A DNA Origami Platform for Single-Pair Förster Resonance Energy Transfer Investigation of DNA–DNA Interactions and Ligation

2019 ◽  
Vol 142 (2) ◽  
pp. 815-825 ◽  
Author(s):  
Kira Bartnik ◽  
Anders Barth ◽  
Mauricio Pilo-Pais ◽  
Alvaro H. Crevenna ◽  
Tim Liedl ◽  
...  
Keyword(s):  
Energy Transfer ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Dna Origami ◽  
Forster Resonance Energy Transfer ◽  
Förster Resonance Energy Transfer ◽  
Single Pair ◽  
Dna Interactions ◽  
Förster Resonance

EXPLORING THE FOLDING FREE ENERGY LANDSCAPE OF SMALL RNA MOLECULES BY SINGLE-PAIR FÖRSTER RESONANCE ENERGY TRANSFER

2008 ◽  
Vol 03 (04) ◽  
pp. 439-457 ◽  
Author(s):  
ANDREI YU. KOBITSKI ◽  
ALEXANDER NIERTH ◽  
MARTIN HENGESBACH ◽  
ANDRES JÄSCHKE ◽  
MARK HELM ◽  
...  
Keyword(s):  
Energy Transfer ◽  
Small Rnas ◽  
Energy Landscape ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Forster Resonance Energy Transfer ◽  
Förster Resonance Energy Transfer ◽  
Single Pair ◽  
Rna Molecules ◽  
Förster Resonance

Proteins and RNA are biological macromolecules built from linear polymers. The process by which they fold into compact, well-defined, three-dimensional architectures to perform their functional tasks is still not well understood. It can be visualized by Brownian motion of an ensemble of molecules through a rugged energy landscape in search of an energy minimum corresponding to the native state. To explore the conformational energy landscape of small RNAs, single pair Förster resonance energy transfer (spFRET) experiments on solutions as well as on surface-immobilized samples have provided new insights. In this review, we focus on our recent work on two FRET-labeled small RNAs, the Diels-Alderase (DAse) ribozyme and the human mitochondrial tRNA Lys . For both RNAs, three different conformational states can be distinguished, and the associated mean FRET efficiencies provide clues about their structural properties. The systematic variation of their free energies with the concentration of Mg 2+ counterions was analyzed quantitatively by using a thermodynamic model that separates conformational changes from Mg 2+ binding. Furthermore, time-resolved spFRET studies on immobilized DAse reveal slow interconversions between intermediate and folded states on the time scale of ~ 100 ms. The quantitative data obtained from spFRET experiments may likely assist in the further development of theories and models addressing the folding dynamics and (counterion-dependent) energetics of RNA molecules.

scholarly journals Directional Photonic Wire Mediated by Homo-Förster Resonance Energy Transfer on a DNA Origami Platform

ACS Nano ◽  
2017 ◽  
Vol 11 (11) ◽  
pp. 11264-11272 ◽  
Author(s):  
Francesca Nicoli ◽  
Anders Barth ◽  
Wooli Bae ◽  
Fabian Neukirchinger ◽  
Alvaro H. Crevenna ◽  
...  
Keyword(s):  
Energy Transfer ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Dna Origami ◽  
Forster Resonance Energy Transfer ◽  
Förster Resonance Energy Transfer ◽  
Photonic Wire ◽  
Förster Resonance

scholarly journals Combining MFD and PIE for Accurate Single-Pair Förster Resonance Energy Transfer Measurements

ChemPhysChem ◽  
2012 ◽  
Vol 13 (4) ◽  
pp. 1060-1078 ◽  
Author(s):  
Volodymyr Kudryavtsev ◽  
Martin Sikor ◽  
Stanislav Kalinin ◽  
Dejana Mokranjac ◽  
Claus A. M. Seidel ◽  
...  
Keyword(s):  
Energy Transfer ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Forster Resonance Energy Transfer ◽  
Förster Resonance Energy Transfer ◽  
Single Pair ◽  
Förster Resonance

scholarly journals Plasmon-assisted Förster resonance energy transfer at the single-molecule level in the moderate quenching regime

Nanoscale ◽  
2019 ◽  
Vol 11 (16) ◽  
pp. 7674-7681 ◽  
Author(s):  
J. Bohlen ◽  
Á. Cuartero-González ◽  
E. Pibiri ◽  
D. Ruhlandt ◽  
A. I. Fernández-Domínguez ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Energy Transfer ◽  
Single Molecule ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Dna Origami ◽  
Forster Resonance Energy Transfer ◽  
Förster Resonance Energy Transfer ◽  
Single Molecule Level ◽  
Förster Resonance

A single molecule “acceptor bleaching” technique is employed to study the effect of gold nanoparticles on FRET using DNA origami templates.

Sign in / Sign up

Export Citation Format

Share Document