DNA base composition of rickettsiae

There is a small but distinct difference in DNA base composition between the typhus and spotted fever groups of rickettsiae. The molar percentages of guanine plus cytosine for Rickettsia prowazeki, R. typhi, and R. canada are approximately 30, for R. rickettsi, R. conori, and R. akari they are about 32.5. The percentage for trench fever rickettsia, Rochalimaea quintana, is 38.6.

5-Hydroxymethyluracil in the DNA of a dinoflagellate

During the characterization of DNA from the dinoflagellate Gyrodinium cohnii, a large discrepancy was detected between the estimation of guanine + cytosine content from the buoyant density of the DNA in CsCl (56.1% G+C) and from the midpoint (T(m)) of its hyperchromicity induced by a thermal gradient (35.6% G+C). Composition analyses of (32)P-labeled nucleotides revealed an actual G+C content of 41.3%, and the presence of an unusual nucleotide amounting to about 37% of the expected thymidylate in unfractionated DNA-a feature that can explain the aberrant behavior of the DNA. The chromatographic properties of the unusual base and UV spectral analyses of the base and its corresponding nucleotide are consistent with its identification as hydroxymethyluracil. This base is not uniformly interspersed with thymine in the DNA. About 10% of Gyrodinium DNA is contributed by a fraction with low hydroxymethyluracil content, which behaves anomalously in Ag(+)-Cs(2)SO(4) density gradients but not in CsCl.

Evidence for the absence of the G-T-psi-C sequence from two mammalian initiator transfer RNAs

Analyses were performed on the purified initiator tRNA from rabbit liver to test for the presence of Psip and Tp in this molecule. Neither of these nucleotides could be detected after hydrolysis by piperidine, NaOH, or T2 RNase. Similarly digestion with venom phosphodiesterase plus phosphatase failed to release any pseudourdine or ribothymidine. Identical results were obtained with the initiator tRNA from sheep mammary gland. The absence of these nucleosides was confirmed by pancreatic and T1 RNase digestion of the rabbit-liver initiator tRNA. The classical G-T-Psi-C sequence was not detected in this molecule. An A-U-C-G sequence has been identified; it may possibly replace the G-T-Psi-C sequence.

Absence of the sequence G-T-psi-C-G(A)- in several eukaryotic cytoplasmic initiator transfer RNAs

The nucleotide sequence G-T-Psi-C-G(A)- has previously been found in every tRNA of known sequence that is active in protein biosynthesis. An exception to this generalization is the recently sequenced initiator tRNA from yeast cytoplasm. It is now reported that cytoplasmic initiator tRNAs from wheat germ, rabbit liver, and sheep mammary gland also lack the G-T-Psi-C-G(A)- sequence. Thus: (i) nucleoside composition analyses show the absence of T in all these tRNAs; (ii) analyses of oligonucleotide fragments produced by T1 ribonuclease show the absence not only of the T-Psi-C-G(A)- sequence, but also of U-Psi-C-G(A)- or U-U-C-G(A)- sequences in such digests. The absence of G-T-Psi-C-G(A)- in the eukaryotic cytoplasmic initator tRNAs is, therefore, not simply due to lack of enzymatic modification of U to T.

The 3'-terminal nucleotide sequences of bacteriophage lambda DNA

Analyses of radioactive oligonucleotides in endonuclease digests of 3'-terminally labeled lambda DNA revealed the 3' terminal sequence -GTTACG for the l strand and -ACCCGCG for the r strand. These sequences, together with those previously known for the 5' cohesive ends, provide a total of 25 known base-pairs in the vicinity of the termini. When the cohesive ends are paired, the sequence between the nicks can be bisected by a 2-fold rotational axis of symmetry. Five of the first eight base-pairs, on either side of the axis, are rotationally symmetric. This symmetry may be involved in the recognition of the site by an enzyme responsible for formation of the cohesive ends.

Nucleotide sequence analysis with polynucleotide kinase and nucleotide "mapping" methods. 5'-Terminal sequences of deoxyribonucleic acid from bacteriophages lambda and 424

The polynucleotide kinase reaction was used in analyses of complex mixtures of oligodeoxynucleotides which were fractionated by various two-dimensional nucleotide ;mapping' procedures. Parallel ionophoretic analyses on DEAE-cellulose paper, pH2, and AE-cellulose paper, pH3.5, of venom phosphodiesterase partial digests of 5'-terminally labelled oligonucleotides enabled the sequence of the nucleotides to be deduced uniquely. A ;diagonal ionophoresis' method has been used with mixtures of nucleotides. Application of these methods to 5'-terminally labelled DNA from bacteriophage lambda gave the terminal sequences pA-G-G-T-C-G and pG-G-G-C-G. Identical 5'-terminal sequences were found with DNA from bacteriophage 424.

