, this strategy offers access to specific targets, a crucial capability for multiplexed single-molecule sensing and for DNA data storage.

scholarly journals Biophysical characterization of DNA origami nanostructures reveals inaccessibility to intercalation binding sites

2019 ◽  
Author(s):  
Helen L. Miller ◽  
Sonia Contera ◽  
Adam J.M. Wollman ◽  
Adam Hirst ◽  
Katherine E. Dunn ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Single Molecule ◽  
Targeted Drug Delivery ◽  
Binding Sites ◽  
Dna Origami ◽  
Target Cells ◽  
Dna Nanostructures ◽  
Synthetic Dna ◽  
Drug Molecules ◽  
Targeted Drug

AbstractIntercalation of drug molecules into synthetic DNA nanostructures formed through self-assembled origami has been postulated as a valuable future method for targeted drug delivery. This is due to the excellent biocompatibility of synthetic DNA nanostructures, and high potential for flexible programmability including facile drug release into or near to target cells. Such favourable properties may enable high initial loading and efficient release for a predictable number of drug molecules per nanostructure carrier, important for efficient delivery of safe and effective drug doses to minimise non-specific release away from target cells. However, basic questions remain as to how intercalation-mediated loading depends on the DNA carrier structure. Here we use the interaction of dyes YOYO-1 and acridine orange with a tightly-packed 2D DNA origami tile as a simple model system to investigate intercalation-mediated loading. We employed multiple biophysical techniques including single-molecule fluorescence microscopy, atomic force microscopy, gel electrophoresis and controllable damage using low temperature plasma on synthetic DNA origami samples. Our results indicate that not all potential DNA binding sites are accessible for dye intercalation, which has implications for future DNA nanostructures designed for targeted drug delivery.

scholarly journals Rational design of DNA nanostructures for single molecule biosensing

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Mukhil Raveendran ◽  
Andrew J. Lee ◽  
Rajan Sharma ◽  
Christoph Wälti ◽  
Paolo Actis
Keyword(s):  
Single Molecule ◽  
Rational Design ◽  
Dna Nanostructures

A Universal Assay for Making DNA, RNA, and RNA–DNA Hybrid Configurations for Single-Molecule Manipulation in Two or Three Steps without Ligation

2019 ◽  
Vol 8 (7) ◽  
pp. 1663-1672 ◽  
Author(s):  
Ya-Jun Yang ◽  
Lun Song ◽  
Xiao-Cong Zhao ◽  
Chen Zhang ◽  
Wen-Qiang Wu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Single Molecule Manipulation

The complex folding behavior of HIV-1-protease monomer revealed by optical-tweezer single-molecule experiments and molecular dynamics simulations

2014 ◽  
Vol 195 ◽  
pp. 32-42 ◽  
Author(s):  
M. Caldarini ◽  
P. Sonar ◽  
I. Valpapuram ◽  
D. Tavella ◽  
C. Volonté ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Single Molecule ◽  
Optical Tweezer ◽  
Dynamics Simulations ◽  
Hiv 1
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