scholarly journals Bench-Top Fabrication of Single-Molecule Nanoarrays by DNA Origami Placement

ACS Nano ◽  
2021 ◽  
Author(s):  
Rishabh M. Shetty ◽  
Sarah R. Brady ◽  
Paul W. K. Rothemund ◽  
Rizal F. Hariadi ◽  
Ashwin Gopinath
Keyword(s):  
Single Molecule ◽  
Dna Origami

Graphene-on-Glass Preparation and Cleaning Methods Characterized by Single-Molecule DNA Origami Fluorescent Probes and Raman Spectroscopy

ACS Nano ◽  
2021 ◽  
Author(s):  
Stefan Krause ◽  
Evelyn Ploetz ◽  
Johann Bohlen ◽  
Patrick Schüler ◽  
Renukka Yaadav ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Single Molecule ◽  
Fluorescent Probes ◽  
Dna Origami ◽  
Glass Preparation ◽  
Cleaning Methods

DNA Origami as a DNA Repair Nanosensor at the Single-Molecule Level

2013 ◽  
Vol 52 (30) ◽  
pp. 7747-7750 ◽  
Author(s):  
Maria Tintoré ◽  
Isaac Gállego ◽  
Brendan Manning ◽  
Ramon Eritja ◽  
Carme Fàbrega
Keyword(s):  
Dna Repair ◽  
Single Molecule ◽  
Dna Origami ◽  
Single Molecule Level

DNA Origami Nanoantennas with over 5000-fold Fluorescence Enhancement and Single-Molecule Detection at 25 μM

Nano Letters ◽  
2015 ◽  
Vol 15 (12) ◽  
pp. 8354-8359 ◽  
Author(s):  
Anastasiya Puchkova ◽  
Carolin Vietz ◽  
Enrico Pibiri ◽  
Bettina Wünsch ◽  
María Sanz Paz ◽  
...  
Keyword(s):  
Single Molecule ◽  
Fluorescence Enhancement ◽  
Dna Origami ◽  
Single Molecule Detection

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.

Single molecule microscopy methods for the study of DNA origami structures

2010 ◽  
Vol 74 (7) ◽  
pp. 688-698 ◽  
Author(s):  
Victoria Birkedal ◽  
Mingdong Dong ◽  
Monika M. Golas ◽  
Bjoern Sander ◽  
Ebbe Sloth Andersen ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Origami ◽  
Single Molecule Microscopy

scholarly journals Arranging Small Molecules with Subnanometer Precision on DNA Origami Substrates for the Single‐Molecule Investigation of Protein–Ligand Interactions

2020 ◽  
Vol 1 (1) ◽  
pp. 2000038
Author(s):  
Jingyuan Huang ◽  
Antonio Suma ◽  
Meiying Cui ◽  
Guido Grundmeier ◽  
Vincenzo Carnevale ◽  
...  
Keyword(s):  
Small Molecules ◽  
Single Molecule ◽  
Dna Origami ◽  
Protein Ligand Interactions ◽  
Ligand Interactions

scholarly journals Direct observation and analysis of TET-mediated oxidation processes in a DNA origami nanochip

2020 ◽  
Vol 48 (8) ◽  
pp. 4041-4051 ◽  
Author(s):  
Xiwen Xing ◽  
Shinsuke Sato ◽  
Nai-Kei Wong ◽  
Kumi Hidaka ◽  
Hiroshi Sugiyama ◽  
...  
Keyword(s):  
Single Molecule ◽  
High Speed ◽  
Excision Repair ◽  
Regulation Of Gene Expression ◽  
Dna Demethylation ◽  
Dna Origami ◽  
Enzymatic Reactions ◽  
Oxidation Reactions ◽  
Methyl Cytosine ◽  
Tet Enzymes

Abstract DNA methylation and demethylation play a key role in the epigenetic regulation of gene expression; however, a series of oxidation reactions of 5-methyl cytosine (5mC) mediated by ten-eleven translocation (TET) enzymes driving demethylation process are yet to be uncovered. To elucidate the relationship between the oxidative processes and structural factors of DNA, we analysed the behavior of TET-mediated 5mC-oxidation by incorporating structural stress onto a substrate double-stranded DNA (dsDNA) using a DNA origami nanochip. The reactions and behaviors of TET enzymes were systematically monitored by biochemical analysis and single-molecule observation using atomic force microscopy (AFM). A reformative frame-like DNA origami was established to allow the incorporation of dsDNAs as 5mC-containing substrates in parallel orientations. We tested the potential effect of dsDNAs present in the tense and relaxed states within a DNA nanochip on TET oxidation. Based on enzyme binding and the detection of oxidation reactions within the DNA nanochip, it was revealed that TET preferred a relaxed substrate regardless of the modification types of 5-oxidated-methyl cytosine. Strikingly, when a multi-5mCG sites model was deployed to further characterize substrate preferences of TET, TET preferred the fully methylated site over the hemi-methylated site. This analytical modality also permits the direct observations of dynamic movements of TET such as sliding and interstrand transfer by high-speed AFM. In addition, the thymine DNA glycosylase-mediated base excision repair process was characterized in the DNA nanochip. Thus, we have convincingly established the system's ability to physically regulate enzymatic reactions, which could prove useful for the observation and characterization of coordinated DNA demethylation processes at the nanoscale.

Atomic force microscopy-based single-molecule force spectroscopy detects DNA base mismatches

Nanoscale ◽  
2019 ◽  
Vol 11 (37) ◽  
pp. 17206-17210 ◽  
Author(s):  
Wenjing Liu ◽  
Yourong Guo ◽  
Kaizhe Wang ◽  
Xingfei Zhou ◽  
Ying Wang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Force Spectroscopy ◽  
Dna Origami ◽  
Single Molecule Force Spectroscopy ◽  
Force Microscopy ◽  
Atomic Force ◽  
Base Pair Mismatch ◽  
Dna Base ◽  
Single Base Pair ◽  
Target Molecules

AFM-based single-molecule-force spectroscopy is limited by low throughput. We introduce addressable DNA origami to study multiple target molecules at once. Target DNAs differing by only a single-base pair mismatch are clearly differentiated.

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