Deoxyadenylate-rich and deoxyguanylate-rich regions in mammalian DNA

Mechanical Stability of DNA Corona Phase on Gold Nanospheres

Noncovalent adsorption of biopolymers on the surface of gold nanoparticles (AuNPs) forms a corona phase that drastically diversify AuNP functions. However, mechanical stabilities of such corona phase are still obscure, hindering the application of biopolymer-coated AuNPs. Here, using optical tweezers, we have observed, for the first time, that DNA corona phase adsorbed on a 5 nm AuNP via two (dA)21 strands in proximity can withstand an average desorption force of 40 pN, which is higher than the stall force of DNA/RNA polymerases. This suggests a new role for AuNPs to modulate replications or transcriptions after binding to prevalent poly(dA) segments in eukaryotic genomes. We have also revealed that with increasing AuNP size (1.8-10 nm), DNA corona becomes harder to remove, likely due to the larger surfaces and flatter facets on bigger AuNPs. These findings provide guidance to design AuNP corona that can withstand harsh environments for biological and materials applications.

Chromosomal organization of simple repeated DNA sequences used for DNA fingerprinting

Stretches of short, simple DNA sequences are widespread in all eukaryote genomes studied so far. Simple sequences are thought to undergo frequent expansion and deletion due to intrinsic genomic mechanisms. Some of the simple sequences were used successfully to detect hypervariable loci in various genomes. Hybridization experiments using synthetic probes not only revealed the informative simple repeats suitable for DNA fingerprinting in a particular species, but also reflected the wide range of distribution of the simple sequences among eukaryotes. The organization of these simple repetitive sequences at the chromosomal loci was investigated using in situ hybridization with chemically synthesized, pure oligonucleotide probes. Both biotin- and digoxigenin-attached probes detected specific chromosomal sites that are enriched in the respective simple-repeat blocks. Depending on the organism and probe used, accumulation of simple DNA sequences at individual or multiple sites on the chromosomes of different vertebrates could be demonstrated. The simple repetitive DNA sequences are located in different chromosomal regions (e.g., heterochromatin on the sex chromosomes, nucleolus organizer regions, and R-band sites), which are constrained considerably during evolution.

Mononucleotide repeats are an abundant source of length variants in mouse genomic DNA

Microsatellite sequences, such as dinucleotide repeats, show a high degree of polymorphism in eukaryotic DNA. These sequences are convenient as genetic markers and can be analyzed by the polymerase chain reaction (PCR). We have assessed the frequency of length variants in 18 mononucleotide repeats in mouse DNA and find that the variability is similar to that reported for dinucleotide repeats. Nine of the 18 repeat sequences (50%) have three or more alleles in the strains tested. Ten of these repeat sequences have been mapped using strain distribution patterns (SDPs) in recombinant inbred (RI) strains.

Long poly(A) tracts in the human genome are associated with the Alu family of repeated elements

Long poly(dA).poly(dT) tracts (poly(A) tracts), regions of DNA containing at least 20 contiguous dA residues on one strand and dT residues on the complementary strand, are found in about 2 X 10(4) copies interspersed throughout the human genome. Using poly(dA).poly(dA) as a hybridization probe, we identified recombinant lambda phage that contained inserts of human DNA with poly(A) tracts. Three such tracts have been characterized by restriction mapping and sequence analysis. One major poly(A) tract is present within each insert and is composed of from 28 to 35 A residues. In each case, the poly(A) tract directly abuts the 3' end of the human Alu element, indicating that the major class of poly(A) tracts in the human genome is associated with this family of repeats. The poly(A) tracts are also adjacent to A-rich sequences and, in one case, to a polypurine tract, having the structure GA3-GA3-GA4-GA6-GA5-GA4. We suggest that repetitive cycles of unequal crossing over may give rise to both the long poly(A) and polypurine tracts observed in this study.

Simple sequences are ubiquitous repetitive components of eukaryotic genomes

Simple sequences are stretches of DNA which consist of only one, or a few tandemly repeated nucleotides, for example poly (dA) X poly (dT) or poly (dG-dT) X poly (dC-dA). These two types of simple sequence have been shown to be repetitive and interspersed in many eukaryotic genomes. Several other types have been found by sequencing eukaryotic DNA. In this report we have undertaken a systematical survey for simple sequences. We hybridized synthetical simple sequence DNA to genome blots of phylogenetically different organisms. We found that many, probably even all possible types of simple sequence are repetitive components of eukaryotic genomes. We propose therefore that they arise by common mechanisms namely slippage replication and unequal crossover and that they might have no general function with regards to gene expression. This latter inference is supported by the fact that we have detected simple sequences only in the metabolically inactive micronucleus of the protozoan Stylonychia, but not in the metabolically active macronucleus which is derived from the micronucleus by chromosome diminution.

