Quantitative enzymatic hydrolysis of tRNAs : Reversed-phase high-performance liquid chromatography of tRNA nucleosides

A rapid quantitative method for enzymatic hydrolysis of microgram amounts of tRNA has been developed, specifically to take full advantage of our precise, accurate, and selective reversed-phase high-performance liquid chromatographic (HPLC) system for separation and measurement of the major and modified nucleosides in tRNA. After study of several enzyme systems, nuclease P1 and bacterial alkaline phosphatase were selected and the hydrolysis parameters were systematically studied. Optimized hydrolysis conditions give quantitative hydrolysis in 2 h and this short incubation time prevents loss of unstable nucleosides. The chromatographic system can tolerate relatively high levels of protein in the sample allowing high enzyme—substrate ratios and direct injection of hydrolysates. This enzymatic hydrolysis—HPLC method is the best described to date for quantitative determination of the nucleoside composition of tRNAs and has already provided important information for investigation of the role of modification in the function of RNAs.     

A modified procedure for the preparation of di- and triribonucleotides from pancreatic ribonuclease digest of RNA.

A novel procedure for the separation of oligonucleotides from pancreatic RNase-digest of RNA is described. The method involves a group-separation of uracil-containing and of cytosine-containing nucleotides on Dowex 50W. The obtained groups are further separated on DEAE-Sephadex A-25 by a linear gradient of NH4HCO3.     

DNA sequence analysis: a general, simple and rapid method for sequencing large oligodeoxyribonucleotide fragments by mapping

Several electrophoretic and chromatographic systems have been investigated and compared for sequence analysis of oligodeoxyribonucleotides. Three systems were found to be useful for the separation of a series of sequential degradation products resulting from a labeled oligonucleotide: (I) 2-D electrophoresis†; (II) 2-D PEI-cellulose; and (III) 2-D homochromatography. System (III) proved generally most informative regardless of base composition and sequence. Furthermore, only in this system will the omission of an oligonucleotide in a series of oligonucleotides be self-evident from the two-dimensional map. The sequence of up to fifteen nucleotides can be determined solely by the characteristic mobility shifts of its sequential degradation products distributed on the two-dimensional map. With this method, ten nucleotides from the double-stranded region adjacent to the left-hand 3′-terminus and seven from the right-hand 3′-terminus of bacteriophage λ DNA have been sequenced. Similarly, nine nucleotides from the double-stranded region adjacent to the left-hand 3′-terminus and five nucleotides from the right-hand terminus of bacteriophage 80 DNA have also been sequenced. The advantages and disadvantages of each separation system with respect to sequence analysis are discussed.     

Chromatographic separation as selection process for prebiotic evolution and the origin of the genetic code

A model for the evolution of a translation apparatus has been suggested where oligonucleotides in a hairpin conformation act as primordial adapters. Specifically activated amino acids are assumed to be attached to these hairpin molecules. For the specific activation, a chromatographic separation of, e.g. ala and CMP from gly and GMP can be accomplished on silica (e.g. of volcanic origin) with aqueous salt solutions. Other adsorbents like clays (kaolin, bentonite, montmorillonite), different silicates (florisil, magnesium trisilicate, calcium silicate, talc), hydroxyapatite, barium sulfate, calcium carbonate, calcium fluoride and titanoxide have been examined as model systems for the separation of nucleotides, nucleosides and amino acids on mineral surfaces. The possible role of chromatographic separation of amino acids for the formation of proteinoids, composed of selected amino acids, is also considered.     

Analysis of the free nucleotide pools of mammalian tissues by high-pressure liquid chromatography

Perchloric acid extracts of tissues were neutralized with tri-N-octylamine and, after removal of ClO₄^?, subjected to preliminary purification on a Cu²⁺-loaded column of Chelex 100. A high-pressure liquid chromatographic (HPLC) anion-exchange procedure was developed and gave good resolution of the naturally occurring free nucleotides on a single column. Where heterogeneous peaks eluted, an effective supplementary analysis was achieved by reverse-phase HPLC. An HPLC paired-ion technique was also evaluated for use in nucleotide analysis. Although anion-exchange was best for overall separation of nucleotides, both reverse-phase and paired-ion chromatography gave excellent separation of cyclic nucleotides. Reduced pyridine nucleotides were detected and measured in the form of their acid-decomposition products. The recovery of nucleotides was examined throughout the described analytical techniques and shown to be quantitative.     

