FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids.

ABSTRACT: Förster resonance energy transfer (FRET) is a technique commonly used to unravel the structure and conformational changes of biomolecules being vital for all living organisms. Typically, FRET is performed using dyes attached externally to nucleic acids through a linker that complicates quantitative interpretation of experiments because of dye diffusion and reorientation. Here, we report a versatile, general methodology for the simulation and analysis of FRET in nucleic acids, and demonstrate its particular power for modelling FRET between probes possessing limited diffusional and rotational freedom, such as our recently developed nucleobase analogue FRET pairs (base-base FRET). These probes are positioned inside the DNA/RNA structures as a replacement for one of the natural bases, thus, pr

SUBMITTER: Preus S 

PROVIDER: S-EPMC3592456 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature