Studies on nucleic acid reassociation kinetics: empirical equations describing DNA reassociation

Advances in plant genome sequencing

The study of plant biology in the 21st century is, and will continue to be, vastly different from that in the 20th century. One driver for this has been the use of genomics methods to reveal the genetic blueprints for not one but dozens of plant species, as well as resolving genome differences in thousands of individuals at the population level. Genomics technology has advanced substantially since publication of the first plant genome sequence, that of Arabidopsis thaliana, in 2000. Plant genomics researchers have readily embraced new algorithms, technologies and approaches to generate genome, transcriptome and epigenome datasets for model and crop species that have permitted deep inferences into plant biology. Challenges in sequencing any genome include ploidy, heterozygosity and paralogy, all which are amplified in plant genomes compared to animal genomes due to the large genome sizes, high repetitive sequence content, and rampant whole- or segmental genome duplication. The ability to generate de novo transcriptome assemblies provides an alternative approach to bypass these complex genomes and access the gene space of these recalcitrant species. The field of genomics is driven by technological improvements in sequencing platforms; however, software and algorithm development has lagged behind reductions in sequencing costs, improved throughput, and quality improvements. It is anticipated that sequencing platforms will continue to improve the length and quality of output, and that the complementary algorithms and bioinformatic software needed to handle large, repetitive genomes will improve. The future is bright for an exponential improvement in our understanding of plant biology.

The effects of oligonucleotide overhangs on the surface hybridization in DNA films: an impedance study

While oligonucleotide hybridization and effects of nucleobase mismatches have been the intense focus of a number of electrochemical studies, the effects of the target strand length on the electrochemical response of oligonucleotide films have not been addressed yet. In this report, we have studied the electrochemical impedance of the oligonucleotide films having overhangs on either the target or the surface bound capture strand. Each system gives different impedance responses, which were interpreted with the help of modified Randles' equivalent. Results indicate that comparable sizes of target and capture strands ensure the higher hybridization efficiency and film order. The presence of nucleobase overhangs at the bottom of the film causes lower changes in charge transfer resistance (ΔR(CT)) after hybridization due to lower hybridization efficiency and presumably non-uniformity in the film. Nucleobase overhangs at the top of the film result in higher ΔR(CT) due to higher film order and accumulation of negative charges but appear not to cause any steric congestion.

Rare genomic deletions and duplications and their role in neurodevelopmental disorders

Copy number variations (CNVs) are deletions and duplications of DNA sequences that vary in length from a few base pairs to several million. While these structural variations are often benign, they can disrupt vital biological functions and result in disease. CNVs have been identified as causal in a number of neurodevelopmental disorders (NDs), including but not limited to, autism, attention-deficit/hyperactivity disorder (ADHD), and schizophrenia. Here, we examine CNV research into these disorders, and discuss relevant methodological considerations. By identifying specific rare deletions and duplications, we may be better able to determine the etiology of neurodevelopmental disorders and identify appropriate treatments.

Mechanism of thermal renaturation and hybridization of nucleic acids: Kramers' process and universality in Watson-Crick base pairing

Renaturation and hybridization reactions lead to the pairing of complementary single-stranded nucleic acids. We present here a theoretical investigation of the mechanism of these reactions in vitro under thermal conditions (dilute solutions of single-stranded chains, in the presence of molar concentrations of monovalent salts and at elevated temperatures). The mechanism follows a Kramers' process, whereby the complementary chains overcome a potential barrier through Brownian motion. The barrier originates from a single rate-limiting nucleation event in which the first complementary base pairs are formed. The reaction then proceeds through a fast growth of the double helix. For the DNA of bacteriophages T7, T4, and phiX174, as well as for Escherichia coli DNA, the bimolecular rate k2 of the reaction increases as a power law of the average degree of polymerization <N> of the reacting single-strands: k2 is proportional to <N> alpha. This relationship holds for 100 < or = <N> < or = 50,000 with an experimentally determined exponent alpha = 0.51 +/- 0.01. The length dependence results from a thermodynamic excluded-volume effect. The reacting single-stranded chains are predicted to be in universal good solvent conditions, and the scaling law is determined by the relevant equilibrium monomer contact probability. The value theoretically predicted for the exponent is alpha = 1 - nutheta2, where nu is Flory's swelling exponent (nu approximately equal 0.588), and theta2 is a critical exponent introduced by des Cloizeaux (theta2 approximately equal 0.82), yielding alpha = 0.52 +/- 0.01, in agreement with the experimental results.

