Three structural biology papers in the latest issue of NAR cite 3DNA

While browsing the latest 39(2) January 2011 issue of Nucleic Acids Research (NAR), I found, to my great surprise, three papers that cite 3DNA. These papers, all under the "structural biology" section, are of interest to me from their titles and abstracts, so I downloaded the PDF versions and read through each of them.

For this blog post, #100 by incidence, it would be intriguing to look into the context to see how 3DNA is cited.

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"Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI" by Vanamee et al. (Mount Sinai School of Medicine, and New England Biolabs):

Analysis of the stereochemical quality of the protein model and assignment of secondary structure were conducted with PROCHECK (13). DNA analysis was performed with 3DNA (14). Solvent-accessible surface areas were calculated in CNS with the algorithm of Lee and Richards employing a 1.4-Å probe(15). Figures were prepared using PyMOL (www.pymol.org). [p713, from bottom left to middle right]

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"DNA intercalation without flipping in the specific ThaI–DNA complex" by Firczuk et al. (Poland, Germany and UK):

An oligoduplex with the correct sequence in standard B-DNA geometry was generated with the program 3DNA (44), and manually adjusted to fit the highly distorted DNA in the structure. ... The programs COOT (45), REFMAC (46) and CNS (47) were used for refinement. [p747, top left]

Analysis with the 3DNA software (44) shows that the intercalation increases the rise between base pairs to about 7 Å or approximately twice its usual value (Figure 5B). Phosphorus–phosphorus (Pn–Pn+1) distances in the DNA backbone are only mildly altered (values range from 5.6 to 7.0 Å). Instead, the extra height of the two CG steps comes at the expense of the twist, which is reduced from its usual value of about 36° (360°/10) to between 10 and 15°. A view toward the major groove shows that the inner base pairs of the recognition sequence are strongly tilted (Figure 5). According to the 3DNA software (44), the first CG step has a negative tilt of about ~12°, which results in the oblique orientation of the following base pairs. The central GC step is characterized by a tilt close to 0°, reflecting the nearly parallel arrangement of the middle bases. Finally, the second CG step has a positive tilt of about 15° which restores the standard orientation of the downstream base pairs. A side view of the DNA indicates a bend at the center of the recognition sequence which is primarily due to the positive ~12° roll of the central GC step into the major groove (Table 1). The 3DNA program also indicates that the propeller twist is positive for the specifically recognized sequence, and (as expected for the standard B-DNA) negative for most of the flanking base pairs. [p749, top right]

Table 1. DNA distortion in complex with ThaI restriction endonuclease: all parameters were calculated with the 3DNA software (44). [p750, middle left]

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"On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics" by Fadda and Pomès (Ireland and Canada):

MD simulations were run with versions 3.3.3 up to 4.0.4 of the GROMACS software package (47,48).

Structural parameters were determined with the 3DNA software package (51,52). The pymol (www .pymol.org) software package was used to generate figures. [p769, bottom right]

Established in 1974 and currently with an impact factor of 7.479, NAR has also been chosen by the Special Libraries Association as one of the top 100 most influential journals in medicine and biology over the last 100 years. The citations by the three papers in the latest issue of NAR illustrate unambiguously 3DNA's big impact in structural biology.