Distribution of poly(A)-containing RNA during normal pollen development and during induced pollen embryogenesis in Hyoscyamus niger

The distribution of poly(A)-containing RNA [poly(A)+RNA] in pollen grains of Hyoscyamus niger during normal gametophytic development and embryogenic development induced by culture of anther segments was followed by in situ hybridization with [3H]-polyuridylic acid as a probe. No binding of the isotope occurred in pollen grains during the uninucleate phase of their development. Although [3H]polyuridylic acid binding sites were present in the generative and vegetative cells of maturing pollen grains, they almost completely disappeared from mature grains ready to germinate. During pollen germination, poly(A)+RNA formation was transient and was due to the activity of the generative nucleus, whereas the vegetative nucleus and the sperm cells failed to interact with the applied probe. In cultured anther segments, moderate amounts of poly(A)+RNA were detected in the uninucleate, nonvacuolate, embryogenically determined pollen grains. Poly(A)+RNA accumulation in these grains was sensitive to actinomycin D, suggesting that it represents newly transcribed mRNA. After the first haploid mitosis in the embryogenically determined pollen grains, only those grains in which the generative nucleus alone or along with the vegetative nucleus accumulated poly(A)+RNA in the surrounding cytoplasm were found to divide in the embryogenic pathway. Overall, the results suggest that, in contrast to normal gametophytic development, embryogenic development in the uninucleate pollen grains of cultured anther segments of H. niger is due to the transcriptional activation of an informational type of RNA. Subsequent divisions in the potentially embryogenic binucleate pollen grains appeared to be mediated by the continued synthesis of mRNA either in the generative nucleus or in both the generative and vegetative nuclei.

Purine base composition analysis of normal and tumor rat DNA

Chemical and viral induced rat tumors were analyzed for their purine base composition and compared to normal tissue DNA'S. The tumors were induced by 7,12-dimethylbenz[a]anthracene (DMBA), 20-methylcholanthrene (MC), 3,4-benzopyrene (BP), 1,2-dimethylhydrazine (DMH) and Rous sarcoma virus (RSV). Normal DNAs were extracted from colon, caecum, liver, spleen and embryo and used as reference standards for base composition of normal rat DNA. The composition of purines was obtained by spectrophotometric estimation of the total adenine and guanine (A/G) contents after depurination of the DNA with 66% formic acid at 30 degrees C for 18 h and passage over a cationic exchange resin. Statistical comparison of the A/G molar ratios in normal rat DNAs (1.271) to those of chemical-induced primary tumors (1.342) has shown a highly significant increase. No significant differences could be detected when the base composition of the normals were compared to transplanted tumors, whether chemically or virally induced. Possible explanations from a mutational point of view are discussed.

Genome modification in two lines of baby hamster kidney fibroblasts (BHK-21)

Reasons for the different levels of 5-methyl cytosine encountered in the DNA of two baby hamsters kidney fibroblast lines, BHK-21/C13 and BHK-21/PyY have been investigated. From enzymic studies it does not seem that there are large numbers of potentially methylatable cytosine residues in the C13 line DNA which contains a lower level of 5-methyl cytosine. Rather it is possible that the difference may be due to the reiteration in the PyY strain of certain sequences containing 5-methyl cytosine which simply occur less frequently in the other line.

Interaction of anthracyclines with DNA and chromosomes

Daunomycin and adriamycin were previously found to produce Q-like banding patterns on chromosomes. The interaction of several anthracyclines with both natural and synthetic DNAs and chromosomes has been investigated in more detail. Daunomycin fluorescence is almost completely quenched by natural DNAs with varying base composition from 31 to 72% G-C and by the alternating polymer poly-d(G-C).poly-d(G-C). In contrast, daunomycin fluorescence is quenched by only 50% when the dye interacts with synthetic A-T polymers. Thus, differential quenching of daunomycin fluorescence can account for the production of bright bands at contiguous A-T sequences along the chromosome. Slight differences in fluorescence quenching between the repeating and homopolymeric A-T duplex DNAs were observed which can be attributed to differences in affinity of daunomycin for these DNAs. The aminosugar moiety of daunomycin, daunosamine, increases the binding of daunomycin to DNA and also enhances chromosome banding.--Nogalamycin, which displays no differential quenching with the different DNAs in solution, also fails to produce bands on chromosomes.--These findings suggest that non-random nucleotide sequence arrangements along the chromosome are a basic determinant for dye interaction to produce the observed banding patterns. Specific banding procedures may determine the accessibility of these sites within the chromosomal DNA.

