The reaction of adenine and cytosine residues in tRNA with chloroacetaldehyde

The reaction of Lupinus luteus tRNAPhe with 1 M chloroacetaldehyde in the pH range of 4 - 6 at 25 degrees C was studied. It was found that earlier difficulties lowering the utility of the reagent for structural studies of nucleic acids were caused by the formation of the stable reaction intermediates. In order to eliminate these difficulties the simple procedure of so-called maturation of the chloroacetaldehyde-modifies tRNA is proposed. It consists in further incubation of the short-term modified tRNA in water at 50 degrees C in the absence of the reagent. During the maturation step the stable intermediates are quantitatively converted into final ethenoderivatives. New HPLC conditions on Aminex A-6 were worked out which enable rapid separation of both ethenoadenosine and ethenocytidine from natural tRNA nucleosides.

Systematic punctuation of eukaryotic DNA by A+T-rich sequences

Isodenaturation of avian and mammalian DNA of Mr greater than 2.5 X 10(8) in 85% (vol/vol) formamide led to the observation by electron microscopy of A+T-rich zones ("AT-rich linkers") of 300-3000 base pairs which are distributed over the entire genome in a characteristic pattern. Linkers of mean length 800 base pairs are found either isolated or in clusters of about four to six linkers of more heterogeneous size separated on average by 2500 base pairs (in duck DNA). In between clusters, single linkers segment the DNA at distances of 10 to more than 100 kilobase pairs, with a majority in the range of 10-30 kilobase pairs. An analogous organization of linkers is found in rat and mouse DNA. The internal organization of the clusters varies, however, in a fashion that might be related to the large amount of light satellite DNA in the mouse and its apparent absence in rat and avian DNA. It is possible to fragment the DNA under appropriate conditions by the single-strand-specific nuclease S1 at the site of these A+T-rich zones and to obtain, on alkaline sucrose gradients, a bimodal pattern of DNA fragments of the size corresponding to the pattern observed by electron microscopy. The implications of this observation for DNA organization, chromatin structure, units of transcription and replication, and possible targets of A+T-specific drugs are discussed.

Inhibition of the release of virion-associated murine leukemia virus genomic RNA by vesicular stomatitis virus

The genomic RNAs of murine leukemia virus (MuLV) and vesicular stomatitis virus (VSV) were distinguishable based on a difference in sedimentation coefficient, polyadenylic acid content, and nucleotide sequence homology. Applying these biochemical characteristics, we found that the release of virion-associated MuLV genomic RNA from virus-producing cells was inhibited by VSV as early as 2 h after superinfection. This finding offers an explanation to our previous inability to detect MuLV(VSV) pseudotype formation during mixed infection with VSV and MuLV.

Intraspecific diversity of nucleotide sequences within the adenine + thymine-rich region of mitochondrial DNA molecules of Drosophila mauritiana, Drosophila melanogaster and Drosophila simulans

Mitochondrial DNA (mtDNA) molecules from Drosophila mauritiana, D. melanogaster, and D. simulans contain a single adenine + thymine (A+T)-rich region, which is similarly located in all molecules, but varies in size among these species. Using agarose gel electrophoresis and electron microscopy, a difference in occurrence of one EcoRI site, and a difference in size (approximately 0.7 kb) of the A+T-rich regions was found between mtDNA molecules of flies of two female lines of D. mauritiana. In heteroduplexes constructed between these two kinds of mtDNA molecules, two or three regions of strand separation, each comprising single strands of unequal length, were apparent near the center of the A+T-rich region. Using the structural differences between D. mauritiana mtDNA molecules it was demonstrated the mtDNA of this species is maternally inherited. Differences in length of A+T-rich regions were also found between mtDNA molecules of two geographically separated strains of D. melanogaster, and between mtDNA molecules of two geographically separated strains of D. simulans. However, in both cases, in heteroduplexes constructed between mtDNA molecules of different strains of one species, the A+T-rich regions appeared completely paired.

Inability of Chinese hamster ovary cells to excise O6-alkylguanine

The capacity of Chinese hamster ovary cells for excising alkylated bases from their DNA was investigated. Cells were treated with N-methyl-N-nitrosourea or N-ethyl-N-nitrosourea, and the amounts of 3-alkyladenine, 7-alkylguanine, and O6-alkylguanine in DNA were compared immediately after the treatment and after a 20-hr incubation. Cells were able to excise 3-alkyladenine and 7-alkylguanine, but there was no loss of O6-alkylguanine, after correction for dilution, due to DNA synthesis during posttreatment incubation. The inability of Chinese hamster ovary cells fail to show growing point mutagenesis after treatment with N-ethyl-N-nitrosourea.