The problem of the eukaryotic genome size

The current state of knowledge concerning the unsolved problem of the huge interspecific eukaryotic genome size variations not correlating with the species phenotypic complexity (C-value enigma also known as C-value paradox) is reviewed. Characteristic features of eukaryotic genome structure and molecular mechanisms that are the basis of genome size changes are examined in connection with the C-value enigma. It is emphasized that endogenous mutagens, including reactive oxygen species, create a constant nuclear environment where any genome evolves. An original quantitative model and general conception are proposed to explain the C-value enigma. In accordance with the theory, the noncoding sequences of the eukaryotic genome provide genes with global and differential protection against chemical mutagens and (in addition to the anti-mutagenesis and DNA repair systems) form a new, third system that protects eukaryotic genetic information. The joint action of these systems controls the spontaneous mutation rate in coding sequences of the eukaryotic genome. It is hypothesized that the genome size is inversely proportional to functional efficiency of the anti-mutagenesis and/or DNA repair systems in a particular biological species. In this connection, a model of eukaryotic genome evolution is proposed.

Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways

The renaturation/denaturation of DNA oligonucleotides is characterized in the context of expanded ensemble (EXE) and transition path sampling (TPS) simulations. Free energy profiles have been determined from EXE for DNA sequences of varying composition, chain length, and ionic strength. TPS simulations within a Langevin dynamics formalism have been carried out to obtain further information of the transition state for renaturation. Simulation results reveal that free energy profiles are strikingly similar for the various DNA sequences considered in this work. Taking intact double-stranded DNA to have an extent of reaction ξ = 1.0, the maximum of the free energy profile appears at ξ≈0.15, corresponding to ∼2 base pairs. In terms of chain length, the free energy barrier of longer oligonucleotides (30 versus 15 base pairs) is higher and slightly narrower, due to increased sharpness associated with the transition. Low ionic strength tends to decrease free energy barriers, whereby increasing strand rigidity facilitates reassociation. Two mechanisms for DNA reassociation emerge from our analysis of the transition state ensemble. Repetitive sequences tend to reassociate through a non-specific pathway involving molecular slithering. In contrast, random sequences associate through a more restrictive pathway involving the formation of specific contacts, which then leads to overall molecular zippering. In both random and repetitive sequences, the distribution of contacts suggests that nucleation is favored for sites located within the middle region of the chain. The prevalent extent of reaction for the transition state is ξ≈0.25, and the critical size of the nucleus as obtained from our analysis involves ∼4 base pairs.

Isolation and characterization of the highly repeated fraction of the banana genome

Although the nuclear genome of banana (Musa spp.) is relatively small (1C approximately 610 Mbp for M. acuminata), the results obtained from other sequenced genomes suggest that more than half of the banana genome may be composed of repetitive and non-coding DNA sequences. Knowledge of repetitive DNA can facilitate mapping of important traits, phylogenetic studies, BAC-based physical mapping, and genome sequencing/annotation. However, only a few repetitive DNA sequences have been characterized in banana. In this work, we used DNA reassociation kinetics to isolate the highly repeated fraction of the banana genome (M. acuminata 'Calcutta 4'). Two libraries, one prepared from Cot </=0.05 DNA (2,688 clones) and one from Cot </=0.1 sequences (4,608 clones), were constructed, and 614 DNA clones were chosen randomly for sequencing and further characterization. Dot-plot analysis revealed that 14% of the sequenced clones contained various semi-tandem and palindromic repeated sequences. 'BLAST' homology searches showed that, in addition to tandem repeats, the Cot libraries were composed mainly of different types of retrotransposons, the most frequent being the Ty3/gypsy type monkey retrotransposon. Selected sequences displaying tandem organization properties were mapped by PRimed IN Situ DNA labeling (PRINS) to the secondary constriction on metaphase chromosomes of M. acuminata 'Calcutta 4'. Southern hybridization with selected BAC clones carrying 45S rDNA confirmed the presence of the tandem repeats in the 45S rDNA unit. This work significantly expands the knowledge of the repetitive fraction of the Musa genome and organization of its chromosomes.