The isolation of duplex DNA fragments containing (dG.dC) clusters by chromatography on poly(rC)-Sephadex

Duplex DNA containing oligo(dG.dC)-rich clusters can be isolated by specific binding to poly(rC)-Sephadex. This binding, probably mediated by the formation of an oligo(dG.dC)rC+ triple helix, is optimal at pH 5 in 50% formamide, 2 M LiCl; the bound DNA is recovered by elution at pH 7.5. Using this method we find that the viral DNAs PM2, lambda and SV40 contain at least 1, 1 and 2 sites for binding to poly(rC)-Sephadex, respectively. These binding sites have been mapped in the case of SV40; the binding sites can in turn be used for physical mapping studies of DNAs containing (dG.dC) clusters. Inspection of the sequence of the bound fragments of SV40 DNA shows that a (dG.dC)6-7 tract is required for the binding of duplex DNA to poly(rC)-Sephadex. Although about 60% of rabbit DNA cleaved with restriction endonuclease KpnI binds to poly(rC)-Sephadex, no binding is observed for the 5.1 kb DNA fragment generated by KpnI digestion, which contains the rabbit beta-globin gene. This indicates that oligo(dG.dC) clusters are not found close to the rabbit beta-globin gene.

Prevention of G:C pairing in mouse DNA by complete blocking of guanine residues with glyoxal. Availability of cytosine, adenine and thymine for hydrogen bonding with added unmodified polynucleotides

We have developed conditions for the reaction of single-stranded DNA with glyoxal which permit blocking of essentially all guanine residues. This procedure effectively prevents base pairing involving these guanine residues, yet permits cytosine, thymine and adenine residues in the DNA to pair with added polynucleotides. Modification of DNA with glyoxal greatly reduces intrastrand helical regions, resulting in a very low binding to hydroxyapatite, as compared to unmodified DNA. Annealing of modified DNA with some synthetic polynucleotides of restricted composition (but not others) leads to a significant increase in binding, presumably because mouse DNA has sequences not containing guanine which are capable of hydrogen bonding to the added polynucleotides. This relatively simple procedure may allow isolation and further study of these guanine-free sequences in DNA.

The selective isolation of the uterine oestradiol-receptor complex by binding to oligo(dT)-cellulose. The mediation of an essential activator in the transformation of cytosol receptor

The [3H]oestradiol-receptor complex was selectively isolated from rat uterus cytosol by column chromatography on oligo(dT)-cellulose. Optimal conditions are described for the binding of the complex to oligo(dT)-cellulose, which is shown to be similar to its binding to DNA-cellulose. The cytosol complex has an apparent mol. wt. of 50,000-60,000 in high salt concentrations, as determined by Sephadex G-100 chromatography. This corresponds to the 4S cytoplasmic oestradiol receptor. In binding to oligo(dT)-cellulose the receptor is transformed into a form with an apparent mol.wt. of 100,000-120,000, corresponding to the 5S nuclear receptor complex. This transformation mimics the conversion in vivo of the cytoplasmic oestradiol receptor into the nuclear form. The binding of the complex to oligo(dT)-cellulose as a 5S nuclear form is unequivocally demonstrated to require the mediation of an activating present in the cytosol. The requirement for an activating factor is discussed in relation to reports that nuclear binding of the oestradiol-receptor complex is not dictated solely by the availability of the cytoplasmic oestradiol receptor.

The presence of (dA.dT)20-25 tracts in the DNA of primitive eukaryotes

Previous work by Jacobson et al. (1) has shown that the number and distribution of (dA.dT)25 tracts in the nuclear DNA of the slime mold Dictyostelium discoideum reflects the number and the distribution of transcriptional units. To investigate whether this is a general phenomenon we compared the nuclear DNAs of other primitive eukaryotes with respect to their content of large (dA.dT)n tracts via the thermal stability of their hybrids with poly(rA). The results of our analysis indicate that all nuclear DNAs tested have (dA.dT)20-25 tracts, but the frequency of such tracts varies from one per 5.4 X 10(6) daltons in Dictyostelium nuclear DNA to one per 2.8 X 10(8) daltons in Crithidia luciliae nuclear DNA. We conclude that the presence of (dA.dT)20-25 tracts is not an obligatory characteristic of the transcriptional unit in primitive eukaryotes. Chromatography of native DNAs on poly(rU) Sephadex columns shows that the large (dA.dT)n tracts occurring in the genomes of both primitive and higher eukaryotes are widely distributed throught these genomes.

