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PubMed2006

Compositional and structural engineering of DNA multilayer films.

We report the layer-by-layer (LbL) preparation of multilayered thin films that consist solely of DNA. The properties of the films were varied by assembling the layers from different oligonucleotide building blocks, which are composed of repeating homopolymeric units of nucleotides [adenosine (A), cytosine (C), guanine (G), and thymidine (T)] or "random" sequences. Films assembled from oligonucleotides with a single complementary unit did not show continual layer buildup. To form a repeating multilayer system, it was necessary for single-stranded DNA to be available for subsequent layers to hybridize. By using oligonucleotides with multiple nucleotide units, multilayer films were successfully assembled. We demonstrate that the thickness and swellability of the films can be controlled by the extent of hydrogen bonding (the G/C content of the oligonucleotide) and orientation of the oligomers. We have examined the stability and swellability of the films in solutions of varying salt concentration as well as in a denaturing urea solution. Stable, hollow DNA capsules were also formed by preparing the films on sacrificial colloidal templates, followed by removal of the core. The assembly of propagating structures through DNA hybridization paves the way for the engineering of DNA films with tailored composition, structure, and permeability, making them likely to find application in drug/gene delivery and biomolecular sensing.

Base Composition↗
PubMed1995

Catalytic cleavage of an RNA target by 2-5A antisense and RNase L.

2-5A antisense (2-5A-AS) molecules are chimeric oligonucleotides that cause 2-5A-dependent RNase (RNase L) to catalyze the selective cleavage of RNA in human cells. These composite nucleic acids consist of a 5'-monophosphorylated, 2',5'-linked oligoadenylate known as 2-5A (an activator of RNase L) covalently attached to antisense 3',5'-oligodeoxyribonucleotides. Here, we characterize the targeted cleavage of the double-stranded RNA-dependent protein kinase (PKR) mRNA by purified, recombinant human RNase L. A 2-5A-AS chimera, which contains complementary sequence to PKR mRNA, and unmodified 2-5A, which causes general RNA decay, were about 20- and 40-fold more active, respectively, than 2-5A-AS chimeras in which the DNA domains are not complementary to sequences in PKR mRNA. Directed cleavage was efficient because each 2-5A-AS chimera targeted many RNA molecules. Moreover, RNase L caused the catalytic cleavage of the RNA target (kcat of approximately 7 s-1). The precise sites of PKR mRNA cleavage caused by 2-5A-AS were mapped, using a primer extension assay, to phosphodiester bonds adjacent to the 3' terminus of the chimera binding site (5' on the RNA target) as well as within the chimera's oligonucleotide binding site itself. The selectivity of this approach is shown to be provided by the antisense arm of the chimera, which places the RNA target in close proximity to the RNase.

Base Sequence↗
PubMed1992

Incorporation of hexose nucleoside analogues into oligonucleotides: synthesis, base-pairing properties and enzymatic stability.

Oligonucleotides containing 1-(2,4-dideoxy-beta-D-erythro-hexopyranosyl)thymine (2) and 1-(3,4-dideoxy-beta-D-erythro-hexopyranosyl)thymine (3) were synthesized on a solid support using the phosphoramidite approach. The properties of these oligonucleotides were compared with the earlier reported characteristics of oligonucleotides containing 1-(2,3-dideoxy-beta-D-erythro-hexopyranosyl) thymine (1). The order in enzymatic stability of end-substituted oligonucleotides is 3 greater than 1 much greater than 2. The hybridization properties of the modified oligonucleotides are in reverse order: 2 much greater than 1 greater than 3.

Alkaline Phosphatase↗
PubMed1978

Mapping of deoxydi- and trinucleotides liberated by the action of endonucleases from the silkworm and Aspergillis oryzae.