Identification of the synthesis of guanosine tetraphosphate (MS I) as insertion of a pyrophosphoryl group into the 3'-position in guanosine 5'-diphosphate

The phosphate transfer system of Haseltine et al., consisting of a ribosomal wash obtained from a stringent strain of Escherichia coli, washed ribosomes, GTP, and ATP, was used to prepare large quantities of guanosine tetra- and pentaphosphates, the magic spot compounds MS I and MS II of Cashel and Gallant. In our hands, the Haseltine et al. system yielded predominantly guanosine tetraphosphate, ppGpp. This system was used exclusively in the described experiments, with ATP labeled with (32)P in the beta- and gamma-positions as donor. The beta-label was found to produce a ppG[unk]p and the gamma-label a ppGp 0001000 1101011 0011100 0011100 1101011 0001000 0000000 0101100 1110010 0100001 0100001 0100001 0110010 0101100 0100000 0100000 1110000 . Furthermore, [(3)H]GDP + [gamma-(32)P]ATP yielded ppGpp in a (3)H:(32)P ratio of 1:1. The results indicate a transfer of the terminal pyrophosphoryl group of ATP as a unit. The position of the transferred pyrophosphoryl was assayed for by preparation of pG from ppGp with Zn(++)-activated inorganic pyrophosphatase from yeast. The pG was then assayed with 3'-nucleotidase, which liberated practically all the labeled phosphate. This result indicate that the phosphate transfer from ATP to GDP yields guanosine 5'-diphosphate-3'-diphosphate.

Polyadenylic acid sequences in the virion RNA of poliovirus and Eastern Equine Encephalitis virus

Poliovirus virion RNA contains a single covalently bound sequence of polyadenylic acid which is approximately 49 nucleotides long. A single, slightly longer polyadenylic acid sequence is contained in Eastern Equine Encephalitis virus RNA. Since these viruses are otherwise dissimilar these sequences may play a common role in viral replication, possibly in translation of the viral RNA.

Studies with cholroplast and mitochondrial DNA. I. Evidence of sequence homology between chloroplast and nuclear DNA (Broad Bean) and between mitochondrial and nuclear DNA (rat liver)

A mixture of broad bean chloroplast and nuclear DNA or rat liver mitochondrial and nuclear DNA was taken through a heating and annealing cycle, and examined by CsCl density gradient centrifugation. The formation of intermediates between the two DNAs during joint annealing was used as a method of detecting sequence homology in different DNA samples. Homology was found between chloroplast and nuclear DNA from broad bean and between mitochondrial and nuclear DNA from rat liver. Since this method produces only qualitative data no implication for possible nucleocytoplasmic relationship can be assessed.

Determination of the backbone structure of nucleic acids and nucleic acid oligomers by laser Raman scattering

Raman spectra of fibers of DNA that have been prepared in the A, B, and C forms are presented and compared with Raman spectra of DNA and RNA in dilute solution. It is shown that the phosphate vibrations in the region 750-850 cm(-1) are very sensitive to the specific conformation of the phosphate group in the backbone chain and are virtually independent of all ohter factors. Thus, a very simple method for the determination of the specific conformation of the backbone chain of nucleic acids, at least so far as the sugar-phosphate chain is concerned, appears available. The method is applied to short oligomers and dimers of ribonucleosides. It is found that at low temperatures, at pH 7, the phosphate group goes into the geometry of the A conformation when the stacking forces between the bases are sufficiently strong.

Quinacrine, a chromosome stain specific for deoxyadenylate-deoxythymidylaterich regions in DNA

Fluorescence of quinacrine in the presence of different polynucleotides was studied to attempt to identify the specific nucleotides responsible for the fluorescence of stained chromosome preparations. A marked enhancement of fluorescence was seen in the presence of bihelical polynucleotides, such as poly(dA-dT), poly(dA).poly(dT), and poly(rA).poly(rU), but not in the presence of single-stranded polynucleotides, such as poly(dA), poly(dT), poly(rA), or poly(rU) alone. The higher was the GC content of natural DNAs, the more they quenched. Quenching was also seen with poly(dG) or poly(rG) alone, but not with poly(dC) or poly(rC) alone. Native and denatured DNA were both effective in quenching fluorescence. Thus, a bihelical conformation is not required for fluorescence quenching. Nearly all of these properties are shared with proflavine. In contrast, acridine orange, which stains most areas of chromosome preparations, shows enhanced fluorescence in the presence of all members of a series of natural DNAs. These data suggest that base-pairs composed of AT (rather than GC) residues are responsible for the observed fluorescence of specific chromosome regions after treatment with quinacrine, and support the proposal of Ellison and Barr (Chromosoma, in press) that the highly localized quinacrine fluorescence in their cytological preparations reflects the presence of DNA that has a high (A + T)/(G + C) ratio.