INTERACTION BETWEEN DENATURED DNA, POLYRIBONUCLEOTIDES, AND RIBOSOMAL RNA: ATTEMPTS AT PREPARATIVE SEPARATION OF THE COMPLEMENTARY DNA STRANDS

Transforming Activity in Both Complementary Strands of Bacillus subtilis DNA

Under conditions favoring single-strand transformation, the two complementary strands of Bacillus subtilis DNA, separated by differential complexing with polyriboguanylic acid, have identical transforming activity. Moreover separated single strands, upon renaturation with unmarked (recipient) DNA, form heteroduplex molecules with similar double-strand transformin activity. These findings bear upon the mechanism of DNA integration.

In vivo cleavage of cytosine-containing bacteriophage T4 DNA to genetically distinct, discretely sized fragments

Mutants of bacteriophage T4D that are defective in genes 42 (dCMP hydroxymethylase), 46 (DNA exonuclease), and 56 (dCTPase) produce limited amounts of phage DNA in Escherichia coli B. In this DNA, glucoylated 5-hydroxymethylcytosine is completely replaced by cytosine. We found that this DNA rapidly becomes fragmented in vivo to at least 16 discrete bands as visualized on agarose gels subjected to electrophoresis. The sizes of the fragments ranged from more than 20 to less than 2 kilobase pairs. When DNAs from two of these bands were radioactively labeled in vitro by nick translation and hybridized to XbaI restriction fragments of cytosine-containing T4 DNA, evidence was obtained that the two bands are genetically distinct, i.e., they contain DNA from different parts of the T4 genome. Mutational inactivation of T4 endonuclease II (gene denA) prevented the fragmentation. Three different mutations in T4 endonuclease IV (gene denB) caused the same minor changes in the pattern of fragments. We conclude that T4 endonuclease II is required, and endonuclease IV is involved to a minor extent, in the in vivo production of these cytosine-containing T4 DNA fragments. We view these DNA fragments as "restriction fragments" since they represent degradation products of DNA "foreign" to T4, they are of discrete size, and they are genetically distinct. Thus, this report may represent the first, direct in vivo demonstration of discretely sized genetically distinct DNA restriction fragments.

The interactions of the separated strands of satellite DNAs with other DNAs: 1. Conditions for associations of the alpha-satellite of the guinea pig with heterologous double-stranded DNAs

The separated H- and L-strands of the alpha-satellite of the guinea pig, Cavea porcellus, recovered from centrifugation in alkaline CsC1 gradients, from complexes with 7 different double-stranded (ds) DNAs including those of 1 bacteriophage, 2 prokaryotes, 2 invertebrates and 2 mammals. The complexes are not artifacts due to in vitro labeling of the satellite, methods of collection, the presence of divalent cations, or the fact that trace amounts of single-stranded (ss) DNAs are used. More complex dsDNAs, such as that recovered from nicked RF M13, do not associate with dsDNAs.

Proteins from human cerebrospinal fluid: binding with nucleic acids

Cerebrospinal fluid (CSF) contains two groups of proteins that bind tightly to DNA and to polyriboguanylic acid, respectively. In certain diseases the amounts of a given nucleic acid bound by a constant volume of CSF may increase, while in others the amount of such proteins may be reduced. Binding of polyriboguanylic acid increased in CSF samples from patients with brain tumors, stroke, multiple sclerosis, and communicating hydrocephalus, but it significantly decreased in CSF samples from patients with obstructive hydrocephalus. These increases may or may not be proportional to the rise in total CSF proteins characteristic for these diseases. Elevated binding of DNA was observed in samples from patients with hydrocephalus, epilepsy, and cortical atrophy. The technique described may be applicable to the diagnosis of a variety of diseases of the central nervous system.

Evidence for conversion of heteroduplex transforming DNAs to homoduplexes by recipient pneumococcal cells (DNA strand resolution-DNA repair-bacterial transformation-genetic recombination)

Heteroduplex molecules of pneumococcal DNA, prepared by cross-annealing resolved complementary strands, have been used as donors in transformation. A number of pairs of genetic markers are situated exclusively in the trans configuration in these heteroduplexes. Insertion of two markers from trans configuration into opposite DNA strands of a recipient genome should result in their segregation after one replication cycle. As a consequence, doubly transformed progeny would not appear, or would be markedly decreased. Contrary to these expectations, transformations with the heteroduplex DNAs give as many doubly transformed progeny for unlinked marker pairs as do homoduplex DNAs. For a pair of markers that normally are weakly linked, the frequencies of cotransfer are actually greater than those observed for a mixture of two singly marked homoduplex DNAs. These results lead to the conclusion that the heteroduplex DNAs are acted upon by repair enzymes of recipient cells so that markers introduced in the trans configuration are frequently converted to the cis configuration, either before or during integration. The efficiency of this conversion suggests that the repair and integration processes may be intimately connected. It is also concluded that complete breakdown of one strand of donor heteroduplex DNA does not occur during DNA uptake by recipient cells.

Correlation between rate of cell growth and rate of DNA synthesis in Escherichia coli B-r

The rates of cell growth and of DNA synthesis have been measured in synchronized cultures of Escherichia coli B/r growing with three different doubling times, from 27 to 80 min. Cell volume was found to increase linearly over the cell cycle, the rate of increase doubling at a precise cell age for each growth rate. The time at which the rate of cell growth doubled was also found to be the time at which new rounds of DNA synthesis were initiated. However, it was found that these two events could be separated in time by inhibiting DNA synthesis for a short period by the addition of nalidixic acid. It is concluded that neither event is the direct trigger for the other.

