Direct observation of spatial configuration and structural stability of locked Y-shaped DNA structure

RSC Advances ◽  
2016 ◽  
Vol 6 (105) ◽  
pp. 103270-103274 ◽  
Author(s):  
Tapas Paul ◽  
Padmaja P. Mishra
Keyword(s):  
Structural Properties ◽  
Structural Stability ◽  
Direct Observation ◽  
Single Molecule ◽  
Building Block ◽  
Spatial Configuration ◽  
Three Dimensional ◽  
Dna Structure ◽  
Bottom Up ◽  
Single Molecule Fret

A new building block unit (locked Y-DNA) and its structural properties for self-assembled, bottom-up, three-dimensional supramolecular nanoarchitectural probe ​have been introduced using single-molecule FRET imaging.

Empirical and Theoretical Evaluation of a Tree-Shaped DNA Nanostructure with a Looped Arm (L-DNA)

2021 ◽  
Vol 13 (8) ◽  
pp. 1452-1457
Author(s):  
Jeonghun Kim ◽  
So Yeon Ahn ◽  
Soong Ho Um
Keyword(s):  
Melting Temperature ◽  
Structural Stability ◽  
Building Block ◽  
Dna Structure ◽  
Secondary Structures ◽  
Theoretical Evaluation ◽  
Single Stranded Dna ◽  
Practical Applications ◽  
Dna Nanostructure ◽  
Specific Selectivity

Several nanostructures have been created with the advent of nanotechnology. DNA has been recognized as a new building block material in addition to its genetic coding role because of its unique features (e.g., intrinsic biocompatibility, precise tenability, specific selectivity). DNA can be organized into a variety of self-assembled nanomaterials including a sphere, a ball, and even an emoticon. In particular, a tree-shaped DNA structure possessing characteristic fractural patterns is easily controlled by size and functionality and can be exploited in various fields. Here, we report an empirical and theoretical evaluation of a Y-shaped tree DNA nanostructure with a looped arm (L-DNA). The synthesized L-DNAs were analyzed for thermal and structural stability. The melting temperature (Tm) of a Y-shaped DNA (Y-DNA) as a core unit and a model DNA nanostructure comprising of central Y-DNA and looped arm were measured individually. According to the complexity (e.g., increased length of the single stranded DNA (ssDNA) used), its yield suddenly decreased with the generation of ssDNAs with distinctive secondary structures. A complicated DNA product is predicted by considering the Tm of expected secondary structures, with increased Tm with respect to variation in salt concentrations. Therefore, the new DNA nanostructure may be utilized as a platform for various practical applications.

scholarly journals Three-dimensional molecular modeling with single molecule FRET

2011 ◽  
Vol 173 (3) ◽  
pp. 497-505 ◽  
Author(s):  
Axel T. Brunger ◽  
Pavel Strop ◽  
Marija Vrljic ◽  
Steven Chu ◽  
Keith R. Weninger
Keyword(s):  
Molecular Modeling ◽  
Single Molecule ◽  
Three Dimensional ◽  
Single Molecule Fret

Direct observation of structural properties and fluorescent trapping sites in macrocyclic porphyrin arrays at the single-molecule level

2016 ◽  
Vol 18 (5) ◽  
pp. 3871-3877 ◽  
Author(s):  
Sujin Ham ◽  
Ji-Eun Lee ◽  
Suhwan Song ◽  
Xiaobin Peng ◽  
Takaaki Hori ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Structural Properties ◽  
Direct Observation ◽  
Single Molecule ◽  
Site Selection ◽  
Wide Field ◽  
Single Molecule Level ◽  
Selection For ◽  
Trapping Sites

By utilizing single-molecule defocused wide-field fluorescence microscopy, we have investigated the molecular structural properties and ascertained site selection for fluorescent trapping sites in multichromophoric systems.

scholarly journals Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication

2020 ◽  
Author(s):  
Benjamin M. Akiyama ◽  
Monica E. Graham ◽  
Zoe O′Donoghue ◽  
J. David Beckham ◽  
Jeffrey S. Kieft
Keyword(s):  
Single Molecule ◽  
Conformational Changes ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Reading Frame ◽  
X Ray Crystallography ◽  
Single Molecule Fret ◽  
High Sequence Conservation ◽  
Rna Genome ◽  
Viral Lifecycle

ABSTRACTMosquito-borne flaviviruses (MBFVs) including dengue, West Nile, yellow fever, and Zika viruses have an RNA genome encoding one open reading frame flanked by 5′ and 3′ untranslated regions (UTRs). The 3′ UTRs of MBFVs contain regions of high sequence conservation in structured RNA elements known as dumbbells (DBs) that regulate translation and replication of the viral RNA genome, functions proposed to depend on the formation of an RNA pseudoknot. To understand how DB structure provides this function, we used x-ray crystallography and structural modeling to reveal the details of its three-dimensional fold. The structure confirmed the predicted pseudoknot and molecular modeling revealed how conserved sequences form a four-way junction that appears to stabilize the pseudoknot. Single-molecule FRET suggests that the DB pseudoknot is a stable element that can regulate the switch between translation and replication during the viral lifecycle by modulating long-range RNA conformational changes.

Direct observation of the formation of DNA triplexes by single-molecule FRET measurements

2012 ◽  
Vol 12 (4) ◽  
pp. 1027-1032 ◽  
Author(s):  
Il Buem Lee ◽  
Ja Yil Lee ◽  
Nam-Kyung Lee ◽  
Seok-Cheol Hong
Keyword(s):  
Direct Observation ◽  
Single Molecule ◽  
Dna Triplexes ◽  
Single Molecule Fret

scholarly journals Direct Observation of pre-mRNA Arrangements During Spliceosome Assembly Using Single Molecule FRET

2011 ◽  
Vol 100 (3) ◽  
pp. 233a
Author(s):  
Daniel J. Crawford ◽  
Larry J. Friedman ◽  
Aaron A. Hoskins ◽  
Jeff Gelles ◽  
Melissa J. Moore
Keyword(s):  
Direct Observation ◽  
Single Molecule ◽  
Spliceosome Assembly ◽  
Single Molecule Fret

A New 1000kv Electron Microscope

1969 ◽  
Vol 27 ◽  
pp. 100-101
Author(s):  
J.L. Williams ◽  
K. Heathcote ◽  
E.J. Greer
Keyword(s):  
Electron Microscope ◽  
Direct Observation ◽  
High Voltage ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Specimen Thickness ◽  
Voltage Electron ◽  
High Voltage Electron Microscope ◽  
Dynamic Experiments ◽  
Conventional Instrument

High Voltage Electron Microscope already offers exciting experimental possibilities to Biologists and Materials Scientists because the increased specimen thickness allows direct observation of three dimensional structure and dynamic experiments on effectively bulk specimens. This microscope is designed to give maximum accessibility and space in the specimen region for the special stages which are required. At the same time it provides an ease of operation similar to a conventional instrument.

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