scholarly journals Single molecule analysis of structural fluctuations in DNA nanostructures

Nanoscale ◽  
2019 ◽  
Vol 11 (39) ◽  
pp. 18475-18482 ◽  
Author(s):  
Mette D. E. Jepsen ◽  
Rasmus Schøler Sørensen ◽  
Christopher Maffeo ◽  
Aleksei Aksimentiev ◽  
Jørgen Kjems ◽  
...  
Keyword(s):  
Single Molecule ◽  
Local Structure ◽  
Brownian Dynamics ◽  
Dna Origami ◽  
Coarse Grain ◽  
Dna Nanostructures ◽  
Single Molecule Fret ◽  
Structural Fluctuations ◽  
Single Molecule Analysis

The local structure of DNA origami boxes shows fluctuations, visualized through single molecule FRET and coarse grain Brownian dynamics.

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 Single-molecule Analysis Using DNA Origami Nanostructures

2013 ◽  
Vol 53 (3) ◽  
pp. 153-157 ◽  
Author(s):  
Masayuki ENDO ◽  
Hiroshi SUGIYAMA
Keyword(s):  
Single Molecule ◽  
Dna Origami ◽  
Single Molecule Analysis

scholarly journals Expanding the Scope of Single Molecule FRET with DNA Origami

2011 ◽  
Vol 100 (3) ◽  
pp. 368a
Author(s):  
Carlos E. Castro ◽  
Hendrik Dietz
Keyword(s):  
Single Molecule ◽  
Dna Origami ◽  
Single Molecule Fret

Single-Molecule Analysis Using DNA Origami

2011 ◽  
Vol 51 (4) ◽  
pp. 874-890 ◽  
Author(s):  
Arivazhagan Rajendran ◽  
Masayuki Endo ◽  
Hiroshi Sugiyama
Keyword(s):  
Single Molecule ◽  
Dna Origami ◽  
Single Molecule Analysis

Single‐Molecule FRET Ruler Based on Rigid DNA Origami Blocks

ChemPhysChem ◽  
2011 ◽  
Vol 12 (3) ◽  
pp. 689-695 ◽  
Author(s):  
Ingo H. Stein ◽  
Verena Schüller ◽  
Philip Böhm ◽  
Philip Tinnefeld ◽  
Tim Liedl
Keyword(s):  
Single Molecule ◽  
Dna Origami ◽  
Single Molecule Fret

scholarly journals Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding

2019 ◽  
Author(s):  
Ikenna C Okafor ◽  
Digvijay Singh ◽  
Yanbo Wang ◽  
Minhee Jung ◽  
Haobo Wang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Engineering ◽  
Dna Unwinding ◽  
Dependent Manner ◽  
Guide Rnas ◽  
Single Molecule Fret ◽  
Wide Range ◽  
The Cost ◽  
Single Molecule Analysis ◽  
Target Activity

Abstract Cas9 has made a wide range of genomic manipulation possible. However, its specificity continues to be a challenge. Non-canonical gRNAs and new engineered variants of Cas9 have been developed to improve specificity, but at the cost of the on-target activity. DNA unwinding is a checkpoint before cleavage by Cas9, and was shown to be made more sensitive to sequence mismatches by specificity-enhancing mutations in engineered Cas9s. Here we performed single-molecule FRET-based DNA unwinding experiments using various combinations of non-canonical gRNAs and different Cas9s. All engineered Cas9s were less promiscuous than wild type when canonical gRNA was used, but HypaCas9 had much-reduced on-target unwinding. Cas9-HF1 and eCas9 showed the best balance between low promiscuity and high on-target activity with canonical gRNA. When extended gRNAs with one or two non-matching guanines added to the 5′ end were used, Sniper1-Cas9 showed the lowest promiscuity while maintaining high on-target activity. Truncated gRNA generally reduced unwinding and adding a non-matching guanine to the 5′ end of gRNA influenced unwinding in a sequence-context dependent manner. Our results are consistent with cell-based cleavage data and provide a mechanistic understanding of how various Cas9/gRNA combinations perform in genome engineering.

ChemInform Abstract: Single-Molecule Analysis Using DNA Origami

ChemInform ◽  
2012 ◽  
Vol 43 (19) ◽  
pp. no-no
Author(s):  
Arivazhagan Rajendran ◽  
Masayuki Endo ◽  
Hiroshi Sugiyama
Keyword(s):  
Single Molecule ◽  
Dna Origami ◽  
Single Molecule Analysis

scholarly journals Single-molecule DNA origami aptasensors for real-time biomarker detection

2020 ◽  
Vol 8 (30) ◽  
pp. 6352-6356
Author(s):  
Keitel Cervantes-Salguero ◽  
Mark Freeley ◽  
Jorge L. Chávez ◽  
Matteo Palma
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Conformational Changes ◽  
Dna Origami ◽  
Biomarker Detection ◽  
Dna Nanostructures

DNA nanostructures as platforms to monitor the inherent conformational changes of aptamers upon analyte binding, with single-molecule resolution and real-time capability.

Reversible Reconfiguration of DNA Origami Nanochambers Monitored by Single-Molecule FRET

2015 ◽  
Vol 54 (12) ◽  
pp. 3592-3597 ◽  
Author(s):  
Barbara Saccà ◽  
Yuji Ishitsuka ◽  
Rebecca Meyer ◽  
Andreas Sprengel ◽  
Elisa-Charlott Schöneweiß ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Origami ◽  
Single Molecule Fret
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