Immunochemical detection of N6-methyladenine in DNA

Antibodies to N6-methyladenosine were produced in rabbit by means of immunization with N6-methyladenosine coupled to bovine serum albumin via periodate oxidation. Cross-reacting antibodies were removed by bovine serum albumin-Sepharose and appropriate nucleoside-human serum albumin absorbents. Nucleoside-specific antibodies were isolated by affinity chromatography of N6-methyladenosine-human serum albumin-Sepharose. The specificity of the purified antibodies has been demonstrated by complement fixation inhibition analyses using nucleoside analogues as inhibition than dAMP. Anti-N6-methyladenosine was used to detect N6-methyladenine in denatured DNAs from various sources by complement fixation. Practically no complement fixation has been found with DNAs containing no N6-methyladenine, such as calf thymus, salmon sperm, Micrococcus radiodurans, Streptomyces chrysomallus and Streptomyces hygroscopicus, whereas a weak reactivity occurred in the case of Bacillus subtilis DNA and Sarcina maxima DNA. For DNA from Proteus mirabilis, Escherichia coli K-12, E. coli B, E. coli WF+, lambda, T2 phages quantitative differences in the immunochemical reactivity were observed, which only partially correlate with the N6-methyladenine content of the DNAs. Other factors, influencing the accessibility of N6-methyladenine to the antibody-combining site have to be taken into consideration.

The methylated purines of Tetrahymena pyriformis transfer ribonucleic acid

By phenol extraction and DEAE cellulose column chromatography, tRNA was isolated from Tetrahymena pyriformis strain GL. Following acid hydrolysis of the tRNA, the methylated purine content was determined by Dowex 50 column chromatography and paper chromatography. The most abundant methylated guanine derivative was found to be N2-DMG. Also present were 1-MG, N2-MG, and 7-MG. The most abundant methylated adenine was found to be 1-MA; no 2-MA was detected. Small amounts of the N6-methyladenines were detected.

Influence of A-T content on the fractionation of DNA restriction fragments by RPC-5 column chromatography

The properties of the fractionated Hae III fragments of pRZ2 DNA (Patient, R.K., Hardies, S.C., and Wells, R.D. (1979) J. Biol. Chem. 254, 5542-5547) were studied in an effort to determine why several of the fragments bind more tightly to RPC-5 than expected on the basis of their length. The purified fragments were analyzed for their nucleotide composition by direct determination of their constituent mononucleotides and by analytical CsCl and Cs2SO4 density gradient analyses. A-T-rich fragments elute at higher salt concentrations than fragments of equivalent size which are not A-T-rich. In addition, denaturation mapping studies by electron microscopy indicate that an A-T-rich run within an otherwise G-C-rich fragment can give rise to delayed elution. At least one other factor influences the separation of DNA restriction fragments by RPC-5 chromatography. Some of the fragments in this digest which elute later than predicted from their size either contain known genetic regulatory sites or bind regulatory proteins.

The stability of methylated purines and of methylphosphotriesters in the DNA of V79 cells after treatment with N-methyl-N-nitrosourea

V79-379A cells growing in suspension culture were treated with N-methyl-N-nitrosourea at concentrations of 0.6 and 1.2 mM. After incubation for periods from 1 to 48 h DNA was isolated from the cells and the concentrations of 7-methylguanine, O6-methylguanine, 3-methyladenine and methyl phosphotriesters were determined. After correction for dilution resulting from DNA synthesis during the incubation it was found that no loss of O6-methylguanine or methylphosphotriesters occurred; 7-methylguanine disappeared with a half-life of 22 h and 3-methyladenine was detectable only immediately after the initial treatment. The results show that these cells eliminate 7-methylguanine and 3-methyladenine from DNA by a repair process but are unable to excise or repair O6-methylguanine or methyl phosphotriesters.

Rapid determination of methylated purines in DNA treated with N-methyl-N-nitrosourea using high-performance liquid chromatography

A method for determining methylated purine bases in [3H]N-methyl-N-nitrosourea (MeNOUr) treated DNA is described. The method combines reversed-phase high performance liquid chromatography (HPLC) of methylated DNA after hydrolysis in dilute acid with the determination of radioactivity in the fractionated eluates. The peaks of the respective methylated purines were indentified by the use of internal standards. The method allows quantitative separation of 3-methyl-adenine (m3Ade), 7-methyl-adenine (m7Ade), 3-methyl-guanine (m3Gua), 7-methyl-guanine (m7Gua) and O6-methyl-guanine (m6Gua) within 20 min. Thus the total time required for determination of methylated purines is limited only by radioactivity measurements in the respective fractions.

