Analysis Of DNA Structure Research Articles

Analysis of DNA structure as a 2D random walk by complex wavelet transform

Analysis of DNA structure as a 2D random walk by complex wavelet transform

Analysis of DNA structure as a 2D random walk by complex wavelet transform

AbstractWe propose the original method of the time-scale wavelet analysis of DNA sequence represented as a 2D walk on a complex plane. Namely, we consider the mapping of two irreducible A − T and G − C sequences into a walk trajectory in the plane AGTC (firstly proposed by M. Gates) as a unique complex-valued function. This function is processed with the new algorithm of the continuous wavelet transform with the Morlet wavelet. This method is based on the representation of the transform’s result as a solution of the specific Cauchy problem for the system of PDE. As an example, we applied the described algorithm to a part of the telomer region of the 22 human chromosome and demonstated the high exactness. Moreover, it is very fast and it provides wide opportunities for the analysis of large genome data samples.

P.266 Analysis of DNA structure in odontogenic keratocysts with morphometric methods

P.266 Analysis of DNA structure in odontogenic keratocysts with morphometric methods

An algorithmic analysis of DNA structure

Bilinearity, complementarity and antiparallelism of the double stranded DNA structure are proved, in a general and abstract setting, as requirements of an efficient duplication algorithm for ‘mobile strings’.

The place of capillary electrophoresis techniques in screening for haemoglobinopathies

Capillary zone electrophoresis (CZE) methods are new laboratory diagnostic tools. The screening of haemoglobin (Hb) variants by a battery of two automated CZE methods at alkaline and acid pH, followed by micellar electrokinetic capillary chromatography (MECC), has been evaluated. Three hundred and ninety-two patients' samples with an abnormal haemoglobin fraction, detected either by isoeletric focusing (IEF) or by automated cation-exchange exchange high-performance liquid chromatography (automated HPLC), were tested by both CZE methods. Their performances were compared with IEF and automated HPLC techniques. The place of MECC has been evaluated. Using both CZE methods, the clinically relevant variants (HbS, HbC, etc.) as well as 15 of 20 clinically silent variants tested were separated from HbA. Using the alkaline CZE method, a presumptive identification of Hb Bart's, HbH and Hb Constant Spring was obtained. Complementary testing by MECC has demonstrated it to be an aid in distinguishing the globin chain mutations before confirmation by DNA or protein structure analysis. Using only one device, alkaline CZE, acid CZE and MECC methods offer high resolution, automated sampling and rapid analysis. They are good tools for screening of haemoglobinopathies and can replace conventional techniques.

Chemical probing and electron microscopic analysis of alternative DNA structure formed in an inverted repeat sequence.

Chemical probing and electron microscopic analysis of alternative DNA structure formed in an inverted repeat sequence Shingo Hokabe, Theodor D. Gurkov, Hiroshi Okawara, Kuniaki Nagayama, Shinsei Minoshima, Nobuyoshi Shimizu and Mikio Kato department of Life Sciences, Osaka Prefecture University, College of Integrated Arts and Sciences, Sakai 599-8531, Japan, Center for Integrative Bioscience, Okazaki National Research Institutes, Okazaki 444-8585, Japan and department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan

Transcription initiation in vivo without classical transactivators: DNA kinks flanking the core promoter of the housekeeping yeast adenylate kinase gene, AKY2, position nucleosomes and constitutively activate transcription.

The housekeeping gene of the major adenylate kinase in Saccharomyces cerevisiae (AKY2, ADK1) is constitutively transcribed at a moderate level. The promoter has been dissected in order to define elements that effect constitutive transcription. Initiation of mRNA synthesis at the AKY2 promoter is shown to be mediated by a non-canonic core promoter, (TA)(6). Nucleotide sequences 5' of this element only marginally affect transcription suggesting that promoter activation can dispense with transactivators and essentially involves basal transcription. We show that the core promoter of AKY2 is constitutively kept free of nucleosomes. Analyses of permutated AKY2 promoter DNA revealed the presence of bent DNA. DNA structure analysis by computer and by mutation identified two kinks flanking an interstitial stretch of 65 bp of moderately bent core promoter DNA. Kinked DNA is likely incompatible with packaging into nucleosomes and responsible for positioning nucleosomes at the flanks allowing unimpeded access of the basal transcription machinery to the core promoter. The data show that in yeast, constitutive gene expression can dispense with classical transcriptional activator proteins, if two prerequisites are met: (i) the core promoter is kept free of nucleosomes; this can be due to structural properties of the DNA as an alternative to chromatin remodeling factors; and (ii) the core promoter is pre-bent to allow a high rate of basal transcription initiation.

Distribution patterns of over-represented k-mers in non-coding yeast DNA.

Over-represented k-mers in genomic DNA regions are often of particular biological interest. For example, over-represented k-mers in co-regulated families of genes are associated with the DNA binding sites of transcription factors. To measure over-representation, we introduce a statistical background model based on single-mismatches, and apply it to the pooled 500 bp ORF Upstream Regions (USRs) of yeast. More importantly, we investigate the context and spatial distribution of over-represented k-mers in yeast USRs. Single and double-stranded spatial distributions of most over-represented k-mers are highly non-random, and predominantly cluster into a small number of classes that are robust with respect to over-representation measures. Specifically, we show that the three most common distribution patterns can be related to DNA structure, function, and evolution and correspond to: (a) homologous ORF clusters associated with sharply localized distributions; (b) regulatory elements associated with a symmetric broad hill-shaped distribution in the 50-200 bp USR; and (c) runs of As, Ts, and ATs associated with a broad hill-shaped distribution also in the 50-200 bp USR, with extreme structural properties. Analysis of over-representation, homology, localization, and DNA structure are essential components of a general data-mining approach to finding biologically important k-mers in raw genomic DNA and understanding the 'lexicon' of regulatory regions.

