While browsing the latest issue (May 2017) of the RNA journal, I came across the paper titled The structure of an E. coli tRNAfMet A1–U72 variant shows an unusual conformation of the A1–U72 base pair by Monestier et al.. Reading through the text, I am pleasantly surprised by the two references to DSSR as shown below:
An analysis using DSSR (Lu et al. 2015) identifies all the secondary structure elements characteristic of the classical cloverleaf secondary structure as well as usual tertiary interactions that stabilize the L-shaped tertiary fold of the molecule.
As a consequence, the opening parameter (Lu et al. 2015) of the A1–U72 base pair becomes unusually high (153.42°). The NH2 group of A1 points toward the minor groove of the acceptor helix. An interaction between the N1 of A1 and the O2 of U72 (d = 3.0 Å) is observed which requires protonation of the N1 atom of A1.
The PDB id for the deposited structure is 5l4o. Running DSSR on this structure is straightforward:
x3dna-dssr -i=5l4o.pdb --more. As with the classic yeast phenylalanine tRNA (PDB id: 1ehz), DSSR identifies two helices, three hairpin loops, one [2,1,5,0] four-way junction loop, among other features.
With regard to the unusual A1-U72 pair highlighted in the title of the paper, DSSR provides the following information. Note the
* in the unconventional
1 A.A1 A.U72 A+U -- n/a tWW tW+W [-14.4(...) ~C3'-endo lambda=32.9] [-172.4(anti) ~C3'-endo lambda=65.0] d(C1'-C1')=10.80 d(N1-N9)=9.19 d(C6-C8)=10.68 tor(C1'-N1-N9-C1')=173.6 H-bonds: "N1*O2(carbonyl)[2.99]" interBase-angle=6 Simple-bpParams: Shear=3.53 Stretch=1.71 Buckle=2.0 Propeller=-6.0 bp-pars: [-0.32 3.91 0.01 6.32 -0.26 153.56]
This citation is yet another example of DSSR’s adoption by experimental biologists. I can only expect to see more such type of DSSR usages in the coming years.