Structure of M1 RNA as determined by psoralen cross-linking

Biochemistry. 1988 Jan 26;27(2):570-5. doi: 10.1021/bi00402a011.

Abstract

The RNA moiety of ribonuclease P from Escherichia coli (M1 RNA) has been photoreacted with 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen (HMT) and long-wave UV light (320-380 nm) in a buffer containing 60 mM Mg2+, where the RNA moiety acts as a true catalyst of tRNA processing. Limited specific digestion and two-dimensional gel electrophoresis yield fragments cross-linked by HMT. By photoreversal of the isolated cross-linked fragments and enzymatic sequencing of the fragments, the positions of the cross-links have been elucidated. This method allows us to locate the cross-link to +/- 15 nucleotides. Further assignments of the exact locations of the cross-links have been made on the basis of the known photoreactivity of the psoralen with different bases. Nine unique cross-links have been isolated in the M1 RNA including four long-range interactions. The short-range interactions are discussed here in detail.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • Cross-Linking Reagents*
  • Electrophoresis, Polyacrylamide Gel
  • Endoribonucleases* / isolation & purification
  • Escherichia coli Proteins*
  • Furocoumarins*
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • RNA, Bacterial*
  • Ribonuclease P
  • Trioxsalen* / analogs & derivatives

Substances

  • Cross-Linking Reagents
  • Escherichia coli Proteins
  • Furocoumarins
  • RNA, Bacterial
  • hydroxymethyltrioxsalen
  • Endoribonucleases
  • Ribonuclease P
  • ribonuclease P, E coli
  • Trioxsalen