Curves+ and 3DNA are currently the most widely used programs for analyzing nucleic acid structures (predominantly double helices). As noted in my blog post, Curves+ vs 3DNA, these two programs also complement each other in terms of features. It thus makes sense to run both to get a better understanding of the DNA/RNA structures one is interested in.
Indeed, over the past few years, I have seen quite a few articles citing both 3DNA and Curves+. Listed below are three recent examples:
- Structures and energetics of four adjacent G·U pairs that stabilize an RNA helix by Gu et al. (2015) in J Phys Chem B.
The helical parameters were measured with 3DNA33 and Curves+.34 The local helical parameters are defined with regard to base steps and without regard to a global axis.
- 5-Formylcytosine alters the structure of the DNA double helix by Raiber et al. (2015) in Nat Struct Mol Biol.
Structure analysis. Helix, base and base pair parameters were calculated with 3DNA or curve+ software packages23,24.
- Structural insights into the effects of 2′-5′ linkages on the RNA duplex by Sheng et al. (2014) in Proc Natl Acad Sci USA.
The major global difference between the native and mixed backbone structures is that the RNA backbone is compressed or kinked in strands containing the modified linkage (Fig. 3 B and C, by CURVES) (30). … To compare the three RNA structures at a more detailed and local level, we calculated the base pair helical and step parameters for all three structures using the 3DNA software tools (31) (Fig. 4 and Table S2). [In the Results section]
For each snapshot, the structural parameters—including six base pair parameters, six local base pair step parameters, and pseudorotation angles for each nucleotide—were calculated using 3DNA (31). The two terminal base pairs are omitted for the 3DNA analysis, because they unwind frequently in the triple 2′-5′-linked duplex. [In the Materials and Methods section]
Reading through these papers, however, it is not clear to me if the authors took advantage of the
find_pair -curves+ option in 3DNA, as detailed in Building a bridge between Curves+ and 3DNA. Hopefully, this post will help draw more attention to this connection between Curves+ and 3DNA.