Rodent DNA reassociation kinetics

The kinetics of reassociation of the nuclear DNA of eight rodents has been examined to determine the amount and repetition frequency of various DNA fractions. Each rodent had at least two distinct, repeated DNA fractions, one group repeated about 300 times and the other repeated about 50,000 times. As shown, the actual repetition frequencies and the amount of the various DNA fractions varied from one species to another. Genetic implications of these results are discussed.     

DNA reassociation kinetics of closely related species

The kinetics of reassociation of the DNA of three groups of closely related organisms were examined. The laboratory mouse was compared to an Asiatic mouse, whose chromosome number is the same but whose chromosome organization is different. Chinese hamster (2N=22) was compared to Syrian hamster (2N=44), and Haplopappus gracilis (2N=4) was compared to H. ravenit (2N=8). It was found that the most highly repeated DNA fractions of the three comparative sets of organisms differ in their reaction rates. However, these fractions of the related hamsters, haplopappi, and probably the mice, do not differ in the amount of DNA composing the fractions. The intermediately fast reassociating DNA and the unique DNA do not differ between members of related pairs of organisms. The implication of these results is that a short sequence of DNA may be highly copied in one organism, while in a related organism a longer DNA sequence is repeated a fewer number of times, and the total amount of repeated DNA may be the same in both related organisms.     

Fluorometric measurement of DNA reassociation kinetics.

A new radioimmunoassay (RIA) method is proposed, utilizing cellulose disks coated with a ${}^{125}\text{I-}\text{Ag}\text{Ab}$ complex as a single reagent. The labeled antigen is released into the incubation medium proportionally to the concentration of the corresponding antigen in the sample. The method is comparable to the classical RIA with regard to sensitivity, precision, and specificity, but it has the advantage of a wide range of nondependence on the sample volume and greater practicability (the analysis is performed using a single-step procedure). The assay of human chorionic somatomammotropin is adopted as a model.     

DNA reassociation kinetics and hybridization in different angiosperms

Reassociation kinetics ofDaucus carota andPetroselinum crispum (Apiaceae), andDatura innoxia (Solanaceae) are presented. Hybridization of³H-labelled DNA of two carrot cultivars indicate strong qualitative homologies of DNA sequences; nevertheless, certain quantitative differences in some Cotregions seem to exist. However, homologous sequences ofDaucus DNA with DNA ofDatura, and, suprisingly, even with DNA ofPetroselinum are very restricted: between 8% in the repeated regions and ca. 7–9% in the unique regions.     

Cytoplasmic DNA: Differentiation by reassociation kinetics

Rat liver nuclear and cytoplasmic DNA samples were denatured and the kinetics of their reassociation was measured. About 85% of the soluble cytoplasmic (mitochondrial) DNA reannealed rapidly with a $\text{C}{}_{\mathrm{o}}\text{t}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{= 0.03}$ while 65% of the particulate (microsomal) DNA reassociated with a $\text{C}{}_{\mathrm{o}}\text{t}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{= 0.14}$ Both nucleic acids were clearly differentiated from nuclear DNA in their reassociation kinetics. The results indicate that both mitochondrial and microsomal DNA consist mainly of single components or closely related families with repetitive sequences.     

DNA reassociation kinetics in diploid and phylogenetically tetraploid cyprinidae.

Four diploid and three phylogenetically tetraploid Cyprinidae (Ostariophysi) have been characterized as for nuclear DNA content, modal chromosome number and DNA reassociation kinetics (hydroxyapatite chromatography). Among the diploid species nuclear DNA content (10(-12) g DNA/2C) was 1.62 for Tinca tinca, 1.87 for Scardinius erythrophthalmus, 2.53 for Leuciscus cephalus and 2.75 for Alburnus alburnus, while the phylogenetically tetraploid species Carassius auratus, Barbus barbus and Cyprinus carpio attained 3.40, 3.66 and 3.80 respectively. Modal chromosome number was 2n = 48-50 for diploid individuals and 2n = 100-104 for phylogenetically tetraploid ones. In all the species 5--8% of the genome is represented by highly repetitive and foldback DNA. In DNA reassociation kinetics of phylogenetically tetraploid Cyprinidae a distinct plateau separates an intermediate reassociating sequence fraction (about 22% of the genome; with average repetition frequencies between 1,000 and 1,400) from a slow reassociating one (unique DNA; about 72% of the genome). These two genome fractions are not clearly distinguishable from each other in Cot curves of the diploid Cyprinidae, where a similar plateau is not evident. Since simple ploidy changes are not expected to affect DNA reassociation kinetics we suggest a different evolution in the genome organization of the two ploidy groups. Some possible hypotheses are discussed.     