Genomic rearrangements and gene copy-number alterations as a cause of nervous system disorders

Genomic disorders are a group of human genetic diseases caused by genomic rearrangements resulting in copy-number variation (CNV) affecting a dosage-sensitive gene or genes critical for normal development or maintenance. These disorders represent a wide range of clinically distinct entities but include many diseases affecting nervous system function. Herein, we review selected neurodevelopmental, neurodegenerative, and psychiatric disorders either known or suggested to be caused by genomic rearrangement and CNV. Further, we emphasize the cause-and-effect relationship between gene CNV and complex disease traits. We also discuss the prevalence and heritability of CNV, the correlation between CNV and higher-order genome architecture, and the heritability of personality, behavioral, and psychiatric traits. We speculate that CNV could underlie a significant proportion of normal human variation including differences in cognitive, behavioral, and psychological features.

Response to Comment by Volkov et al . on "Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil"

Volkov et al . claim that significant conclusions about the total number of species ( S ) cannot be made because different abundance models cannot be distinguished and the sensitivity of the chi-square measure to changes in estimates of S is low. We point out that currently available data do not support these claims.

Leafing through the genomes of our major crop plants: strategies for capturing unique information

Crop plants not only have economic significance, but also comprise important botanical models for evolution and development. This is reflected by the recent increase in the percentage of publicly available sequence data that are derived from angiosperms. Further genome sequencing of the major crop plants will offer new learning opportunities, but their large, repetitive, and often polyploid genomes present challenges. Reduced-representation approaches - such as EST sequencing, methyl filtration and Cot-based cloning and sequencing - provide increased efficiency in extracting key information from crop genomes without full-genome sequencing. Combining these methods with phylogenetically stratified sampling to allow comparative genomic approaches has the potential to further accelerate progress in angiosperm genomics.

Enrichment of gene-coding sequences in maize by genome filtration

Approximately 80% of the maize genome comprises highly repetitive sequences interspersed with single-copy, gene-rich sequences, and standard genome sequencing strategies are not readily adaptable to this type of genome. Methodologies that enrich for genic sequences might more rapidly generate useful results from complex genomes. Equivalent numbers of clones from maize selected by techniques called methylation filtering and High C0t selection were sequenced to generate approximately 200,000 reads (approximately 132 megabases), which were assembled into contigs. Combination of the two techniques resulted in a sixfold reduction in the effective genome size and a fourfold increase in the gene identification rate in comparison to a nonenriched library.

High-Cot sequence analysis of the maize genome

Higher eukaryotic genomes, including those from plants, contain large amounts of repetitive DNA that complicate genome analysis. We have developed a technique based on DNA renaturation which normalizes repetitive DNA, and thereby allows a more efficient outcome for full genome shotgun sequencing. The data indicate that sequencing the unrenatured outcome of a Cot experiment, otherwise known as High-Cot DNA, enriches genic sequences by more than fourfold in maize, from 5% for a random library to more than 20% for a High-Cot library. Using this approach, we predict that gene discovery would be greater than 95% and that the number of sequencing runs required to sequence the full gene space in maize would be at least fourfold lower than that required for full-genome shotgun sequencing.

Genome architecture, rearrangements and genomic disorders

An increasing number of human diseases are recognized to result from recurrent DNA rearrangements involving unstable genomic regions. These are termed genomic disorders, in which the clinical phenotype is a consequence of abnormal dosage of gene(s) located within the rearranged genomic fragments. Both inter- and intrachromosomal rearrangements are facilitated by the presence of region-specific low-copy repeats (LCRs) and result from nonallelic homologous recombination (NAHR) between paralogous genomic segments. LCRs usually span approximately 10-400 kb of genomic DNA, share >or= 97% sequence identity, and provide the substrates for homologous recombination, thus predisposing the region to rearrangements. Moreover, it has been suggested that higher order genomic architecture involving LCRs plays a significant role in karyotypic evolution accompanying primate speciation.

PAGE analysis of the heteroduplexes formed between PCR-amplified 16S rRNA genes: estimation of sequence similarity and rDNA complexity

Analysis of the 16S rRNA genes retrieved directly from different environments has proven to be a powerful tool that has greatly expanded our knowledge of microbial diversity and phylogeny. It is shown here that sequence similarity between 80 and 100% among 16S rDNAs can be estimated by the electrophoretic migration of their heteroduplexes. This was measured by hybridization and electrophoresis in polyacrylamide gels of the product obtained after PCR amplification of almost the entire 16S rRNA gene from different bacterial species. These heteroduplexes were also observed after amplification of samples containing DNA from two or more bacterial species and a procedure was applied to identify reliably heteroduplexes among the amplification products. The electrophoretic migration of the heteroduplexes observed after PCR was used to detect the presence of 16S rDNAs with different sequences in DNA extracted from both a mixture of two bacterial species and samples containing a natural bacterial community.