Preferential transcription of Bacillus subtilis light deoxyribonucleic acid strands during sporulation

Messenger ribonucleic acid (RNA) from log and sporulation stages of growth were transcribed mainly from the heavy strand of the complementary strands of Bacillus subtilis deoxyribonucleic acid (DNA). During sporulation a slight transcription shift from heavy to light DNA strands was observed. RNA-DNA hybrid competition experiments revealed that this shift was due to sporulation-specific transcription from light-DNA strands.

Control of initiation of DNA synthesis in Escherichia coli B-r

The pattern of new growing forks in the Escherichia coli genome after a period of inhibition of DNA synthesis has been examined. Synchronous cultures of E. coli B/r were treated with nalidixic acid to stop DNA synthesis for various lengths of time. After removal of the nalidixic acid the location of active growing forks was determined by measuring the reversion rate of a histidine requirement induced by the "growing-point mutagen," nitrosoguanidine. It was found that the ability to initiate a new round of DNA synthesis upon release from the nalidixic acid block was attained at the cell age at which a new round of replication would have been initiated had DNA synthesis not been blocked. However, if the nalidixic acid was removed before the normal initiation age, the initiation of the next round of synthesis was delayed past the normal time, which indicates that initiation of new rounds is not completely independent of DNA synthesis.

Ribosomal RNA genes in bacteria: evidence for the nature of the physical linkage between 16S and 23S RNA genes in Bacillus subtilis

The nature of the arrangement of 16S and 23S ribosomal RNA genes on the Bacillus subtilis chromosome was studied by means of a Cs(2)SO(4) density gradient centrifugation technique after complexing DNA-(ribosomal) RNA hybrids with mercuric ions. It was observed that the same fragments of single-stranded DNA with an average molecular weight of 1.9 x 10(6) which hybridize with 23S RNA also hybridize with 16S RNA. This indicates that genes for both these species of ribosomal RNA are physically linked on such DNA fragments. Some evidence suggests that the two types of genes are interspersed with each other, perhaps in sets, each of which contains a 16S and a 23S ribosomal RNA gene.

Evidence for multiple growing points on the genome of rapidly growing E. coli B-r

Synchronized cultures of rapidly growing E. coli B/r cells were starved for a required amino acid at various cell ages to allow ongoing chromosome replication to be completed without initiation of new replication cycles. It has been found that when such synchronized cultures are exposed to the mutagen nitrosoguanidine, genetic markers just in the process of replication show a markedly higher mutation rate than markers elsewhere on the chromosome. The number of growing points on the chromosome at each cell age can then be determined by observing the nitrosoguanidine-induced mutation rates for specific genetic markers on the genome. These experiments indicate that there exist multiple growing points on the genome for about ten minutes during the life cycle when the cells are growing with a doubling time of 28 minutes.

The transcribing strands of bacillus subtilis DNA for ribosomal and transfer RNA

H(3)-labeled purified 16S and 23S ribosomal RNA's and transfer RNA's were found to hybridize exclusively with the H strand of the separated complementary strands of B. subtilis DNA. These results indicate that these RNA's are transcribed in vivo from a strand with a composition similar to that from which messenger RNA's are copied and presumably by the same mechanism.

Fractionated strands of bacterial deoxyribonucleic acid. 3. Transformation efficiencies and rates of phenotypic expression

Preferential binding of guanine-rich ribopolymers to one of the complementary strands of denatured deoxyribonucleic acid (DNA) of Diplococcus pneumoniae permitted the fractionation of the complements in CsCl density gradients. Phenotypic expression of the newly acquired genes for four drug resistances was more rapid in cells transformed by the heavy fractions than in those transformed either by light fractions or by unfractionated DNA. The efficiencies of transformation with the two complements were nearly equal for the four markers tested. Both efficiency and expression results were the same whether we assayed the residual activity or the activity obtained by annealing the fractions with excess recipient DNA.

Heterogeneity of the conserved ribosomal ribonucleic acid sequences of Bacillus subtilis

Doi, Roy H. (University of California, Davis), and Richard T. Igarashi. Heterogeneity of the conserved ribosomal ribonucleic acid sequences of Bacillus subtilis. J. Bacteriol. 92:88-96. 1966.-Hybrid formation was demonstrated between Bacillus subtilis ribosomal ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) from various bacterial species. The high degree of complementarity between B. subtilis ribosomal RNA and the DNA from B. cereus and B. stearothermophilus suggested a method to test whether the same RNA sequences were hybridizing with the DNA from these two species. Saturation studies with 16S and 23S RNA preparations from B. subtilis showed that a definite number of complementary sites was present in each DNA. Base composition analyses of the RNA in the hybrid demonstrated that ribosomal RNA sequences were involved. Hybrid competition studies revealed that B. stearothermophilus ribosomal RNA could compete totally against B. subtilis ribosomal RNA for B. stearothermophilus DNA, although it could compete only partially against the B. subtilis ribosomal RNA hybridizing with B. cereus DNA. These observations were made independently with both 16S and 23S ribosomal RNA preparations. These results revealed that different nucleotide sequences of B. subtilis ribosomal RNA were hybridizing with the DNA from B. cereus and B. stearothermophilus. Two possible interpretations of these results are: (i) different nucleotide sequences from a homogeneous ribosomal RNA population are hybridizing with heterologous DNA preparations, and (ii) ribosomal RNA cistrons are heterogeneous.