A rapid computer analysis for multicomponent DNA reassociation kinetics

An iterative program, Gaushaus, has been adapted to analyze complex DNA reassociation kinetics. With valid experimental data, rapid convergence to a solution is always achieved by this program even when the starting parameters are grossly in error. The output of the program also includes useful statistical information.     

Length dependence in reassociation kinetics of radioactive tracer DNA.

The reassociation kinetics have been measured for radioactive Escherichia coli DNAs (tracers) of various average single-strand lengths reassociated alone and in the presence of excess unlabeled DNA (driver) of two different average lengths. Hydroxylapatite binding was used to follow the reaction time course. The length-dependence of the rate constant determined in the tracer self-reassociation reactions is in agreement with the square-root dependence previously determined (Wetmur, J. G., & Davisond, N. (1968) J. Mol. Biol. 31, 349-370) using optical methods to follow the time course. However, for the driver-tracer reactions, where the radioactive DNA reassociates largely with DNA of a different average length, the dependence of the rate constant upon average tracer length is increased and approaches an L to the first power dependence. In 0.18 M Na+, the variation of the rate constant for tracer reassociation with the lengths of the reassociating strands has been shown to fit the simple equation k = (9.0077).(L T 0.55 + 1/L D 0.55), where k is the observed rate constant in L mol-1 s-1 and L(T)and L(D) are the weight average tracer and driver lengths, respectively, in nucleotides. This dependence suggests that the rate of nucleation of two free strands is proportional to the sum of the reciprocals of the hydrodynamic radii of the two strands.     

Method for determination of nucleotide sequence homology between viral genomes by DNA reassociation kinetics.

A model and appropriate equations were derived for the quantitative estimation of nucleotide sequence homology between two partially related viral genomes by measurement of the initial rate of reassociation of one labeled DNA in the presence of a second unlabeled DNA. The validity and usefulness of this procedure were demonstrated by the analysis of the reassociation kinetics of labeled adenovirus 7 DNA in the presence of unlabeled adenovirus 2 DNA. Based on DNA reassociation, the extent of homology between adenovirus 2 and 7 genomes was found to be 10 to 12%. The duplex formed between adenovirus 2 and 7 DNA had the appropriate thermal stability for a well-matched DNA-DNA hybrid.     

The Bombyx mori genome: analysis by DNA reassociation kinetics

The size and nucleotide sequence complexity of the Bombyx mori genome has been determined from the kinetics of reassociation of its DNA. Nonrepeated DNA comprises 55% of the genome, and the remainder is divided equally between sequences repeated roughly 500 and 50000 times. Non-repeated sequence DNA virtually free of repeated sequences was prepared by partial reassociation and subsequent fractionation on hydroxyapatite. The nucleotide sequence complexity of this component was determined relative to DNA from B. subtilis and E. coli. After correction for the size of the repeated sequence fraction, the DNA content of the Bombyx mori genome was calculated to be 0.53±0.02×10^?12 g. This value compares favorably with the DNA content of haploid B. mori spermatids and mature sperm determined cytophotometrically by Rasch (1973).     

Application of DNA sonication in the study of reassociation kinetics]

Single-stranded breaks arising is DNA under sonication divide the molecule in short double-stranded regions of lengths depending on sonication conditions. The reassociation rate of DNA with single-stranded breaks is considerably lowered as compared with intact DNA of the same length. For sonicated DNA the slowing of reassociation and the deflection to higher orders of C(o)t of the reaction is observed at the late stages. Further process of sonication occurs likely on single-stranded breaks and DNA fragments obtained as a result of infinite sonication are practically intact. Reassociation of DNA, degraded to a "saturation", proceeds as a second order reaction in precise accordance with the obtained fragment length.     