Phylogenetic relationship of the green alga Nanochlorum eukaryotum deduced from its chloroplast rRNA sequences

The marine green coccoidal alga Nanochlorum eukaryotum (N.e.) is of small size with an average diameter of 1.5 microns. It is characterized by primitive-appearing biochemical and morphological properties, which are considerably different from those of other green algae. Thus, it has been proposed that N.e. may be an early developed algal form. To prove this hypothesis, DNA of N.e. was isolated by a phenol extraction procedure, and the chloroplast DNA separated by preparative CsCl density-gradient centrifugation. The kinetic complexity of the nuclear and of the chloroplast DNA was evaluated by reassociation kinetics to 3 x 10(7) bp and 9 x 10(4) bp, respectively. Several chloroplast genes, including the rRNA genes, were cloned on distinct fragments. The order of the rRNA genes corresponds to the common prokaryotic pattern. The 16S rRNA gene comprises 1,548 bases and is separated from the 23S rRNA gene with its 2,920 bases by a short spacer of 460 bases, which also includes the tRNA(Ile) and tRNA(Ala) genes. The 5S rRNA gene has not been found; it must start further than 500 bases downstream from the 3'-end of the 23S rRNA gene. From the chloroplast rRNA sequences, we have deduced secondary structures of the 16S and 23S rRNAs, which are in agreement with standard models. The rRNA sequences were aligned with corresponding chloroplast sequences; phylogenetic relationships were calculated by several methods. From these calculations, we conclude that N.e. is most closely related to Chlorella vulgaris. Therefore, N.e. does not represent an early developed algal species; the primitive-appearing morphological and biochemical characteristics of N.e. must rather be explained by secondary losses.

A kinetic model for subtractive hybridization

Nucleic acid sequences that differ in abundance between two populations (target sequences) can be cloned by multiple rounds of subtractive hybridization and amplification by PCR. These sequences can be cDNAs representing up-regulated mRNAs, or genomic DNAs from deletion mutants. We have derived an equation that describes the recovery of such sequences, and have used this to simulate the outcome of up to 10 rounds of subtractive hybridization and PCR amplification. When the model was tested by comparing its predictions with the published results from genomic and cDNA subtractions, the predictions of the model were generally in good agreement with the published data. We have modelled the outcomes of genomic subtractions, for a variety of genomes, and have used it to compare various strategies for enriching targets. The model predicts that for genomes of less than 5 x 10(8) bp, deletions of as small as 1 kbp should represent > 99% of the DNA after three to six rounds of hybridization (depending on the enrichment procedure). As genomes increase in size, the kinetics of hybridization become an important limiting factor. However, even for genomes as large as 3 x 10(9) bp, it should be possible to isolate deletions of 5 kbp using the appropriate conditions. These simulations suggest that such methods offer a realistic alternative to chromosome walking for identifying genomic deletions for which there are known phenotypes, thereby considerably reducing time and effort. For cDNA subtractive hybridization, the model predicts that after six rounds of hybridization, sequences that do not differ in abundance between the tester and driver populations (the background) will represent < 1% of the subtracted population, and even quite modestly upregulated cDNAs should be successfully enriched. Where several up-regulated cDNAs are present, the predicted final representation is dependent on both the initial abundance and the degree of up-regulation.

Kaposi's sarcoma. IV. Detection of CMV DNA, CMV RNA and CMNA in tumor biopsies

In order to determine whether human cytomegalovirus- (CMV) DNA homologous sequences as well as CMV-specific RNA(s) and antigen(s) exist in tumor biopsies of Kaposi's sarcoma (KS) DNA-DNA reassociation, RNA-DNA in situ cytohybridization and anticomplement immunofluorescence test (ACIF) tests were applied. Three of 10 DNAs extracted from Kaposi sarcoma biopsies contained DNA sequences homologous to radioactively labelled human CMV DNA probe. The amount of CMV DNA in these sarcoma tissues was calculated to range from 0.7 to 1 genome equivalent per diploid cell. The presence of virus-specific RNA was also demonstrated in section from five of 10 tumor biopsies. CMV-determined nuclear antigen(s) CMNA) present in variable degrees were also demonstrated. In contrast, we could not detect any herpes simple virus type II (HSV-2) or Epstein-Barr virus (EBV) DNA sequences in DNA of these tumor biopsies. Furthermore, there were no detectable HSV-2 or EBV-specific RNA or virus-specific antigens in sections of these biopsies. These results provide new lines of evidence for the relationship between CMV and Kaposi's sarcoma.