Both silkworm nuclease and nuclease O of Aspergillus oryzae mycelia hydrolyse DNA endolytically to di- and trinucleotides terminating in 5'-phosphate. These oligonucleotides were fractionated first be DEAE-cellulose chromatography with 7 M urea into the respective isoplithic groups and then analysed for the composition and isomerism: each group was labeled 5'-terminally by the [gamma-32P]ATP-polynucleotide kinase reaction and then electrophoresed monodimensionally for the dinucleotides and two-dimensionally for the di- and trinucleotides mixtures, respectively, followed by elution and digestion with snake venom exonuclease. Both nucleases gave rather similar simple maps in which all sixteen dinucleotides and almost all the possible trinucleotides were identified, indicating their random mode of actions.

Animals↗
PubMed2006

Probing the W chromosome of the codling moth, Cydia pomonella, with sequences from microdissected sex chromatin.

The W chromosome of the codling moth, Cydia pomonella, like that of most Lepidoptera species, is heterochromatic and forms a female-specific sex chromatin body in somatic cells. We collected chromatin samples by laser microdissection from euchromatin and W-chromatin bodies. DNA from the samples was amplified by degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) and used to prepare painting probes and start an analysis of the W-chromosome sequence composition. With fluorescence in situ hybridization (FISH), the euchromatin probe labelled all chromosomes, whereas the W-chromatin DNA proved to be a highly specific W-chromosome painting probe. For sequence analysis, DOP-PCR-generated DNA fragments were cloned, sequenced, and tested by Southern hybridization. We recovered single-copy and low-copy W-specific sequences, a sequence that was located only in the W and the Z chromosome, multi-copy sequences that were enriched in the W chromosome but occurred also elsewhere, and ubiquitous multi-copy sequences. Three of the multi-copy sequences were recognized as derived from hitherto unknown retrotransposons. The results show that our approach is feasible and that the W-chromosome composition of C. pomonella is not principally different from that of Bombyx mori or from that of Y chromosomes of several species with an XY sex-determining mechanism. The W chromosome has attracted repetitive sequences during evolution but also contains unique sequences.

Animals↗
PubMed2001

Detection of single base alterations in genomic DNA by solid phase polymerase chain reaction on oligonucleotide microarrays.

DNA microarray technology holds significant promise for human DNA diagnostics. A number of technical approaches directed at the parallel identification of mutations or single nucleotide polymorphisms make use of polymerase-based specificity, like minisequencing or allele-specific primer elongation. These techniques, however, require separate laborious sample amplification, preparation, and purification steps, making large-scale analyses time and cost consuming. Here, we address this challenge by applying an experimental setup using simultaneous solid and liquid phase PCR on polyethyleneimine-coated glass slides, a novel microarray support allowing on-chip amplification reactions with exquisite specificity. A gene-specific oligonucleotide tiling array contains covalently attached allele-specific primers which interrogate single nucleotide positions within a genomic region of interest. During a thermal cycling reaction amplification products remain covalently bound to the solid support and can be visualized and analyzed by the incorporation of fluorescent dyes. Using the described procedure we unequivocally defined the presence of point mutations in the human tumor suppressor gene p53 directly from a natural DNA source. This semi-multiplex solid phase amplification format allowed the rapid and correct identification of 20 nucleotide positions from minute amounts of human genomic DNA. Our results suggest that this approach might constitute a vital component of future integrated DNA chip devices used in gene analysis.

Base Composition↗
PubMed1999

Mechanistic studies on the base-catalyzed transformation of neocarzinostatin chromophore: roles of bulged DNA.