Complete analysis of cellular nucleotides by two-dimensional thin layer chromatography

We describe methods for the complete analysis of cellular nucleotides from as few as 10(6) 32Pi-labeled cells in a simple 2-day experiment. Nucleotides are extracted with acid, neutralized, and resolved by two-dimensional thin layer chromatography on polyethyleneimine cellulose. In the first dimension the nucleotides are separated based on the negative charge of their phosphate groups (i.e. cyclic, mono-, di, and triphosphates) and in the second dimension on their content of nucleobases (i.e. Ura, Cyt, Thy, Gua, and Ade). Because the separation is logical, one can predict the chromatographic migration of most nucleotides. By running standards we have determined the chromatographic location of over 90 biologically important nucleotides, nucleotide derivatives, and modified nucleotides from tRNA. We also developed a set of enzymatic and chemical methods to be used in conjunction with the chromatographic separations for verifying the identity of nucleotides and characterizing novel nucleotides. In this paper we use these methods to analyze and inventory the nucleotide content of Salmonella typhimurium in balanced log phase growth. Other potential uses of the method are also described.     

Negative electrospray ionization mass spectrometry of synthetic and chemically modified oligonucleotides.

We report here on the analysis of synthetic oligonucleotides by electrospray ionization mass spectrometry (ESI-MS). After intensive removal of salt ions (especially sodium cations), negative ion mass spectra, allowing mass measurement with an accuracy of 0.01%, were obtained on several oligonucleotides up to 80 nucleotides. In most cases, the resolution was sufficient to observe n-1 and n-2 forms due to internal deletions during automated synthesis, and to identify the missing nucleotides. A 132-mer, whose size is close to the limit of automated chemical synthesis, was also successfully mass measured. A quantitative study showed that ESI-MS can provide quantitative data on oligonucleotides of similar size and structure. The described methodology is used to characterize oligonucleotide analogues such as phosphorothioate oligonucleotides designed for antisense applications. Finally, analyses in the positive ion mode on a trimer TpTpT in the presence of different amine bases were performed and allowed a better understanding of the influence of these bases on the ions formation.     

Analysis of free amino acids in mammalian brain extracts

An optimized method for analysis of free amino acids using a modified lithium-citrate buffer system with a Hitachi L-8800 amino acid analyzer is described. It demonstrates clear advantages over the sodium-citrate buffer system commonly used for the analysis of protein hydrolysates. A sample pretreatment technique for amino acid analysis of brain extracts is also discussed. The focus has been placed on the possibility of quantitative determination of the reduced form of glutathione (GSH) with simultaneous analysis of all other amino acids in brain extracts. The method was validated and calibration coefficient (K _GSH) was determined. Examples of chromatographic separation of free amino acids in extracts derived from different parts of the brain are presented.     

Isolation and some properties of a deoxyribonuclease from Turbo cornutus.

1. Four DNases were found in the dried liver extract of a top shell, Turbo cornutus. The major one was purified 120-fold by phosphocellulose column chromatography, sulfoethylcellulose column chromatography and gel-filtration on Sephadex G-150. The yield was 2.7%. 2. The enzyme activity was not affected by Mg2+ (10(-3)--10(-2)M), EDTA (10(-3)--10(-2)M), or NaCl (10(-1)M). It showed a pH optimum of 4.7--4.8. Ionic strength was found to be critical for the maximal activity. The isoelectric point was 8.5--9.0. On heating at 50 degrees C C for 5 min the enzymic activity fell to half the initial value. 3. The enzyme preparation degraded native as well as heat-denatured DNA, but not RNA. It degraded heat-denatured DNA endonucleolytically to give oligonucleotides with 3'-phosphates. 4. The 3'-phosphate and 5'-hydroxy termini of oligonucleotides were investigated. At both the 3'- and 5'-terminal positions, purine nucleotides were predominant.     

Neighboring nucleotide interactions during DNA sequencing gel electrophoresis.

Electrophoretic separation of oligonucleotides in denaturing polyacrylamide gels is primarily a function of length-dependent mobility. The 3' terminal nucleotide sequence of the oligonucleotide is a significant, secondary determinant of mobility and separation. Oligomers with 3'-ddT migrate more slowly than expected on the basis of length alone, and thus are better separated from the preceding, shorter oligomers in the sequencing ladder. Oligomers with 3'-ddC are relatively faster than expected, and are therefore less separated. At the 3' penultimate position, -dC- increases and -dT- reduces separation. Purines at the 3' terminal or penultimate positions of oligonucleotides affect separation less than the pyrimidines. These results suggest specific interactions among neighboring nucleotides with important effects on the conformation of oligonucleotides during electrophoresis. These interactions are compared to compression artifacts, which represent more extreme anomalies of length-dependent separation of oligonucleotides. Knowledge of base-specific effects on electrophoretic behavior of DNA oligomers supplements the usual information available for determination of sequences; additionally it provides an avenue to thermodynamic and hydrodynamic investigations of DNA structure.     

