Isolation of transfer RNA isoacceptors by chromatography on dihydroxyboryl-substituted cellulose, polyacrylamide, and glass

Applications of reversible covalent chemistry in analytical sample preparation

Reversible covalent chemistry (RCC) adds another dimension to commonly used sample preparation techniques like solid-phase extraction (SPE), solid-phase microextraction (SPME), molecular imprinted polymers (MIPs) or immuno-affinity cleanup (IAC): chemical selectivity. By selecting analytes according to their covalent reactivity, sample complexity can be reduced significantly, resulting in enhanced analytical performance for low-abundance target analytes. This review gives a comprehensive overview of the applications of RCC in analytical sample preparation. The major reactions covered include reversible boronic ester formation, thiol-disulfide exchange and reversible hydrazone formation, targeting analyte groups like diols (sugars, glycoproteins and glycopeptides, catechols), thiols (cysteinyl-proteins and cysteinyl-peptides) and carbonyls (carbonylated proteins, mycotoxins). Their applications range from low abundance proteomics to reversible protein/peptide labelling to antibody chromatography to quantitative and qualitative food analysis. In discussing the potential of RCC, a special focus is on the conditions and restrictions of the utilized reaction chemistry.

Boronate affinity adsorption of RNA: possible role of conformational changes

Batch equilibrium adsorption isotherm determination is used to characterize the adsorption of mixed yeast RNA on agarose-immobilized m-aminophenylboronic acid. It is shown that the affinity-enhancing influence of divalent cations depends strongly on the precise nature of the cation used, with barium being far more effective than the conventionally-used magnesium. This adsorption-promoting influence of barium is suggested to arise primarily from ionic influences on the structure and rigidity of the RNA molecule, as the adsorption of ribose-based small molecules is not similarly affected. The substitution of barium for the standard magnesium counterion does not greatly promote the adsorption of DNA, implying that the effect is specific to RNA and may be useful in boronate-based RNA separations. RNA adsorption isotherms exhibit sharp transitions as functions of temperature, and these transitions occur at different temperatures with Mg2+ and with Ba2+. Adsorption affinity and capacity were found to increase markedly at lower temperatures, suggestive of an enthalpically favored interaction process. The stoichiometric displacement parameter, Z, in Ba2+ buffer is three times the value in Mg2+ buffer, and is close to unity.

The role of the CCA sequence of tRNA in the peptidyl transfer reaction

Peptidyl transfer is a key step in the process of protein biosynthesis. To examine the role of the universal CCA terminal sequence of tRNA in the process of peptidyl transfer, various mutant transcripts of Escherichia coli valine tRNA were constructed. Peptidyl transferase activity, monitored by the 'fragment reaction' with a slight modification, was decreased by mutation at any one base of CCA. The effect of mutation was moderate in the UCA, CUA and CCG mutants. Replacement of A76 by a pyrimidine nucleotide, or replacement of either C74 or C75 by a purine nucleotide caused a marked decrease in the activity. These findings suggested that the universal CCA terminus of tRNA makes a functional interaction with ribosomal RNA by base-pairing.

Resolution of RNA using high-performance liquid chromatography

High-performance liquid chromatographic techniques can be very effective for the resolution and isolation of nucleic acids. The characteristic ionic (phosphodiesters) and hydrophobic (nucleobases) properties of RNAs can be exploited for their separation. In this respect anion-exchange and reversed-phase chromatography have been successfully employed in the analysis and/or isolation of RNAs. In some cases, particularly tRNAs, chromatographic separations which rely upon multiple interactions between the solute and mobile and/or stationary phases have been highly effective. Mixed-mode chromatography involving simultaneous ionic and hydrophobic interactions, has been employed to resolve complex mixtures of tRNAs. Hydrophobic-interaction chromatography using gradients of decreasing salt concentration and weakly hydrophobic stationary phases has allowed the resolution of some tRNA mixtures as well as the analysis of modified materials.

High-performance liquid chromatography of transfer RNAs. Separation of transfer RNAs from mammalian sources

A survey of recent advances in high-performance liquid chromatography (HPLC) of tRNA is presented here. The polystyrene and reversed-phase anion exchangers are discussed for their ability to resolve tRNAs without loss of the aminoacyl-tRNA bond. The HPLC of a tRNA of choice, based on the affinity principle, is studied. Both chemical (boronate) and biological (plant lectins) affinity groups for the tRNA interaction are described. A comprehensive scheme is presented for the separation of four mammalian tRNAs. Scope of future research in this area is also discussed.

m-Aminophenylboronate agarose specifically binds capped snRNA and mRNA

m-Aminophenylboronate-substituted agarose binds specifically RNA chains carrying a mature 5' cap. The binding occurs most effectively at pH greater than 8 and involves diester formation between the negatively charged tetrahedric boronate group and the cisdiol of the ribose of the cap. The positive charge introduced by the m7G methylation is necessary for efficient binding although two closely spaced cis-diol groups alone (as in the cap analog NADH) are sufficient for binding. Non-capped RNA (like poly (U) and rRNA) or decapped RNA are not bound. It is shown that the matrix can be used for the isolation of capped small nuclear RNA and mRNA.

