Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins

Abstract

The conformations of biological macromolecules are intimately related to their cellular functions. Conveniently, the well-characterized dipole–dipole distance-dependence of Förster resonance energy transfer (FRET) makes it possible to measure and monitor the nanoscale spatial dimensions of these conformations using fluorescence spectroscopy. For this reason, FRET is often used in conjunction with single-molecule detection to study a wide range of conformationally dynamic biochemical processes. Written for those not yet familiar with the subject, this review aims to introduce biochemists to the methodology associated with single-molecule FRET, with a particular emphasis on how it can be combined with biomolecular simulations to study diverse interactions between nucleic acids and proteins. In the first section, we highlight several conceptual and practical considerations related to this integrative approach. In the second section, we review a few recent research efforts wherein various combinations of single-molecule FRET and biomolecular simulations were used to study the structural and dynamic properties of biochemical systems involving different types of nucleic acids (e.g., DNA and RNA) and proteins (e.g., folded and disordered).

Spatiotemporal Theranostic Nanoprobes Dynamically Monitor Targeted Tumor Therapy

“…As shown in Figure 1h–j, when the excitation wavelength ( λ ex ) was 405 nm, the emission wavelength ( λ em ) was successfully redshifted from 422 to 810 nm, the same as that of ICG following the self‐assembly of DDASI‐NPs, owing to the increasing RIM through the aggregation of DAS dimer, [ 15 ] thus improving the total fluorescence intensity and facilitating the calculation of that by simple addition. [ 26 ] Notably, on one hand, as displayed in Figure 1k, the fluorescence intensity of ICG in DDASI‐NPs became weaker due to the ACQ, but AIE enhanced their overall fluorescence intensity, promoting stronger in vivo tracing. On the other hand, as seen in Figure 1l,m, the fluorescence intensity of AIE was rapidly quenched within 6 h and that of ICG returned to normal as a result of the disintegration of nanoprobes triggered by the intracellular microenvironment, causing the overall intracellular fluorescence intensity to first decrease and then increase.…”

FRET-mediated quenching of BODIPY fluorescent nanoparticles by methylene blue and its application to bacterial imaging

“…The FRET process is broadly used in bioimaging [39] or biosensing [40], especially to track the binding of proteins or DNA to specific ligands [41]. However, there are fewer examples of the use of energy transfer to improve the contrast in bioimaging.…”

Fluorescence lifetime analysis of smFRET with contribution of PIFE on donor and acceptor

“…Also, mechanisms underlying reactions, e.g., protein-nucleic acid and protein-protein interactions, can now be observed in real time. 4,[7][8][9][10][11][12][13][14][15][16][17][18][19] Singlemolecule FRET (smFRET) has been used to answer fundamental questions about replication, recombination, transcription, translation, RNA folding and catalysis, non-canonical DNA dynamics, protein folding and conformational changes, various motor proteins, membrane fusion proteins, ion channels, signal transduction, to name just a few with this list growing rapidly. 18,[20][21][22][23][24] FRET signals must be interpreted carefully in order to avoid the effect of other photo-physical events on the results.…”