Determination of the naturally occurring monoacetyl derivatives of di- and polyamines

A method is described for the determination of pmol quantities of monoacetylputrescine, N¹-acetylspermidine, N⁸-acetylspermidine and related compounds. The method is based on the derivatization of these compounds with 5-dimethylaminonaphthalene-1-sulphonyl-chloride, followed by thin-layer chromatographic separation. Cleanup steps allow the application of the method to urine analyses. From the repeated determination of acetylated polyamines in the urine of healthy individuals it can be concluded that these conjugates are the major excretory form of di- and polyamines.The cleanup steps used in this procedure and the method described for the stabilization of 5-dimethylaminonaphthalene-1-sulphonyl derivatives on thin-layer plates are advantageous also for the analyses of total polyamines in urine hydrolysates, and in related applications of the dansylation method.     

Rapid print-readout technique for sequencing of RNA's containing modified nucleotides.

A rapid, simple, and highly sensitive method for sequence analysis of RNA was developed, which consists of the following steps: (i) controlled hydrolysis of the RNA by brief heating in water; (ii) (32P)-labeling of 5'-hydroxyl groups of the fragments produced in (i); (iii) resolution of labeled fragments by size on polyacrylamide gels giving the familiar "ladder"; (iv) contact transfer ("print") of the ladder from the gel to a PEI-cellulose thin layer; (v) in situ treatment of the ladder with RNase T2 resulting in the release of 5'-(32P)-labeled nucleoside-3',5' diphosphates; (vi) contact transfer and thin-layer separation of (32P)-labeled nucleotides on PEI-cellulose in ammonium sulfate and ammonium formate solvents; (vii) autoradiography. The chromatographic behavior of the 4 major and 18 modified nucleotides was determined. The positions of major and modified nucleotides in the sequence can be read directly from the separation patterns displayed on X-ray film. As this is the only sequencing method presently available that allows one to display and identify directly the positions in the RNA chain of major and modified nucleotides, no additional procedures are required to analyze the latter.     

The non-enzymic hydroxylation of phenylalanine to tyrosine by 2-amino-4-hydroxy-6,7-dimethyl-5,6,7,8-tetrahydropteridine

1. Phenylalanine is converted into tyrosine by incubation in air with 6,7-dimethyltetrahydropterin, which is a cofactor for the enzymic hydroxylation. This can cause serious inaccuracies in assays of phenylalanine hydroxylase. 2. The non-enzymic reaction is not specific for l-phenylalanine. 3. m-Tyrosine, o-tyrosine and dihydroxyphenylalanines are formed in addition to p-tyrosine; their chromatographic separation and assay are described. 4. l-[(14)C]Phenylalanine as purchased or soon after purification contains p- and m-tyrosine, both of which can cause errors in the assay of phenylalanine hydroxylase. 5. Catalase prevents the non-enzymic hydroxylation. Thiol compounds in low concentrations stimulate the reaction but in high concentrations are inhibitory. Fe(2+) and metal complexing agents have small stimulatory effects. 6. The mechanism of the non-enzymic reaction and its possible relation to the enzymic hydroxylation of phenylalanine are discussed; it is suggested that phenylalanine is attacked by a peroxide of the cofactor.     

The identification and quantitation of connective tissue hexosamines using a combination of gas liquid chromatographic and colorimetric procedures.

Due to interactions between amino sugars, amino acids, and/or carbohydrate breakdown products from acid hydrolysis, the quantitation of individual amino sugars from connective tissue hydrolysates, requires a number of indirect steps involving separation and purification of the hexosamines prior to gas-liquid chromatography. In this paper, a method is reported which permits the direct quantitation of galactosamine and glucosamine from connective tissue hydrolysates, utilising a combination of both gas-liquid chromatographic and colorimetric procedures. A two-phase extraction system which selectively eliminates pyridine and amino acids from the T.M.S. ethers of glucosamine and galactosamine is also described.     

Purification and properties of myosin light-chain kinase from fast skeletal muscle.

1. A procedure is described for the isolation of myosin light-chain kinase from rabbit fast skeletal muscle as a homogeneous protein. 2. Myosin light-chain kinase is a monomeric enzyme of mol.wt. 77000. Under some conditions of storage it is converted into components of mol.wts. about 50000 and 30000 that possess enzymic activity. 3. The enzyme is clearly different in structure and properties from any other protein kinase so far isolated from muscle. 4. The enzyme is highly specific for the P-light chain (18000-20000-dalton light chain) of myosin and requires Ca2+ for activity. 5. The P-light chain is phosphorylated at a similar rate whether isolated or associated with the rest of the myosin molecule. 6. The effects of pH, bivalent cation and other nucleotides on the enzymic activity are described. 7. The role of the phosphorylation of the P-light chain of myosin in muscle function is discussed.     

