title: Carbodiimide modification analysis of aminoacylated yeast phenylalanine tRNA: evidence for change in the apex region.
abstract: The G- and U-specific reagent, carbodiimide was used to probe the solution structure of aminoacylated yeast phenylalanine tRNA. Both quantitative and qualitative changes in modification were observed when the modification patterns of tRNA-CCA(3'OH), tRNA-CCA(3'NH2) and phe-tRNA-CCA(3'NH2) were compared. Five nucleotides were modified in all cases, D16 and G20 in the D-loop, U33 and Gm34 in the anticodon loop and U47, in the region of the extra arm. Small changes occurred in the D-loop with incorporation of the adenosine analogue manifest as new, low levels of modification of G22 (D-stem) and a loss of sensitivity to Mg+2 in modification of D16. Aminoacylation resulted in new modification of G19, modification of a residue in the T psi CG sequence, and a 2.5-fold increase in modification of G22. Taken together the results show that aminoacylation causes increased exposure of bases in the apex region of the L-shaped molecule where the D- and psi-loops are joined. The effects observed could occur as a consequence of stable or dynamic changes in conformation.
mesh_terms: D003028:CME-Carbodiimide / Q000031:analogs & derivatives; D002234:Carbodiimides; D055598:Chemical Phenomena; D002621:Chemistry; D003839:Deoxyadenosines / Q000031:analogs & derivatives*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010761:Phosphorus Radioisotopes; D012346:RNA, Transfer, Amino Acyl; D012441:Saccharomyces cerevisiae; D013329:Structure-Activity Relationship
chemical_list: D002234:Carbodiimides; D003839:Deoxyadenosines; D010761:Phosphorus Radioisotopes; D012346:RNA, Transfer, Amino Acyl; D003028:CME-Carbodiimide; C019247:3'-amino-3'-deoxyadenosine