Base-stacking interactions stabilize nucleic acid structures. Many ways exist to account for such interactions, including quantum chemical calculations (see for example the review by Sponer et al. [2008] on Nature and magnitude of aromatic stacking of nucleic acid bases.). In 3DNA, base-stacking interactions are assessed from planar projections of the ring and exocyclic atoms in consecutive bases or base pairs; the larger the overlap area, the stronger the stacking interactions, and vice versa.
Over the years, I’ve seen a few publications taking advantage of this 3DNA parameter. Here are two recent ones:
To analyze the role of the sequence regularity for the double-helical structure, we calculated the overall overlapping of base pairs (stacking) at every step of the two duplexes of 20mer pG(CUG)6C and the duplex of 19mer pGG(CGG)3(CUG)2CC using the program 3DNA (Lu & Olson, 2003).
Basepair overlap values are calculated by 3DNA software.35
Hopefully, more 3DNA users would notice this ‘little’ feature and make good use of it.
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.
While browsing the August 2012 40(14) issue of Nucleic Acids Research (NAR), I noticed the following four papers that cite 3DNA:
The local base pair step parameters as calculated by x3dna (37,38) are represented in the Supplementary Figure S2.
The initial extended single-stranded DNA structure was obtained using the 3DNA program (15).
DNA structures were analyzed using 3DNA (31).
Each of these DNA structural models consists of values for all base-pair step parameters (roll, twist, tilt, rise, shift and slide) for each dinucleotide or trinucleotide. This enabled us to convert DNA sequences into 3D coordinates by using the rebuilding part of 3DNA (39), a program for analysis, rebuilding and visualization of 3D nucleic acid structures.
The above four NAR papers appear in the sections “Nucleic Acid Enzymes” (1), “Structural Biology” (2) and “Methods Online” (1), and cover research areas of DNA-protein interactions (3) and G-quadruplex structures (1). As quoted above, two papers employ the analyzing components of 3DNA, while the other two take advantage of its rebuilding facilities.
Between the two primary 3DNA publications, the 2003 NAR paper (NAR03) is cited twice, while the 2008 Nature Protocol paper (NP08) is cited three times. Apparently, after some time lag, NP08 has gradually overpassed NAR03 to become the community’s favorite citation for 3DNA.
