FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids
Journal article, 2013

Forster 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, providing unique control of their position and orientation and the advantage of reporting from inside sites of interest. In demonstration studies, not requiring molecular dynamics modelling, we obtain previously inaccessible insight into the orientation and nanosecond dynamics of the bases inside double-stranded DNA, and we reconstruct high resolution 3D structures of kinked DNA. The reported methodology is accompanied by a freely available software package, FRETmatrix, for the design and analysis of FRET in nucleic acid containing systems.

double-stranded dna

geometry

resonance energy-transfer

dependence

orientation

acceptor

visualization

helices

base analog

hydrogen-bonds

Author

S. Preus

University of Copenhagen

K. Kilsa

University of Copenhagen

Francois-Alexandre Miannay

Chalmers, Chemical and Biological Engineering, Physical Chemistry

Bo Albinsson

Chalmers, Chemical and Biological Engineering, Physical Chemistry

Marcus Wilhelmsson

Chalmers, Chemical and Biological Engineering, Physical Chemistry

Nucleic Acids Research

0305-1048 (ISSN) 1362-4962 (eISSN)

Vol. 41 1 Article Number: e18-

Areas of Advance

Nanoscience and Nanotechnology (2010-2017)

Life Science Engineering (2010-2018)

Subject Categories

Physical Chemistry

Biochemistry and Molecular Biology

Biophysics

Chemical Sciences

DOI

10.1093/nar/gks856

More information

Latest update

5/8/2018 1