title: Specificity of the photoreaction of 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen with ribonucleic acid. Identification of reactive sites in Escherichia coli phenylalanine-accepting transfer ribonucleic acid.
abstract: In order to test the potential of psoralen photoaddition for the probing of RNA conformation at sequence resolution, we have analyzed the specificity of the reaction of 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen (HMT) with Escherichia coli tRNAPhe. The sites of HMT covalent addition have been identified by a combination of analytical techniques involving chemical cleavage of the tRNAPhe molecule at the m7G site and gel electrophoresis of RNase T1 digests together with paper electrophoretic characterization of HMT-modified nucleotides and oligonucleotides. In addition, we have taken advantage of the alteration of the cleavage rate of pancreatic RNase adjacent to a photoadduct. HMT photoaddition shows a very high preference for uracil residues. However, important differences in HMT photoreactivity are observed for various U sites of the tRNAPhe molecule. Reactivity of specific bases has been correlated with partial melting of the molecule. Data available so far indicate a strong preference of the photoreactive probe for a "loose" helical conformation as compared with a tight helix, whereas a random coil appears poorly reactive.
mesh_terms: D001665:Binding Sites; D004926:Escherichia coli / Q000378:metabolism*; D011564:Furocoumarins / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D010777:Photochemistry; D012329:RNA, Bacterial / Q000378:metabolism*; D012346:RNA, Transfer, Amino Acyl / Q000378:metabolism*; D014307:Trioxsalen / Q000031:analogs & derivatives / Q000378:metabolism*
chemical_list: D011564:Furocoumarins; D012329:RNA, Bacterial; D012346:RNA, Transfer, Amino Acyl; C016507:hydroxymethyltrioxsalen; D014307:Trioxsalen