Interspersion and transcription of repeated sequences of rat DNA

Repetitive rat DNA reassociated to Cot=0.1 and deprived of "foldback" sequences showed close interspersion with unique sequences. As measured by electron microscopy, the average length of repetitive segments was about 600 +/- 400, and of unique segments 1800-3600 base pairs. Pyrimidine tracts over 80 nucleotides in length were found mainly in foldback and repetitive fractions. Oligo(dT) tracts, 20-30 bases in length prevailed in the DNA fraction reassociated to Cot=0.1. Repetitive and unique DNA fractions were annealed to Millipore filters and hybridized with hnRNA. Up to 1.6% of repetitive DNA reassociated to Cot=0.05 showed base complementarity with hnRNA, whereas the comparative figures for DNA reassociated to Cot=10 and for the unique fraction were 0.8% and 0.3% respectively. When hybridization of hnRNA was carried out in solution in vast DNA excess, no hybrid formation with repetitive sequences reassociated to Cot=0.1 was observed, although hybridization with DNA reassociated to Cot=10 was noticeable.

Template specific inhibitor of mammalian DNA polymerases

A study of the inhibition of mouse cellular DNA polymerases by poly-nucleotides and their vinyl analogs is presented. Poly(dT)-directed poly(dA) synthesis by representatives of all three classes of cellular DNA polymerase could be completely inhibited by poly(9-vinyladenine), although higher concentrations were required in the case of the gamma class enzyme. Studies on the mechanism of the inhibition using the alpha class DNA polymerase and different templates showed that the enzyme activity was inhibited in all cases where base-pairing between the vinyl polymer and the template occurred; poly(9-vinyladenine) did not interfere with the replication of templates to which it does not bind. The inhibition occurred shortly after addition of poly(9-vinyladenine) to ongoing reactions, yet the enzyme was not displaced from the template - primer complex.

Influence of temperature on the detectibility and chromosomal distribution of specific DNA sequences by in situ hybridisation

Hybridising certain AT-rich satellite complementary RNAs (cRNAs) to their homologous chromosomal DNA sequences at different temperatures of incubation results in a different dispersion of autoradiographic label throughout the karyotypes. The temperature at which most label, or cRNA-DNA hybrid formation, exists corresponds to the optimal rate temperature for the hybridisation of these same satellite cRNA-DNA hybrids as determined by RNA excess filter hybridisation. It is likely that the in situ hybridisation results can therefore be explained by the fact that there is a similar temperature-dependence on the rate of hybrid formation for both in situ and RNA excess hybridisation. This should have important implications for the designing of in situ hybridisation experiments in general.

Hybridization of polyuridylic acid to human DNA immobilized onto nitrocellulose filters

The level of deoxyadenylate (da) regions in human DNA was estimated from formation of poly(U)-poly(da) triplexes on nitrocellulose filters that were RNAase resistant. The (dA) rich sequences were determined following mild ribonuclease treatment of the poly(U)-DNA hybrids (5 mug/ml at 25 degreesC for 30 min), where as exhaustive ribonuclease treatment (5 mug/ml at 25 degrees C for 6 hr) estimated the more (dA) pure sequences. The level of (dA) rich regions was 0.39% of the DNA and for the more (dA) pure regions it was 0.07%. The (dA) regions were widely distributed throughout human DNA regardless of base composition or sequence repetition. However, a concentration of (dA) regions into main band CsC1 gradient fractions of DNA and into repeated DNA was observed.

The hybridisation of [(3)H]poly(uridylic) acid to DNA from Phaseolus aureus Roxb

[5-(3)H]poly(uridylic) acid hybridises to nuclear DNA, suggesting the DNA contains poly (deoxyadenylic) acid sequences. These regions do not appear to be clustered in the DNA. Although the amount of DNA involved is small it is sufficient for thousands of sequences. Thermal dissociation of the hybrids shows that a relatively small number of hydrogen bonds is involved in each and it is concluded that these sequences are relatively short. In view of the fact that much longer poly(adenylic) acid sequences are found in plant RNA it is concluded that these are added after transcription.