Synthesis of a nitrobenzeneboronic acid substituted polyacrylamide and its use in purifying isoaccepting transfer ribonucleic acids

Highly purified isoaccepting species of transfer ribonucleic acid (tRNA) were prepared by use of a polyacrylamide substituted with nitrobenzeneboronic acid functional groups. This method exploits the well-known ability of boronic acids to complex with RNA cis-diols. tRNA isoacceptors were obtained by enzymatically acylating a mixture of tRNA species with a single amino acid and passing the mixture over a solid-state nitrobenzeneboronic acid at pH 6.5 or 7.0. Pure aminoacyl-tRNA eluted at the column liquid volume, and unacylated tRNA species were bound. The bound species were recovered by lowering the pH of the eluant to 4.5. This procedure is uncomplicated, rapid, and applicable to nearly all tRNA isoacceptors. It does not chemically modify the tRNA(s) of interest or adversely affect their ability to be aminoacylated. Since boronic acids must be ionized to complex with cis-1,2-diols, boronic acid derivatives were prepared which ionize at a pH compatible with the stability of the aminoacyl bond. Two isomeric benzeneboronic acids with pKas of 6.8 and 7.4 were synthesized by introducing electron-withdrawing nitro groups into the aromatic ring. The addition of succinyl side chains permitted the nitrobenzeneboronic acids to be coupled to aminoethylpolyacrylamide. The properties of the nitrobenzeneboronic acid substituted acrylamide were illustrated by enriching phenylalanyl-tRNA at pH 7.0 to greater than 95% purity (1.63 nmol of phenylalanine accepted per A260 unit of tRNA) and seryl-tRNA isoacceptors at pH 6.5 to essentially theoretical purity (1.58 nmol of serine accepted per A260 unit of tRNA.

Structural changes in the glutamine-chargeable Escherichia coli transfer RNA-Trp produced by chemical modification with sodium bisulfite

Glutamine-mischargeable tRNA produced by sodium bisulfite-treated Escherichia coli tRNA-Trp was isolated by dihydroxyboryl-cellulose affinity column chromatography. This tRNA was shown to have dual specificity tryptophan and glutamine, and, when charged with either amino acid, bound to ribosomes in response to the non-sense codon UAG but not in response to the tryptophan codon UGG. The results were consistent with the reported properties of Su+7 tRNA. The bisulfite-treated tRNA-Trp migrated as two bands during polyacrylamide gel electrophoresis. The faster moving band (band I) coincided with that of untreated tRNA-Trp. The slower moving band (band II) coincided with the glutamine-chargeable tRNA-Trp. Su+7 tRNA behaved like band II tRNA upon gel electrophoresis. Nucleotide sequence analysis showed that a cytidine-uridine transition occurred at the 1st or the 2n position of the anitcodon of band II tRNA. Band I and band II tRNAs differed from each other in their thermal melting profiles. It is suggested that the single base change in the anticodon is responsible for the altered conformation of band II tRNA.

Ribosome binding site analysis of ovalbumin messenger ribonucleic acid

The region of the ovalbumin messenger ribonucleic acid (mRNAov) molecule bound to the 40S ribosomal subunit and its associated initiation factors in the wheat germ cell-free translation system were isolated and characterized. Two mRNAov fragments, 87 and 92 nucleotides in length, were protected from T1 ribonuclease digestion by binding of guanosine 5',beta,gamma-methylenetriphosphate and were shown by hybridization and fingerprint mapping to be derived from the 5' end of mRNAov. Both these mRNAov fragments were of sufficient length to contain both the cap structure and the AUG initiation codon. Four T1-resistant oligonucleotides, prepared by direct digestion of mRNAov with T1 ribonuclease were also found to bind to the wheat germ 40S ribosomal subunit. Nucleotide sequence analysis of these oligonucleotides revealed (1) that they were not a subset of the ribosome binding fragments described above, (2) that they were derived from within the mRNAov molecule (one from within the coding region and three from the noncoding region at the 3' end of the mRNAov molecule), and (3) that three of the four mRNAov nucleotides contained 3'-terminal AUG trinucleotides. These data suggested that features of the mRNAov molecule in addition to the nucleotide sequence might be important in specifying the correct ribosome binding site for the initiation of protein synthesis. The amount of mRNAov bound to the wheat germ 40S ribosomal subunit in a preinitiation complex was found to vary inversely with the potassium ion concentration. Lowering the potassium concentration to levels suboptimal for translation also resulted in the protection of larger fragments of the mRNAov molecule derived from the same 5'-end region as the ribosome binding fragments described above. The ability of the cap analogue 7-methylguanosine 5'-phosphate (m7G5'p) to reduce the amount of mRNAov bound to the wheat germ 40S ribosomal subunit was found to depend directly on thepotassium concentration. Interestingly, the effects of potassium on the amount of mRNAov bound in a preinitiation complex and the inhibition of this binding by m7G5'p could be observed by changing the potassium concentration after binding had occurred. These data suggested that the interaction between the wheat germ 40S ribosomal subunit and mRNAov was very sensitive to the ionic environment.