A rapid radiometric assay for adenosine deaminase

A rapid radiochemical procedure for the measurement of adenosine deaminase is described. The method employs phospho-Sephadex, a weak cation exchanger, which permits the enzymic product inosine to pass unretarded through the gel while the radioactive substrate adenosine is retained. Use of a Millipore filter manifold permits rapid processing of samples and eliminates time-consuming column chromatographic, electrophoretic, or paper chromatographic techniques required for separation of product and substrate.The activity of adenosine deaminase was examined in spleen cell preparations prepared from normal CBA mice. Excellent agreement of results was obtained when the radioactive method was compared with two other independent assay techniques.     

Preparative isolation of di-, tri- and tetrapyrimidine nucleotides from depurinated herring sperm DNA (author's transl)

The pyrimidine nucleotides p(dT)3, p(dT)2p, pdCp, p(dC)2p and p(dC)3 and the mixtures of sequence isomers p(dC, dT), p(dC, dT)p, p(dT2, dU), (dT2, dU)p, p(dC, dT2), p(dC, dT2)p, p(dC, dT3), p(dC, dT), p(dC2, dT)p, and p(dC2, dT2) are isolated on a preparative scale from depurinated hydrolysates of herring sperm DNA by the following procedure. The DNA hydrolysate is first separated into a low and a high molecular weight mixture of pyrimidine nucleotides by column chromatography on DEAE-cellulose. The nucleoside bisphosphates pdCp and pdTp, the dinucleotides p(dC)2 and p(dT)2 and the sequence isomers p(dC, dT) are largely separated out of the mixture of the low molecular weight pyrimidine nucleotides. The remaining mixture is rechromatographed at pH 3.5 on QAE-Sephadex. This separates the pyrimidine nucleotides containing a majority of cytidylic acid units from those containing more thymidylic acid units, which are then fractionated at pH 7.5 according to the number of bases in the chain. The pyrimidine nucleotides and mixtures of sequence isomers separated to 83-99% purity by column chromatography are further separated by paper chromatography and are obtained in chromatographically pure form after this step. The structures of the isolated DNA fragments are determined from chromatographic data, absorption and enzymatic degradation.     

High-performance liquid chromatographic determination of creatinine in serum, and a correlation of the results with those of the Jaffé and enzymic methods

A high-performance liquid chromatographic method for the determination of creatinine in control sera is reported, based on its separation from deproteinated serum components on the ion-exchange material HEMA Bio 1000 SB and ultraviolet detection at 230 nm. Groups of eleven to fourteen samples of human serum and several control materials were simultaneously analysed by the Jaffé, enzymic ultraviolet and enzymic peroxidase aminophenazone methods. Another group (52–115 sera) was analysed for correlations with spectrophotometric methods. The precision of the chromatographic method ranges between 2.0 and 1.0% (relative standard deviation) for serum creatinine concentrations of 115.1 to 471 μmol/l, respectively. A very good accuracy was found in analyses of reference materials Kontrollogen-L and -LP. Some results of analyses of the other control sera were higher and the other lower than those obtained by the Jaffé and enzymic methods, because both interferences and enzyme inhibitors were encountered. Correlations between the chromatographic and spectrophotometric methods were good.     

A thin-layer chromatographic method for separation of thymidine and deoxyuridine nucleotides

A thin-layer chromatographic method for the separation of thymidine and deoxyuridine nucleotides and nucleosides is described. This procedure involves the following sequence of steps: (i) Ion-exchange thin-layer chromatography to afford separation into fractions of increasing degree of phosphorylation, (ii) conversion of each fraction into an equivalent mixture of thymine and uracil through the combined actions of alkaline phosphatase and thymidine phosphorylase, and (iii) partition thin-layer chromatographic separation of thymine and uracil. A key feature of the method is the specificity afforded by the second step which converts only thymidine and deoxyuridine nucleotides and nucleosides to the corresponding pyrimidine bases. An application of the method to the study of [³H]deoxyuridine metabolism in L1210 cells, as well as the effect of methotrexate on this metabolism is also described.     

Quantitative Parametrs of Cooperative Interactions of the Oligodeoxyribonucleotides on the Complementary Template

Abstract

The cooperative interactions of oligonucleotides on the complementary template were studied using the quantitative analysis of the template alkylation with the oligonucleotides bearing covalently attached 4-[N-(2-chloroethyl)-N-methylamino]benzyl group at 5′-end. The influence of the mismatched nucleotides and the stabilizing N-(2-hydroxyethyl)phenazinium group at the 5′- and 3′-ends of the oligonucleotides on the parameters of cooperativity was evaluated.