While browsing the latest issue (May 2017) of the RNA journal, I came across the paper titled The structure of an E. coli tRNA_f^Met 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 N1*O2 H-bond.

   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[1]: "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.