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 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.

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.

scholarly journals Encoding Multiple Virtual Signals in DNA Barcodes with Single-Molecule FRET

Nano Letters ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1694-1701 ◽  
Author(s):  
Sung Hyun Kim ◽  
Hyunwoo Kim ◽  
Hawoong Jeong ◽  
Tae-Young Yoon
Keyword(s):  
Single Molecule ◽  
Dna Barcodes ◽  
Single Molecule Fret

Single-Molecule FRET-Based Dynamic DNA Sensor

ACS Sensors ◽  
2021 ◽  
Author(s):  
Anoja Megalathan ◽  
Kalani M. Wijesinghe ◽  
Soma Dhakal
Keyword(s):  
Single Molecule ◽  
Dna Sensor ◽  
Single Molecule Fret

scholarly journals Single-molecule FRET dynamics of molecular motors in an ABEL trap

Methods ◽  
2021 ◽  
Author(s):  
Maria Dienerowitz ◽  
Jamieson A.L. Howard ◽  
Steven D. Quinn ◽  
Frank Dienerowitz ◽  
Mark C. Leake
Keyword(s):  
Single Molecule ◽  
Molecular Motors ◽  
Single Molecule Fret
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