Cytomegalovirus: detection in human colonic and circulating mononuclear cells in association with gastrointestinal disease

The specificity and strength of the reported association between cytomegalovirus (CMV) and colonic adenocarcinoma were tested by analysis of a consecutive series of surgically resected colons for: CMV-DNA by a DNA-DNA reassociation kinetics (hybridization) procedure; latent virus by co-cultivation of fresh tissue with indicator fibroblasts; and CMV viral antigens by immunofluorescence. Ten of 13 cancer patients whose colonic tissue was able to be examined by all techniques showed evidence of active or prior CMV infection. Four cancer specimens were CMV-DNA (hybridization)- positive; an additional specimen from a cancerous colon was culture-positive. In six instances, CMV DNA was detected in mucosal cells adjacent to colon adenocarcinoma. In tissue from one of three patients with ulcera tive colitis and two of seven patients with other non-neoplastic colonic disease, CMV DNA was also detected. No fresh colonic tissues were demonstrated to have CMV surface or nuclear antigens when examined by immunofluorescence. Culture of peripheral lymphocytes was positive for CMV in three of 14 cancer patients. A CMV specific defect in humoral immunity could not be documented in that most cancer patients, as well as cancer-free patients, exhibited circulating specific antibody to CMV and had a normal capacity for CMV-specific antibody-dependent cellular cytotoxicity. We conclude that CMV, probably in a latent form, is readily detectable in colonic cells of man, including those derived from malignant, pre-malignant and non-malignant tissues. Neither preferential replication in damaged tissue nor carriage of CMV by peripheral lymphocytes homing to gut appear to explain the presence of CMV in colon cells.

Evolution of sea urchin non-repetitive DNA

New methods have been applied to the determination of single copy DNA sequence differences between the sea urchin species Strongylocentrotus purpuratus, S. franciscanus, S. drobachiensis, and Lytechinus pictus. The thermal stability of interspecies DNA duplexes was measured in a solvent (2.4 M tetraethylammonium chloride) that suppresses the effect of base composition on melting temperature. The lengths of duplexes were measured after digestion with S1 nuclease and correction made for the effect of length on thermal stability. The degree of base substitution that has occurred in the single copy DNA during sea urchin evolution is significantly larger than indicated by earlier measurements. We estimate that 19% of the nucleotides of the single copy DNA are different in the genomes of the two sea urchin congeners, S. purpuratus, and S. franciscanus, which apparently diverged only 15 to 20 million years ago.

Message sequences and short repetitive sequences are interspersed in sea urchin egg poly(A)+ RNAs

At least half of the mass and most of the different single-copy maternal mRNA sequences in the egg are covalently associated with transcripts of short repetitive sequences. Only a restricted group of the diverse genomic repeat families are significantly represented. The messages fall into several hundred sets, each containing transcripts from a different repeat family.

Reassociation Kinetics and Cytophotometric Characterization of Peanut (Arachis hypogaea L.) DNA

The base composition of peanut (var. NC-17) DNA determined from thermal denaturation profiles showed an average guanine plus cystosine content of 34% which was in close approximation to 36% guanine plus cytosine calculated from the buoyant density. Buoyant density also indicated the absence of satellite DNA. The genome size, 2.0 x 10(9) base pairs, as determined by reassociation kinetics of the single copy DNA was close to the genome size determined by cytophotometry, 2.1 x 10(9) base pairs. Peanut DNA averaging 450 to 600 base pairs long, reassociated in phosphate buffer and fractionated by hydroxylapatite, indicated a DNA genome composition of 36% nonrepetitive or single copy DNA; reassociation in formamide and followed by optical methods indicated the repetitive DNA possesses highly repeated, intermediately repeated and rarely repeated components of DNA with DNA sequences repeated on the average about 38,000, 6,700, and 200 times each. Different criteria of reassociation in formamide revealed further subdivisions of these four separate components of DNA. The DNA of above mentioned NC-17 variety compared to Florigiant variety showed no differences in thermal denaturation profiles, buoyant density, or in genome size.