Nucleic acid bulges have been implicated in a number of biological processes and are specific cleavage targets for the enediyne antitumor antibiotic neocarzinostatin chromophore (NCS-chrom) in a base-catalyzed, radical-mediated reaction. Studies designed to elucidate the detailed mechanism of the base-catalyzed activation of NCS-chrom and to evaluate the roles of bulged DNA in its activation are described. They show that nucleobases in the DNA bulge are not required to form an effective bulge pocket but enhance the binding of the wedge-shaped activated drug molecule. Analysis of solvent deuterium isotope effects on NCS-chrom degradation and DNA cleavage efficiency experiments suggests that the spirolactone biradical 6 is a relatively stable species and that intramolecular quenching of the C2 radical of 6 to form the biologically active cyclospirolactone radical 7a occurs first (pathway a in Scheme 2), leaving the C6 radical to abstract the hydrogen atom from the DNA deoxyribose and to form the cyclospirolactone 8. Binding of the activated drug at the bulge site is required, but not sufficient, for efficient 8 formation, whereas cleavage of bulged DNA is not essential. Efficient generation of 8, but inefficient DNA damage generation, comes mainly from the likely high off-rate of 7a binding. The finding that thymidine 5'-carboxylic acid-ended oligonucleotide fragment can be formed in the reaction suggests that the process of DNA cleavage is rather slow and that sequential oxidations of the target 5'-carbon are possible. Study of the effect of solvent (methanol) concentration on NCS-chrom degradation indicates that bulged DNA acts to assist the intramolecular quenching of the radical at C2 by C8' ' of the naphthoate moiety by excluding solvent from the binding pocket, thus preventing the formation of spirolactones 9, and by blocking radical polymerization. Because in the absence or near absence of solvent methanol 8 formation does not reach even 10% that formed in the presence of bulged DNA, it is possible that the DNA bulge also induces a conformational change in the drug to promote the intramolecular reaction.

Base Composition↗
PubMed1990

Telomere G-strand structure and function analyzed by chemical protection, base analogue substitution, and utilization by telomerase in vitro.

Eukaryotic telomeres have a 12-16 nucleotide long deoxyguanosine (dG) rich single-stranded overhang at their molecular termini. Some of the unique features of telomeres are probably attributable to a specialized structure formed by this overhang. In the ciliated protozoan Tetrahymena thermophila, the dG-rich overhang is comprised of approximately two repeats of the sequence d(TTGGGG). Previous work has shown that the synthetic oligonucleotide d(TTGGGG)4 can form an unusual non-Watson-Crick base-paired structure (the "G-strand structure") containing G-G base pairs and syn-guanines. We have tested the susceptibility of various dGs in this structure to methylation by DMS. At 0-10 degrees C one dG residue is hypersensitive to methylation while others are particularly resistant. By systematically substituting deoxyinosine (dI) for dG in d(TTGGGG)4 we identify N2 groups of guanine essential for formation of the G-strand structure. We show that dI-substituted molecules that cannot form the G-strand structure nonetheless function as substrates for telomere repeat addition in vitro by the telomere lengthening enzyme, telomerase. The implications of these data are discussed.

Animals↗
PubMed1990

Oligonucleotide correlations between infector and host genomes hint at evolutionary relationships.

The frequencies of oligonucleotides of length 3-6 were studied in 211 sequences of human DNA (659 kilobases), 22 sequences of DNA of human viruses (120 kbs), in 181 sequences of E. coli (442 kbs), and in 42 sequences of phages of E. coli (137 kbs). The sequences were obtained from Genbank(R) 48. The observed frequencies (O) were compared to the expected frequencies (E) obtained in two ways: 1) according to nucleotide composition for each series, and 2) according to first order Markow chains for triplets, second order for quadruplets, and third order for quintuplets and sextuplets. The ratio O/E was obtained for each oligonucleotide. Then, the correlation between the ratio O/E in a pair of series was calculated. Strong correlations were observed for sequences of man and human viruses, and for E. coli and its phages. Other correlations were small. For higher order Markov chains, there is indication of some correlation also between viruses and phages. It was concluded that through analysis of parallel oligonucleotide series it may be possible to infer some of the complex evolutionary relationships existing between cells and their infectors beyond the level of codon usage.

Base Composition↗
PubMed2000

Analysis of fas ligand gene mutation in patients with systemic lupus erythematosus.