Comparison of theoretical denaturation maps of phiX174 and SV40 with their gene maps

When the theoretical denaturation maps of phiX174 and SV40 are compared with their gene maps, it is observed that the beginning and the end of each gene in these two DNA's fall in a region of lower melting temperatures. Local (A+T)-contents evaluated from the known sequences at these regions support the above implication that the beginnings and the ends of nearly all the genes in phiX174 and SV40 are relatively rich in (A+T)-content.

23S ribosomal ribonucleic acid of macrolide-producing streptomycetes contains methylated adenine

Coresistance to macrolide, lincosamide, and streptogramin B-type (MLS) antibiotics by a common biochemical mechanism characterizes clinically resistant pathogens. Of 10 streptomycetes tested for resistance to macrolide, lincosamide, and streptogramin B-type antibiotics, only 1, Streptomyces erythreus, the organism used for production of erythromycin, was found resistant to all three classes; moreover, it was the only streptomycete in the series tested found to contain N6-dimethyladenine (m62A) in 23S ribosomal ribonucleic acid, the structural alteration of ribosomal ribonucleic acid associated with clinical resistance. Of the seven streptomycetes tested for the presence of m62A and N6-methyladenine (m6A), two, S. fradiae and S. cirratus, which produce the macrolide antibiotics tylosin and cirramycin, respectively, were found to contain m6A, but not m62A. The remaining strains tested, including strains which produce lincomycin and streptogramins, contained neither m6A nor m62A.

Determination of 6-methyladenine in DNA by high-performance liquid chromatography

A method for the determination of 6-methyladenine (6MA) by high-performance liquid chromatography (HPLC) has been developed. DNA bases were separated by using the strong cation-exchange resin Zipax SCX. Purine bases were obtained by hydrolysis and dialysis of DNA and analysed by HPLC. 6MA in DNA from Escherichia coli was determined by the proposed method. It is suggested that the method could be applicable to analyses of 6MA from other biological sources.

High pressure liquid chromatographic determination of arprinocid in feed

Arprinocid [9 - (2 - chloro - 6 - fluorophenylmethyl)-9H-purin-6-amine] is determined in feed by high pressure liquid chromatography with a silica column and ultraviolet detection. The drug is extracted from the feed into chloroform in the presence of pH 7 phosphate buffer, transferred to 0.1N HCl, and separated from interfering substances by partitioning with hexane. The acidic solution is neutralized, and the analyte is extracted into chloroform for injection into the chromatograph. This procedure has been applied to feeds containing 0.0030--0.0090% arprinocid with a precision of less than 5% relative standard deviation at the 0.0060% formulated concentration level. The results of this chromatographic procedure also correlate with those from a colorimetric analysis.

Complete deficiency of adenine phosphoribosyltransferase: a third case presenting as renal stones in a young child

We report a third case of 2, 8-dihydroxyadenine stones in a child with a complete lack of the adenine salvage enzyme--adenine phosphoribosyltransferase (APRT). The propositus, a 20-month-old girl of consanguineous Arab parents, presented with multiple urinary tract infections and supposed 'uric acid' stones in the right renal pelvis and left ureter. Both parents and one brother were heterzygotes for the defect, in keeping with an autosomal recessive mode of inheritance. In contrast with the other purine salvage enzyme disorder of childhood with true uric acid stones (the Lesch-Nyhan syndrome), uric acid excretion was normal in all family members. As in our previous case, treatment with allopurinol, without alkali, has eliminated the urinary excretion of 2, 8-dihydroxyadenine: the stones were removed surgically. 2, 8-Dihydroxyadenine should be considered in any child thought to have uric acid stones and tests made to distinguish the two compounds.

A conserved and unique (AT)-rich segment in yeast mitochondrial DNA

The mtDNA of the cytoplasmic petite mutant of yeast RD1A consists mainly of a perfect head-to-tail repetition of a known sequence of 66 consecutive AT and 2 GC base pairs. We have hybridized complementary RNA made on RD1A mtDNA with the mtDNAs of four different wild-type Saccharomyces strains that differ markedly in restriction fragmentation pattern. The tm's of the four heteroduplexes are identical to the tm of the homoduplex of RD1A mtDNA with complementary RNA of one repeat length. With all four wild-type mtDNAs this complementary RNA hybridizes mainly to a single restriction fragment of about 300 base pairs. This shows the conservation and individuality of at least one (AT)-rich segment in yeast mtDNA. The 300 base pair fragment has been mapped in the vicinity of the oxi-2 locus. The possible role of the (AT)-rich segment in the processing of the primary transcript of this region is discussed.