The sequence organization of bovine DNA

The organization of repetitive DNA sequences has been investigated in bovine DNA. Repetitive sequences of all kinds constitute 25% to 30% of the total. Five density satellites constitute about 20% of the genome, and most of the remainder consists of alternating repeating and nonrepeating sequences. The nonrepeating sequences have a very broad size distribution averaging 4,000 nucleotide paris in length with the longest exceeding 10,000 nucleotide pairs. The interspersed repetitive sequences are much more nearly homogeneous in size, averaging 350 nucleotide pairs in length, and are divided into 8 to 14 sequence families.

Evidence that populations of Dictyostelium single-copy mRNA transcripts carry common repeat sequences

Two recombinant plasmids, M4 and KH10, carrying Dictyostelium DNA inserted into the Eco RI restriction endonuclease site of pMB9 by poly(dA)-poly(dT) tailing, were selected for study because they are complementary to abundant mRNA populations from Dictyostelium. Both plasmids have been shown to hybridize a heterogeneous size class of mRNAs which, in the case of KH10, comprise 5-10% of the pulse-labeled poly(A)+ RNA from vegetative cells. Analysis of the sequence organization of the two pieces of Dictyostelium DNA shows that they consist mostly of single-copy sequences with a short DNA sequence which is repeated in the genome and interspersed with single-copy DNA. These and other results suggest that the majority of the hybridization of pulse-labeled mRNA to M4 and KH10 is to the short "repeated" DNA sequences. In the genome, members of these repeat families appear to be transcribed onto a population of different single-copy mRNAs. Additional results show that M4 DNA contains a sequence which is entirely complementary to a discrete mRNA.

Transcription of the Marek's disease virus genome in virus-induced tumors

Transcription of the Marek's disease virus (MDV) genome in tumor tissues from MDV-infected chickens has been studied by analyzing the hybridization kinetics of (3)H-labeled MDV DNA with unlabeled RNA extracted from these tissues. Lymphoid tumors of ovary, spleen, liver, and kidney contained MDV genomes, but the virus-specific RNA sequences were transcribed from less than 15% of the viral DNA. A virus nonproductive lymphoblastoid cell line, designated MKT-1, has been established from a kidney lymphoma and contains 15 MDV genomes per cell. In these cells, 12 to 14% of the viral DNA was transcribed. Thus transcription of the MDV genome was restricted both in tumor tissues and MKT-1 cells. A hybridization experiment where RNA extracted from MKT-1 cells and RNA extracted from a spleen tumor were mixed and hybridized to (3)H-labeled MDV DNA indicated that the virus-specific RNAs from the two sources were encoded by the same DNA sequences. The polyribosomal fractions of MKT-1 cells and this spleen tumor contained only a portion of the virus-specific RNA sequences found in whole-cell extracts, indicating the existence of a posttranscriptional control mechanism which prevents the transfer of certain viral RNA transcripts to the polyribosomes. The data suggest that the repressed expression of the viral genome in lymphoid tumor tissues and MKT-1 cells may be the result of precise controls within the cell at the transcriptional and posttranscriptional levels.

Herpes simplex virus type 1 Angelotti and a defective viral genotype: analysis of genome structures and genetic relatedness by DNA-DNA reassociation kinetics

DNA-DNA reassociation kinetics of herpes simplex virus type 1 Angelotti DNA and a class of defective viral DNA revealed that the viral standard genome has a total sequence complexity of about 93 X 10(6) daltons and that a portion of 11 X 10(6) daltons occurs twice on the viral genome. These results agree with structural features of herpes simplex virus type 1 DNA derived from electron microscopic studies and restriction enzyme analyses by several investigators. The defective viral DNA (molecular weight, about 97 X 10(6)) displays a sequence complexity of about 11 X 10(6) daltons, suggesting that the molecule is built up by repetitions of standard DNA sequences comprising about 15,000 base pairs. A 2 X 10(6)-dalton portion of these sequences maps in the redundant region and a 9 X 10(6)-dalton portion maps in the unique part of the standard herpes simplex virus type 1 Angelotti DNA, as could be shown by reassociation of viral standard DNA in the presence of defective DNA and vice versa. No cellular DNA sequences could be detected in defective DNA. A 12% molar fraction of the defective DNA consists of highly repetitive sequences of about 350 to 500 base pairs in length.

