FRETmatrix: a methodological platform for the simulation and analysis of FRET in nucleic acids

In the ‘Advance Access’ section of Nucleic Acids Research, published on September 12, 2012 (DOI: 10.1093/nar/gks856), I came across the paper FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids by Søren Preus et al.. In this work, the authors developed a methodological platform (implemented in the Matlab package FRETmatrix’) to simulate the base-base FRET in order to elucidate the structure and dynamics of nucleic acids.

Reading through the text, I am pleased to find that the authors take advantage of the matrix-based Calladine and El Hassen Scheme (CEHS) for ‘building nucleic acid geometrical models’, and kindly cite SCHNArP, 3DNA, and the standard base-reference frame paper. They provide a succinct description of the model building process, and also note the connection between CEHS and SCHNArP. From the very beginning, I appreciated the elegance of the CEHS method — it is simple, mathematical rigorous, and generally applicable for quantifying the relative position and orientation between any two rigid bodies. SCHNAaP/SCHNArP implements the analysis/rebuilding components of CEHS in an expanded form, and CEHS further serves as a corner stone of 3DNA.

Another point worth noting is Figure 3 (see below) where the authors present (a–c) Representative examples of output geometries produced by FRETmatrix (right) along with the block representation of the corresponding structures produced by 3DNA (28) (left). To the best of my memory, this is one of the very few times where 3DNA’s blocview functionality is explicitly cited.

geometrical model building combined with FRET simulations in three model structures





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