Heterogeneity in sensitivity to cleavage by the restriction endonucleases ECORI and HindIII of circular kinetoplast DNA molecules of Crithidia acanthocephali

Kinetoplast DNA (kDNA) of the protozoan Crithidia acanthocephali consists mainly of an association of approximately 27,000 covalently closed, 0.8-micron (1.58 X 10(6) daltons) circular molecules apparently held together in a particular structural configuration by topological interlocking. The sensitivities of circular kDNA molecules to the restriction endonucleases EcoRI and HindIII have been studied using agarose gel electrophoresis and electron microscopy. Digestion with EcoRI or HindIII of collections of single circular molecules obtained from sonicated kDNA associations resulted in a single cleavage of 9.3 and 12% of the molecules, respectively. Digestion of intact kDNA associations with EcoRI or HindIII resulted in cleavage of 9.2 and 10.4%, respectively, of the component circular molecules, but not in detectable disruption of the characteristic structure of the associations. Analysis of the products of sequential digestion of kDNA with the two enzymes indicated that approximately 8% of the circular molecules each contain a single site sensitive to EcoRI and a single site sensitive to HindIII; 1.5-3% contain only an EcoRI-sensitive site; 3-4% contain only a HindIII-sensitive site; and the remainder (approximately 86%) are insensitive to either enzyme. Further, data obtained from sequential digestion experiments and from studies of the partial denaturation products of the circular molecules digested with EcoRI or HindIII indicated that when they occur the EcoRI site and the HindIII site are each at a unique position in all molecules, 10-13% of the circular contour length apart. Similar digestion products were found for kDNAs from different cloned organisms, suggesting that the four different kinds of circular molecules, in regard to EcoRI and HindIII sensitivity, are found in similar proportions in the kDNA association of different organisms.

Purification and properties of nitrogenase from Rhodospirillum rubrum, and evidence for phosphate, ribose and an adenine-like unit covalently bound to the iron protein

1. The molybdenum-iron (Mo-Fe) protein, iron (Fe) protein and the activating factor of nitrogenase from Rhodospirillum rubrum were purified. 2. The Mo-Fe protein has properties similar to those of the Mo-Fe proteins of other nitrogen-fixing organisms. 3. The Fe protein is similar to other Fe proteins with respect to its molecular weight, metal composition and e.p.r. signal. 4. The Fe protein is different from other Fe proteins in that it apparently has two types of subunits rather than one, its u.v. spectrum has an extra peak, and phosphate, ribose and an adenine-like unit are covalently bound to the protein. The presence of these non-protein groups on the protein may explain the requirement for activation of R. rubrum Fe protein.

Comparative study of DNA methylation in three unicellular eucaryotes

We have analyzed the nature/content of methylated bases in the nuclear DNA of three unicellular eucaryotes. The pattern of methylation was different for each of the three organisms studied: Saccharomyces cerevisiae contained only 5-methylcytosine; Tetrahymena pyriformis contained only N6-methyladenine; and Chlamydomonas reinhardi contained both modified bases.

Heterogeneity of Epstein-Barr virus. III. Comparison of a transforming and a nontransforming virus by partial denaturation mapping of their DNAs

The DNAs of a transforming and a nontransforming Epstein-Barr virus strain, B95-8 AND P3HR-1, were compared by partial denturation mapping. B95-8 viral DNA showed a homogeneous denaturation pattern. In contrast, P3HR-1 viral DNA was heterogeneous, containing at least two classes of molecules, classified into groups A and B and present in a ratio of about 2:1 to 3:1. No evidence could be obtained that molecules from both groups A and B contain identical sequences present in different orientations as described for herpes simplex viral DNA. The majority of sequences present in B95-8 and in P3HR-1 viral DNA group A could be correlated by assuming that different sequences, about 12,000 base pairs long, were inserted or deleted, respectively, at different position of both viral genomes.