Adenine + thymine content of different genes located on the broad host range plasmid RP4

The genetic map of plasmid RP4 was correlated with its adenine+thymine (AT) map. For this purpose, RP4 DNA was digested with one or both of the restriction enzymes EcoRI and HindIII and the resulting linear RP4 molecules and fragments were partially denatured, examined in the electron microscope and their AT maps were determined using a computer program. From these AT maps the EcoRI and HindIII restriction sites were located on the AT map of RP4. Since the positions of these restriction sites on the genetic map of RP4 are known, the maps could be compared. They revealed a high AT content for the Tn1 transposon and the kanamycin resistance gene. The tra-1 region is also distinguished by a sharply defined AT-rich region, whereas tra-2 and the tetracycline resistance gene have an AT content which is not distinctly different from the average AT content of RP4.

Sensitive fluorimetry of adenine, its nucleosides and nucleotides

We improved our fluorimetric analysis of adenine compounds by high performance liquid chromatography(HPLC). Bromoacetoaldehyde was better than Chloro- or iodoacetoaldehyde as the reagent of fluorescent derivatization. A moderate reaction for unstable ADP and ATP was found and their fluorescent derivatives were separated by HPLC using Hitachi gel No. 3012-N. The method was applied to determine cAMP in human urines and a catecholamine receptor system. Further, a sensitive fluorescence spectrophotometer was developed. In this micro-HPLC, several ten femtomoles of the adenine compounds were separated.

Spectrum of 2,8-dihydroxyadenine urolithiasis in complete APRT deficiency

APRT deficiency may be totally benign or life threatening. The importance of early recognition/diagnosis is thus stressed. Urolithiasis (2,8-DHA stones: the precipitating factor in all cases) is treatable. With early recognition and treatment allopurinol without alkali and a diet low in purine homozygotes have remained clinically and biochemically normal to date. 'Uric acid' stones in children must always be suspect and subjected to sophisticated analysis. Diagnosis from red cell APRT activity may also have its pitfalls.

Translocation specificity of the Tn3 element: characterization of sites of multiple insertions

247 independent events involving insertion of the TN3 transposable element into a 4 kb constructed plasmid (pTU4) of partially known DNA sequence were studied by restriction endonuclease mapping, and 65 of these insertion sites were examined further by DNA sequence analysis. Our results show that the previously proposed regional specificity for Tn3 insertion is associated with a strong preference for AT-rich segments as insertion sites. Moreover, multiple insertions of the Tn3 occurred at certain AT-rich nucleotide positions, and 23 of 26 independent insertion events at a single nucleotide position were found to be in the same orientation. A region of the recipient plasmid showing major homology with the terminal 18 bp of Tn3 was identified in the vicinity of an 11 nucleotide segment that included three insertional hot spots and 36 independent insertions. Our results indicate that the site and orientation of insertion of Tn3 are at least partly determined by the primary nucleotide sequence of the recipient genome, and suggest that insertional hot spots may result from the combined effects of AT richness plus homology of the recipient genome with the terminal sequences of Tn3.

DNA sequence of the gene for the outer membrane lipoprotein of E. coli: an extremely AT-rich promoter

The outer membrane lipoprotein is the most abundant protein in an E. coli cell. Its structural gene (Ipp) was cloned into a lambda phage vector and the nucleotide sequence of a DNA fragment of 814 bp encompassing the Ipp gene was determined. The promoter region of the gene was found to have the following features. First, a segment of 261 bp preceding the transcription initiation site (-1 to -261) has a very high AT content of 70%, in contrast to 53% for the mRNA region of 322 bp, 44% for a segment of 127 bp after the transcription termination site and 49% for the average AT content of the E. coli chromosome. Second, in particular, of the first 45 bp upstream from the transcription initiation site (-1 to -45), 36 bases (80%) are A or T. Third, there is a heptanucleotide sequence homologous to the "Pribnow box," eight bases apart from the transcription initiation site. Fourth, a sequence homologous to the "RNA polymerase recognition site" exists on both strands between positions -27 and -39. Finally, there is a long dyad symmetry centered at the transcription initiation site.

Is the DNA of virus T7 methylated?

DNA modification of T7 wild type and of T7 M-mutants was studied by determining the percentage of 5-methylcytosine (5MC)/cytosine (C) and N6-aminopurine (6MA)/adenine (A) and by evaluating the plating efficiencies of restriction-sensitive T7 M-mutants on modifying and non-modifying host strains. Only 0.03% adenine and 0.02% cytosine were methylated in the DNA of T7 wild type as well as in T7 M-mutants, which was independent of the host DNA methylation (30- to 50-fold higher). The restriction of T7 M-mutants, determined from the plating efficiencies, was not altered on modifying or non-modifying hosts. These results indicate that host-specific modification is blocked during T7 development and that this is not due to the M-protein.