Student Answers for PS#4: Problem 3

Student Answers for PS#4: Problem 3Highlight a feature of tRNA^Phe not shown in the tRNA structure tutorial.tRNA^Phe images for problem 3 above. Student initials and captions below.

KD: The image shows the unusual base pairing between bases A44 and N,N-dimethly-G26 which is responsible for the 26° kink in the anticodon and D arm helix structures.
Some tertiary base pair interactions found in yeast tRNA that are predicted also to occur in other tRNAs. These features might be common to all species.

PHa: tRNA^Phe is shown in cartoon view (yellow) except for some noted base pairs. The first is the G-C bp between position 15 and 48, in red sticks. It was predicted by Michael Levitt. He noticed that whenever the base in positon 15 is a G, position 48 is C; and whenever 15 is A, 48 is U. However, the two strands containing these bases run in parallel directions. The structure of the base pair formed there is not a Watson-Crick structure. Instead, one base is rotated roughly 180° with respect to the normal W-C position. The resulting structure can be formed essentially the same way by G-C or A-U. However there is no longer a dyad axis, and so C-G or U-A pairs here would require different positions of the phosphodiester backbone. Because these combinations are never observed, the backbone structure in this region probably remains constant.

PHb: The second example is the C13-G22 - m⁷G46 base triple. Here, the first two bases are Watson-Crick paired, whereas the third is not.

WL: Unusual base interaction in tRNA: Base triplet (A9, A23, U12); hydrogen are displayed.

GZa: View of the wireframe bases in CPK mode, with the bases flanking the anticodon in green.
I was interested in the conformation of the tRNA around the anticodons, so I zoomed in on that area. The first feature of note is the kink in the backbone between nucleotides 33 and 34, allowing the RNA to loop around and form a double helix with itself. One question about this area is the source of the stabilization of this kink. Is it stabilized simply by the complementary base pairing of the bases further up on the helix or is there another factor? Another feature of note is the abnormally large sidechain of OMG37. Perhaps this orients the anticodon bases into the proper orientation.

GZb: The same bases in spacefill to show the packing interactions. In this view, one can see definite packing interactions between the OMG37 and nucleotide 36. The long extra side chain appears to interact with the H-bonding area. This needs more examination. However, it appears that U33 does not have stacking interactions - it comes close only to phosphates from the backbone. Thus, it seems that there are no stacking interactions stabilizing the kink in the backbone.