Studies on nucleic acid reassociation kinetics: V. Effects of disparity in tracer and driver fragment lengths

Measurements are described of the kinetics of nucleic acid strand pair reassociation where the complementary strands are of different lengths and are present in different concentrations. Rate constants for the reaction of labelled fragments ("tracer") with excess complementary strands ("driver") were determined, both for driver fragment length greater than tracer fragment length and for the reverse case. Second order reactions and pseudo-first order reactions utilizing strand separated drivers and tracers were studied. The nucleic acids which served for this investigation were phiX174 DNA and RNA, plasmid RSF2124 DNA and E. coli DNA. Approximate empirical expressions relating driver and tracer fragment lengths with the observed rate constants were obtained for practical use. In long tracer-short driver reactions the observed rate constant for the tracer reaction increases proportionately with tracer length. In long driver-short tracer reactions the rate of tracer reaction is retarded. The latter result is unexpected and appears to represent a departure from standard interpretations of the renaturation reaction.

A unified theory of nucleation-rate-limited DNA renaturation kinetics

DNA renaturations under nucleation-rate-limiting conditions on simple DNA such as bacterial and bacteriophage DNA show significant deviation from ideal second-order kinetics when followed by optical density measurements at 260 nm. Ideal second-order kinetics yield linear plots when the data is plotted in the standard reciprocal second-order (RSO) manner. The observed deviations from ideal second-order behavior take the form of steadily downward-curving RSO plots. In this paper, experiments are presented for E. coli and T2 DNA documenting this non-ideal behavior. Since experiments using T4, T5 and B, subtilis DNA yield identical non-ideal behavior, this behavior appears to be a property of DNA renaturation followed by optical density, not a peculiarity of a particular DNA. Identical non-ideal behavior is also seen in kinetics followed by S1 nuclease assay. A theory is developed to explain this deviation from ideal second-order kinetics. The theory also explains why kinetics followed by hydroxyapatite chromatography show nearly ideal second-order kinetics. In contrast to the approach taken by others in developing equations that describe S1 nuclease monitored reactions, our view is that nonideal second-order kinetics are fundamentally due to the reacton of free single strands to yield partially helical duplex species. Later reactions of these species tend to reduce the deviations from non-ideal second-order kinetics.

Chromosomal localization of human beta globin gene on human chromosome 11 in somatic cell hybrids

We have successfully used a DNA.cDNA molecular hybridization assay to directly determine the presence or absence of human beta globin gene sequences in 20 human-mouse somatic cell hybrids, each of which contained a different subset of human chromosomes. The assay is specific for the individual human globin genes and will detect the presence of a globin gene if the relevant chromosome is present in only 10% of the cells of a hybrid population. The content of human chromosomes in each hybrid clone was characterized by Giemsa 11 staining, Giemsa trypsin-Hoechst 33258 staining, and by the use of 22 independent isozyme markers for 17 different human chromosomes. All human chromosomes were present in one or more cell lines devoid of the human beta globin gene except for 6, 8, 9, 11, and 13. Among these latter chromosomes, only chromosome 11 was present in the six hybrid clones that contained the human beta globin gene. In fact, chromosome 11 was the only human chromosome that was present in all of the six hybrid clones found to be positive for the human beta globin gene. Two sister clones, 157-BNPT-1 and 157-BNPT-4, had similar subsets of human chromosomes except that 11 was present only in 157-BNPT-4. 157-BNPT-4 contained the human beta globin gene while 157-BNPT-1 did not. DNA from three hybrid lines was also annealed to purified human gamma globin cDNA; two lines positive for human beta globin gene sequences also contained human gamma globin gene sequences while one line was negative for both beta and gamma gene sequences. On the basis of these results, the human beta and gamma globin genes have been assigned to human chromosome 11.

