A chemical approach to studies of the three-dimensional structure of tRNA - alkylation with a reagent covalently bound to a "peculiar site'

Chemical and computer probing of RNA structure

Ribonucleic acids (RNAs) are one of the most important types of biopolymers. RNAs play key roles in the storage and multiplication of genetic information. They are important in catalysis and RNA splicing and are the most important steps of translation. This chapter describes experimental methods for probing RNA structure and theoretical methods allowing the prediction of thermodynamically favorable RNA folding. These methods are complementary and together they provide a powerful approach to determine the structure of RNAs. The three-dimensional (tertiary) structure of RNA is formed by hydrogen-bonding among functional groups of nucleosides in different regions of the molecule, by coordination of polyvalent cations, and by stacking between the double-stranded regions present in the RNA. The tertiary structures of only some small RNAs have been determined by high-resolution X-ray crystallographic analysis and nuclear magnetic resonance analysis. The most widely used approach for the investigation of RNA structure is chemical and enzymatic probing, in combination with theoretical methods and phylogenetic studies allowing the prediction of variants of RNA folding. Investigations of RNA structures with different enzymatic and chemical probes can provide detailed data allowing the identification of double-stranded regions of the molecules and nucleotides involved in tertiary interactions.

Synthesis and intramolecular crosslinking of chlorambucilyl (prolyl)n [3H]phenylalanyl-tRNAPhe (yeast), n = 0, 5, 11 and 15

Rigid, variable-length oligoproline crosslinking reagents, which we call molecular rulers, are a potentially powerful tool for probing the solution structures of tRNA and other biological macromolecules. We wish to demonstrate the feasibility of molecular rulers on a well-studied model system, yeast phenylalanine tRNA, before applying them to less well understood structures. We have found chlorambucil (4-(4-(bis(2-chloroethyl)amino)phenyl)-butanoic acid) to be suitable for use as an alkylating function attached to the imino end of oligo-L-proline spacers which are peptide bonded at their carboxyl ends to the alpha-amine of [3H]Phe-tRNAPhe (yeast). Chlorambucil and chlorambucilyl oligoprolines may be readily and sensitively assayed by their alkylation kinetics with aqueous pyridine as measured by optical absorbance of the product. The pyridine reaction seemed to be the first order in chlorambucil, k1 = (5.4 +/- 1.0) X 10(-3) min-1, zero order in pyridine, and was strongly inhibited by Me2SO. Filter assays of tRNA alkylation by chlorambucilyl [3H]prolyl proline suggested that this reaction is also first order in alkylation reagent, but somewhat dependent on tRNA concentration, and also strongly inhibited by Me2SO. Full alkylation activity was regained upon removal of Me2SO. Modification of [3H]Phe-tRNAPhe (yeast) with the N-hydroxysuccinimide esters of chlorambucilyl (prolyl)n was accomplished with yields of 100% for n = 0, 92% for n = 5, 94% for n = 11 and 44% for n = 15, in 80% Me2SO/CHCl3 at pH 9, 37 degrees C, conditions under which chlorambucil alkylation of tRNA is strongly inhibited. The rates of intramolecular crosslinking of chlorambucilyl (prolyl)n [3H]Phe-tRNAPhe (yeast) were measured assuming a first-order process, giving K1 = (5.3 +/- 0.2) X 10(-3) min-1 for n = 0, (3.2 +/- 0.4) X 10(-4) min-1 for n = 5, (6.8 +/- 0.8) X 10(-5) min-1 for n = 11 and (1.6 +/- 0.4) X 10(-4) min-1 for n = 15. Yields of intramolecularly crosslinked tRNA were 80% for n = 0 after 4 h in 10 mM NH4OAc (pH 6)/1 mM Mg(OAc)2 at 37 degrees C, 7% for n = 5, 3% for n = 11, and 5% for n = 15.

Molecular rulers for measuring RNA structure: sites of crosslinking in chlorambucilyl-phenylalanyl-tRNAPhe (yeast) and chlorambucilyl-pentadecaprolyl-phenylalanyl-tRNAPhe (yeast) intramolecularly crosslinked in aqueous solution

Intramolecular crosslinking of yeast phenylalanine tRNA in aqueous solution with rigid, variable-length crosslinking reagents, which we call "molecular rulers," has given results in reasonable agreement with the crystal structure. Chlorambucilyl-[3H]phenylalanyl-tRNAPhe crosslinked intramolecularly at G-71 and A-73, whereas chlorambucilyl-pentadecaprolyl-[3H]phenylalanyl-tRNAPhe crosslinked at G-20 and Y-37. The pentadecaprolyl reagent was predicted to be 62 A long, including chlorambucil and phenylalanine; the sites that it reached are 60 A distant from the 3' OH (in the case of G-20) or 80 A distant (in the case of Y-37) in the crystal structure of tRNAPhe. The close agreement between the length of the reagent and the distance of G-20 from the 3' OH in the crystal structure illustrates the rigidity of the tRNAPhe molecule in the dihydrouridine loop region at the corner of the molecule. The apparent ability of the 62-A-long reagent to crosslink to a site, Y-37, that is 80 A distant from the 3' OH in the crystal structure appears to illustrate the flexibility of both the 3' A-C-C-A terminus and the anticodon stem and loop, with respect to the tRNA molecule. These observations demonstrate the utility of oligoproline-based crosslinking reagents as rigid, variable-length molecular rulers for biological macromolecules in solution.

A route to RNA with an alkylating group at the 5'-triphosphate residue

Reaction of ATP with N,N,N'-tris(2-chloroethyl), N' (p-formyl-phenyl)propylenediamine-1,3 (abbreviation C13R) afforded a gamma-ester of ATP (abbreviation C1RpppA) - the product of alkylation by an aliphatic nitrogen mustard residue of C13R. The alkylating activity of the aromatic nitrogen mustard residue of C1RpppA is suppressed by the electron-acceptor effect of the p-formyl group. C1RpppA is a substrate of RNA-polymerase, and affords RNA with C1RpppA-residues at the 5'-termini.

Inhibition of deacylation and improvement in N-hydroxysuccinimide ester modification of phenylalanyl-tRNA by dimethyl sulfoxide

We have found that dimethyl sulfoxide significantly inhibits deacylation of Phe-tRNA. This allows a high pH in N-hydroxysuccinimide ester reactions while maintaining a high level of aminoacylated tRNA, improving the overall yield of the Phe-tRNA modification reaction.