DNA fiber models ABC

Among the 55 fiber models available in 3DNA, the A-, B- and C-DNA types are the most generic – they can be built with bases A, C, G and T in any combination (see table below). Moreover, in addition to the well-known Arnott fiber models (#1, #4 and #7, all from calf thymus), there are newer variants from van Dam & Levitt (#46 and #47) and Premilat & Albiser (#53 to #55).

 1   32.7   2.548  A-DNA (calf thymus)
 4   36.0   3.375  B-DNA (calf thymus)
 7   38.6   3.310  C-DNA (calf thymus)
46   36.0   3.38   B-DNA (BI-type nucleotides)
47   40.0   3.32   C-DNA (BII-type nucleotides)
53  -38.7   3.29   C-DNA (depreciated)
54   32.73  2.56   A-DNA [cf. #1]
55   36.0   3.39   B-DNA [cf. #4]

As shown in Figure 9 of the 3DNA 2003 NAR paper (linked below), the A-, B- and C-DNA fiber models are all right-handed regular straight helices, yet each has distinguished features.

While I could easily envisioned possible applications of the fiber models, especially in connection with analysis and rebuilding routines in 3DNA, it was still a nice surprise to see a recent article by Gossett and Harvey, titled "Computational Screening and Design of DNA-Linked Molecular Nanowires" [Nano Lett., 2011, 11 (2), pp 604–608]. The abstract is quoted below:

DNA can be used as a structural component in the process of making conductive polymers called nanowires. Accurate molecular models could lead to a better understanding of how to prepare these types of materials. Here we present a computational tool that allows potential DNA-linked polymer designs to be screened and evaluated. The approach involves an iterative procedure that adjusts the positions of DNA-linked monomers in order to obtain reasonable molecular geometry compatible with normal DNA conformations and with the properties of the polymer being formed. This procedure has been used to evaluate designs already reported experimentally, as well as to suggest a new design based on pyrrylene vinylene (PV) monomers.

In the article, 3DNA (the web interface version w3DNA) was cited as follows:

The selection of DNA structures is important because the DNA remains fixed throughout the procedure. To reduce the risk of an incorrect result, one should choose a subset of DNA structures that are in some sense representative of DNA conformational space. The DNA structures (A-, B-, and C-form DNA) were obtained using the Web 3DNA web server. We used a poly(dG)-poly(dC) sequence with ideal geometry for each DNA structure. A-DNA was constructed with rise = 2.548 Å and twist = 32.7˚ , B-DNA was constructed with rise = 3.375 Å and twist = 36.0 ˚, and C-DNA was constructed with rise = 3.310 Å and twist = 38.6 ˚.

Indeed, this is a novel application of fiber DNA ABC models!