Analysis of rat repetitive DNA sequences

Parameters of repetitive sequence organization have been measured in the rat genome. Experiments using melting, hydroxylapatite binding, and single strand specific nuclease digestion have been used to measure the number, length, and arrangement of repeated DNA sequences. Renaturation and melting or S1 nuclease digestion of 1.0 kbp DNA fragment show about 20% of rat DNA sequences are 3000-fold repeated. Renatured duplexes from 4.0 kbp DNA fragments display two repetitive size fractions after nuclease digestion. About 60% of the repeated sequences are 0.2-0.4 kbp long while the remainder are longer than 1.5 kbp. The arrangement of the repeated sequences has been measured by hydroxylapatite fractionation of DNA fragments of varying lengths bearing a repeated sequence. Repeated DNA sequences are interspersed among 2.5 kbp long nonrepeated sequences throughout more than 70% of the rat genome. There are approximately 350 different 3000-fold short repeated sequences in the rat interspersed among 600,000 nonrepeated DNA sequences.

Some aspects of the basic mechanisms of chemical carcinogenesis

An extended summary is presented of current progress in research on the basic mechanism of chemical carcinogenesis conducted in the Division of Biophysics, School of Hygiene and Public Health, at the Johns Hopkins University. The first section concerns the involvement of free radicals in benzo[a]pyrene metabolism and carcinogenesis, the second the relationship between neoplastic transformation and somatic mutation, and the third the changes in DNA sequence organization and gene expression in neoplastic transformation.

Studies on nucleic acid reassociation kinetics: retarded rate of hybridization of RNA with excess DNA

The rate of reaction of excess double-stranded bacteriophage phiX174 and plasmid RSF2124 DNA drivers with enzymatically synthesized asymmetric RNA tracers was measured. Other reactions were carried out with excess Escherichia coli DNA and E. coli RNA labeled in vivo. RNA and DNA fragment lengths were held approximately equal. For each case it was shown that in DNA excess the rate constant for RNA-DNA hybridization is 3- to 4.5-fold lower than that of the renaturation rate constant for the driver DNA. This retardation was also observed in pseudo-first-order hybridization reactions driven by excess strand-separated RSF2124 DNA. It was concluded that the rate constant for RNA-DNA by hybridization depends partially on which species is in excess.

A program for least squares analysis of reassociation and hybridization data

A computer program is described for the rapid calculation of least squares solutions for data fitted to different functions normally used in reassociation and hybridization kinetic measurements. The equations for the fraction not reacted as a function of Cot follow: First order, exp(-kCot); second order, (1+kCot)-1; variable order, (1+kCot)-n; approximate fraction of DNA sequence remaining single stranded, (1+kCot)-.44; and a function describing the pairing of tracer when the rate constant for the tracer (k) is distinct from the driver rate constant (kd): (formula: see text). Several components may be used for most of these functional forms. The standard deviations of the individual parameters at the solutions are calculated.

The problem of nuclease activity in nucleic acid hybridization reactions. Theoretical considerations

The presence of nuclease during DNA-DNA or DNA-RNA hybridization reactions alters the kinetics of hybrid formation. Unfortunately, while the effect (even of small amounts of nucleas) on the Cot curve may be large, it may not be readily detectable. The effect of various types of nuclease is shown. As many nucleases cause a shift in the position rather than a change in shape of the curve, all studies involving nucleic acid hybridization should assay for the presence of nucleases and care must be taken to avoid their presence as contaminants.

Studies on nucleic acid reassociation kinetics: rate of hybridization of excess RNA with DNA, compared to the rate of DNA renaturation

The rate of reaction of double-stranded replicative form (RF) [3H]DNA of bacteriophage phiX174 with excess (+)strand DNA and (+)strand RNA was measured by standard methods of hydroxyapatite chromatography. The reactions follow pseudo-first-order kinetics and the observed rate constant for the RNA-DNA reaction differs less than 25% from that of the DNA-DNA reaction. The pseudo-first-order rate constants are close to the value predicted on the basis of the second-order rate constant measured in the renaturation of the double-stranded phiX RF [3H]DNA.

Occurrence of BK virus DNA in DNA obtained from certain human tumors

DNA sequences from BK virus have been detected by measurements of reassociation kinetics in DNA preparations isolated from five of 12 human tumor tissues and three of four human tumor cell lines; no DNA sequences from BK virus could be found using the same assay in DNA samples obtained from nontumor tissues removed from various patients. Whether or not this association is trivial, indicative of infection by BK virus, or correlative with the tumor state must await the testing of additional samples of normal and tumor tissues as well as a definition of the physical state of the genome of BK virus.