OBJECTIVE: To investigate the possible association of a Fas ligand (FasL) gene mutation(s) or polymorphism(s) with systemic lupus erythematosus (SLE). METHODS: For amplification of the introns of the FasL gene, long polymerase chain reaction (PCR) using exon-based primers was utilized, followed by partial sequencing to construct exon-specific oligonucleotide primers for the analyses of FasL genomic DNA in SLE patients. Structural defects were studied by use of a composite analysis of reverse transcriptase-PCR/single-strand conformational polymorphism (SSCP) analysis of messenger RNA (mRNA) transcripts of the FasL gene in 35 SLE patients and PCR/SSCP analysis of FasL genomic DNA in 143 SLE patients. RESULTS: The sizes of the introns were approximately 0.6 kb for intron 1, 4.3 kb for intron 2, and 1.3 kb for intron 3. By SSCP analysis, we did not identify any mutations or polymorphisms in the FasL mRNA transcripts or in any of the 4 exons or areas of the introns adjacent to the exons. CONCLUSION: Using the same methods used in the present studies (PCR/SSCP), one group of investigators identified a structural defect of the FasL molecule in 1 of 75 SLE patients evaluated. Among the 143 SLE patients in the present study, however, we did not identify any mutations or polymorphisms of the FasL gene. Our results suggest that a FasL defect is not the major contributing factor in the pathogenesis of SLE.

DNA Mutational Analysis↗
PubMed2006

Ethanol is a better inducer of DNA guanine tetraplexes than potassium cations.

Guanine tetraplexes are a biologically relevant alternative of the Watson and Crick duplex of DNA. It is thought that potassium or other cations present in the cavity between consecutive guanine tetrads are an integral part of the tetraplexes. Here we show using CD spectroscopy that ethanol induces the guanine tetraplexes like or even better than potassium cations. We present examples of ethanol stabilizing guanine tetraplexes even in cases when potassium cations fail to do so. Hence, besides the A-form or Z-form, ethanol stabilizes another conformation of DNA, i.e., the guanine tetraplexes. We discuss the mechanism of the stabilization. Use of ethanol will permit studies of guanine tetraplexes that cannot be induced by potassium cations or other tetraplex-promoting agents. This work demonstrates that a still broader spectrum of nucleotide sequences can fold into guanine tetraplexes than has previously been thought. Aqueous ethanol may better simulate conditions existing in vivo than the aqueous solutions.

Base Composition↗
PubMed1996

Capture in the gel: intermoleculare triplex formation during gel electrophoresis.

Analysis of unusual gel mobility patterns formed by certain DNA triplexes has revealed that intermolecular triplex formation can occur during gel electrophoresis when a faster migrating single strand overtakes a slower migrating band containing a duplex of appropriate sequence. Control experiments showed that this capture of the third strand occurs by sequence-specific hybridization rather than some nonspecific retardation. This phenomenon can be used to detect triplexes by a gel-shift assay even if their lifetime is much shorter than the time of gel electrophoresis.

Base Composition↗
PubMed1989

Modern coding sequences are in the periodic-to-chaotic transition.

Modern coding sequences are in the periodic-to-chaotic transition. In the case of alpha A-crystallin coding sequence of the chicken, the initial tetrameric periodicity of the primordial tetramer C C T G has been decaying by the golden mean: the 4, 7, 11 rule. Thus, the tetramer has become parts of recurring heptamers, and some heptamers have become parts of the 11-base-long repeating units.

Amino Acid Sequence↗
PubMed2004

The development of a DNA microarray-based assay for the characterization of commercially formulated microbial products.