A-T rich sequences in vertebrate DNA. A possible explanation of q-banding in metaphase chromosomes

Partially denatured DNAs from mouse, cow, and chicken were visualized in the electron microscope by the basic protein film technique and the size and distribution of the denatured regions characterized. A-T rich sequences visualized at 15% denaturation average about 1500 bases in length for all three species and are arranged quite non-randomly in the genome. This arrangement is such that 30--50% of the entire genome contains no A-T rich DNA, and another 20% is composed about one-half of A-T rich sequences and one-half of other sequences. Comparison with DNA denaturation profiles indicates that for each organism these sequences are from 25--30% G+C and that there is very little if any DNA more A-T rich than these. Estimates from published studies of fluorescence enhancement of quinacrine bound to A-T rich DNAs suggest that the observed non-random organization of A-T rich sequences is sufficient to account for Q banding of metaphase chromosomes.

Modified bases in the DNAs of unicellular eukaryotes: an examination of distributions and possible roles, with emphasis on hydroxymethyluracil in dinoflagellates

The occurrence of small amounts of one or more of several modified bases in the DNA of an organism is widespread in nature. Prominent among these bases are 5-methylcytosine, N6-methyladenine and 5-hydroxymethyluracil. All can be found in varying amounts in DNA of viral, prokaryotic and eukaryotic origin. In some organisms, modified nucleotides comprise a large fraction of DNA nucleotides and in others there is complete replacement of one of the common four nucleotides by a modified one. This article discusses the distributions and possible roles of the several modified bases found in prokaryote and eukaryote DNAs. Emphasis is given (1) methylcytosine in a broad variety of eukaryotes, (2) methyladenine in certain protozoa and protophyta and (3) hydroxymethyluracil in dinoflagellates. Attention is focused on the phenomenology and the possible consequences of the presence of hydroxymethyluracil in DNA.

The nucleotide sequence of oocyte 5S DNA in Xenopus laevis. I. The AT-rich spacer

The primary sequence of the principal spacer region in X. laevis oocyte 5S DNA has been determined. The spacer is AT-rich and comprises half or more of each repeating unit. The sequence is internally repetitious; most of it can be represented by the following set of oligonucleotides: CAACAGTTTTCAAAAGGTTTCGAAGTTTTT(T). The spacer, which varies in length from about 360 to 570 or more nucleotides, can be subdivided into a region (A2) which is variable in length in different repeating units, flanked by regions (A1, A3, B1) which are relatively constant in length. The A2 region consists, on the average, of 5-6 tandem copies of the oligonucleotide CAAAGTTTGAGTTTT; variation in the redundancy of this oligonucleotide accounts for much of the repeat length variation in the genomic 5S DNA. Most copies of this oligonucleotide are identical, although several differing by 1 or 2 nucleotides have been detected in plasmid-cloned 5S DNA fragments. Regions A1 and A3 comprise a linear array of similar, but not identical, oligonucleotides; most repeating units contain very similar A1 and A3 sequences. Region B1 is a sequence of 49 nucleotides immediately adjacent to the 5' terminus of the 5S rRNA sequence. It is GC-rich, much less repetitive than the remainder of the spacer and contains several palindromes, but no regions of dyad symmetry. This sequence is identical in all six of the single cloned repeating units of 5S DNA analyzed.

Purification and biochemical properties of Egtved viral RNA

32P-labeled Egtved virus RNA was released from highly purified virus by phenol-SDS extraction. The single-stranded nature of the RNA was demonstrated by (1) its buoyant density of 1.69 g/cm3 in Cs2-SO4, (2) its susceptibility to digestion by pancreatic ribonuclease in either 1 X SSC or 0.01 X SSC (standard saline citrate), (3) its base composition (29.3% C, 23.6% A, 14.5% U. 32.6% G). This Egtved virus is different from the other rhabdoviruses since the base composition of its genomic RNA is lower in its composition of A + U. Such a result could have possible taxonomic implications concerning the orignin and evolution of Egtved Virus relative to the other known rhabdoviruses.

Mapping adenines, guanines, and pyrimidines in RNA

The positions of adenines, guanines, and pyrimidines can be determined by partial nuclease digestion of a terminally labeles RNA molecule. In urea, at elevated temperatures, RNase T1 generates a pattern reflecting cleavage at guanines while RNase U2 cleaves only at adenine. A limited alkaline hydrolysis provides a continuum of fragments derived from breaks at every phosphodiester bond. The reaction products are electrophoretically fractionated by size in adjacent lanes of a polyacrylamide gel. An autoradiograph of the gel displays the sequence up to 100 nucleotides from the end of the molecule, although uracil cannot as yet be distinguished from cytosine. These techniques form the basis of an RNA sequencing method and are demonstrated on yeast 5.8S ribosomal RNA.