Correlation between the species radiosensitivity of animals and concentration of AT-rich sequences in DNA

The authors have revealed a positive and statistically significant correlation between the sum of T-"pure" and T-rich pyrimidine DNA clusters and radiosensitivity of animals of different species. It was demonstrated that the share of a DNA fraction rich in AT-pairs and denaturing within the temperature range from 55 to 75 degrees increases with increasing specific radiosensitivity of animals.     

DNA reassociation kinetics and diversity indices: richness is not rich enough

DNA reassociation kinetics, also known as Cot curves, were recently used by Gans and co-workers to estimate the number of bacterial species present in soil samples. By reanalysing the mathematical model we show that rather than the number of species, Simpson and Shannon diversity indices are encoded in the experimental data. Our main tool to establish this result are the so-called Rényi diversities, closely related to Hill numbers, illustrating the power of these concepts in interpreting ecological data. We argue that the huge diversity encountered in microbial ecology can be quantified more informatively by diversity indices than by number of species.     

Propidium iodide and S1 nuclease: tools for studying DNA reassociation kinetics

A method for the determination of the amount of double-stranded DNA in a reassociation mixture is described. Reassociated DNA resistant to S1 nuclease digestion is measured fluorometrically using propidium iodide. A direct comparison is made between this method and an established method in which radiolabeled Escherichia coli DNA resistant to S1 digestion is measured by scintillation counting after separation of nucleotides by Sephadex G-100 chromatography. Reassociation curves determined for calf thymus and E. coli DNA are presented.     

Preparation of radioiodinated simian virus 40 DNA for use in DNA - DNA reassociation kinetics experiments.

A method is described for the preparation of 125I-labelled SV40 DNA. Using this method, SV40 DNA can be routinely labelled to 15 - 10(6) dpm per mug; much higher specific activities are easily obtained by minor modifications of the method. Once incorporated, the radioactive label dissociates from DNA exceedingly slowly at 4 degrees C or at 68 degrees C. Iodinated SV40 DNA is shown to be useful in the quantitation of viral nucleic acid sequences in SV40-transformed 3T3 cells by DNA - DNA reassociation kinetics.     

DNA reassociation kinetics in relation to genome size in four amphibian species

DNA reassociation kinetics were studied, by means of the hydroxyapatite chromatography method, for four species of Amphibians with different nuclear DNA content: Xenopus laevis (3 pg DNA per haploid genome) and Bufo bufo (7 pg) of the Anura subclass and Trituras cristatus (23 pg) and Necturus maculosus (52 pg) of the Urodela subclass.Within each subclass the two species studied were found to have about the same absolute amount of unique DNA. The differences of total nuclear DNA can be accounted for by quantitative variations of the repetitive sequence classes, at least in part due to changes in the number of copies of the various sequences. On the contrary the great difference in nuclear DNA between the two subclasses, Anura and Urodela, involves all sequence classes in parallel; the slowly reassociating fraction appears to be unique in spite of a tenfold difference in absolute amount.The dependence of reassociation kinetics on DNA fragment length for the four species indicates for all of them an interspersed organization of the various sequence classes.     

Structural characteristics (reassociation and melting kinetics) of kinetoplast DNA from Crithidia oncopelti

A highly purified associate of kinetoplast DNA is isolated from C. oncopelti, and its physico-chemical properties are studied. Both native associate and its ultrasonic fragments are found to have a complex character of melting. 5-6 melting zones (3 of them being the main) are found on the melting curve. Analysis of reassociation kinetics of sonicated associate of kinetoplast DNA has revealed the presence of at least two components: fast reassociating component (65-70% of complex DNA), which reassociation kinetics is equivalent to the unique sequence with molecular weight of 2.3. - 10(6) daltons, and slow reassotiating component (15% of complex DNA), having reassociation kinetics equivalent to unique sequence of 26 - 10(6) daltons. The data obtained suggest that complex associate of kinetoplast DNA is heterogenous for its nucleotide sequence and base composition.