Commercially formulated bioproducts containing a complex consortia of bacteria as an active ingredient pose a significant challenge for regulatory agencies and companies seeking to assess the safety and efficacy of these bioproducts. The main challenge stems from how to characterize the bacterial composition of these products, for which there is presently a lack of suitable methods. A prototype DNA microarray composed of oligonucleotide probes for functional genes, virulence factors, and taxonomic genes for a number of bacterial species was developed to examine the utility of microarray technology as a molecular tool for characterizing consortia bioproducts. The genomic DNA from four different products was extracted by two methods and examined with the microarray prototype and by denaturing gradient gel electrophoresis (DGGE). Although the identity of the consortial species remains unknown, the microarray assay provided unique and reproducible hybridization patterns for all four products, and agreed with the fingerprints generated by DGGE. The ability to differentiate between a variety of consortia products demonstrates that DNA microarrays have the potential to be a powerful tool in monitoring complex microbial communities.

Bacteriological Techniques↗
PubMed2004

8-Oxoguanine induces intramolecular DNA damage but free 8-oxoguanine protects intermolecular DNA from oxidative stress.

7,8-Dihydro-8-oxoguanine (8-oxoguanine; 8-oxo-G), one of the major oxidative DNA adducts, is highly susceptible to further oxidation by radicals. We confirmed the higher reactivity of 8-oxo-G toward reactive oxygen (singlet oxygen and hydroxyl radical) or nitrogen (peroxynitrite) species as compared to unmodified base. In this study, we raised the question about the effect of this high reactivity toward radicals on intramolecular and intermolecular DNA damage. We found that the amount of intact nucleoside in oligodeoxynucleotide containing 8-oxo-G decreased more by various radicals at higher levels of 8-oxo-G incorporation, and that the oligodeoxynucleotide damage and plasmid cleavage by hydroxyl radical were inhibited in the presence of 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxo-dG). We conclude that 8-oxo-G within DNA induces intramolecular DNA base damage, but that free 8-oxo-G protects intermolecular DNA from oxidative stress. These results suggest that 8-oxo-G within DNA must be rapidly released to protect DNA from overall oxidative damage.

Base Composition↗
PubMed1998

Effect of base composition on DNA bending by phosphate neutralization.

Of the many forces involved in DNA bending by proteins, we have focused on the possible role of asymmetric phosphate neutralization due to interactions between the negatively charged phosphate backbone of duplex DNA and cationic amino acids of an approaching protein. The resulting unbalanced charge distribution along the duplex DNA is thought to induce the double helix to collapse toward the neutralized surface. Previous work has confirmed that DNA bending (approximately 20.7 +/- 4 degrees) is induced by asymmetric incorporation of six uncharged racemic methylphosphonate analogs partially neutralizing one face of GC-rich duplex DNA. We have now analyzed DNA duplexes with similar patches of methylphosphonate linkages in an AT-rich sequence context and again observe bending toward the neutralized face, to an extent (20 +/- 0.6 degrees) comparable to that observed for neutral patches in GC-rich DNA. The similar induced bend angles in AT-rich and GC-rich contexts does not reveal increased flexibility in AT-rich sequences, or a particular propensity of A-T base pairs to roll toward the minor groove in the tested sequences.

Base Composition↗
PubMed1995

Incorporation of 2'-deoxy-6-thioguanosine into G-rich oligodeoxyribonucleotides inhibits G-tetrad formation and facilitates triplex formation.

An efficient and expeditious method for the synthesis of S6-(cyanoethyl)-N2-isobutyryl (or trifluoroacetyl)-2'-deoxy-6-thioguanosine (7 and 2) from 2'-deoxyguanosine (G) has been developed. Compound 7 has been incorporated into several G-rich triple-helix-forming oligonucleotides (TFOs) using solid-support, phosphoramidite chemistry. The purified oligonucleotides containing 2'-deoxy-6-thioguanosine (S6-dG) residues in the place of G have been characterized by nucleoside composition analysis. These modified TFOs have been shown to be stable in aqueous, as well as buffered, solutions normally used to assay triple-helix formation. It has also been demonstrated that partial incorporation of S6-dG is effective in inhibiting the formation of G tetrads in G-rich oligodeoxyribonucleotides, thus facilitating triple-helix formation in potassium-containing buffers.

Base Sequence↗