Secondary DNA structure analysis of the coding strand switch regions of five Leishmania major Friedlin chromosomes.

As part of the EULEISH international genome project, a region of 74,674 nucleotides from chromosome 21 of Leishmania major Friedlin was subcloned and sequenced; and 31 new coding sequences were predicted. Of particular interest was a unique coding strand switching region covering 1.6 kb of DNA; and this was subjected to further investigation. Bioinformatic analysis of this region revealed an unusually high AT composition, a lack of putative hairpins and a strong curvature of the DNA in agreement with the structural characteristics of similar regions of other Leishmania chromosomes. These observations and a comparison with the secondary DNA structure of four other Leishmania chromosomes and chromosomes of different organisms could suggest a functional role of this region in transcription and mitotic division.

Conformations of nucleoside analogue 1-(2'-deoxy-beta-D-ribofuranosyl)-1,2,4-triazole-3-carboxamide in different DNA sequence contexts.

The concept of using a dynamic base-pairing nucleobase as a mode for degenerate recognition presents a unique challenge to analysis of DNA structure. Proton and phosphorus NMR studies are reported for two nine-residue DNA oligodeoxyribonucleotides, d(CATGGGTAC).d(GTACNCATG) (1) and d(CATGTGTAC).(GTACNCATG) (2), which contained 1-(2'-deoxy-beta-D-ribofuranosyl)-1,2,4-triazole-3-carboxamide (N) in the center of the helix at position 14. The duplexes were compared to the canonical Watson-Crick duplexes, d(CATGGGTAC).d(GTACCCATG) (3) and d(CATGTGTAC).d(GTACACATG) (4). Two-dimensional NOESY spectra of 1-4 in H(2)O and D(2)O solutions collected at 5 degrees C allowed assignment of the exchangeable and nonexchangeable protons for all four oligodeoxyribonucleotides. Thermodynamic and circular dichroism data indicated that 1-4 formed stable, B-form duplexes at 5 degrees C. Two-dimensional (1)H-(31)P correlation spectra indicated that there were minor perturbations in the backbone only near the site of the triazole base. Strong NOESY cross-peaks were observed between the H5 and H1' of N14 in 1 and, unexpectedly, 2, which indicated that, in both duplexes, N14 was in the syn(chi)() conformation about the glycosidic bond. NOESY spectra of 1 and 2 recorded in 95% H(2)O, 5% D(2)O indicated that the imino proton of the base opposite N14, G5, or T5, formed a weak hydrogen bond with N14. These conformations place the polar carboxamide functional group in the major groove with motional averaging on the intermediate time scale.

Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths.

DNA structure plays an important role in a variety of biological processes. Different di- and tri-nucleotide scales have been proposed to capture various aspects of DNA structure including base stacking energy, propeller twist angle, protein deformability, bendability, and position preference. Yet, a general framework for the computational analysis and prediction of DNA structure is still lacking. Such a framework should in particular address the following issues: (1) construction of sequences with extremal properties; (2) quantitative evaluation of sequences with respect to a given genomic background; (3) automatic extraction of extremal sequences and profiles from genomic databases; (4) distribution and asymptotic behavior as the length N of the sequences increases; and (5) complete analysis of correlations between scales. We develop a general framework for sequence analysis based on additive scales, structural or other, that addresses all these issues. We show how to construct extremal sequences and calibrate scores for automatic genomic and database extraction. We show that distributions rapidly converge to normality as Nincreases. Pairwise correlations between scales depend both on background distribution and sequence length and rapidly converge to an analytically predictable asymptotic value. For di- and tri-nucleotide scales, normal behavior and asymptotic correlation values are attained over a characteristic window length of about 10-15 bp. With a uniform background distribution, pairwise correlations between empirically-derived scales remain relatively small and roughly constant at all lengths, except for propeller twist and protein deformability which are positively correlated. There is a positive (resp. negative) correlation between dinucleotide base stacking (resp. propeller twist and protein deformability) and AT-content that increases in magnitude with length. The framework is applied to the analysis of various DNA tandem repeats. We derive exact expressions for counting the number of repeat unit classes at all lengths. Tandem repeats are likely to result from a variety of different mechanisms, a fraction of which is likely to depend on profiles characterized by extreme structural features.

Molecular Dynamics Simulations of the d(CCAACGTTGG) 2 Decamer: Influence of the Crystal Environment

Molecular dynamics (MD) simulations of the DNA duplex d(CCAACGTTGG) 2 were used to study the relationship between DNA sequence and structure. Two crystal simulations were carried out; one consisted of one unit cell containing two duplexes, and the other of two unit cells containing four duplexes. Two solution simulations were also carried out, one starting from canonical B-DNA and the other starting from the crystal structure. For many helicoidal parameters, the results from the crystal and solution simulations were essentially identical. However, for other parameters, in particular, α, γ, δ, (ϵ − ζ), phase, and helical twist, differences between crystal and solution simulations were apparent. Notably, during crystal simulations, values of helical twist remained comparable to those in the crystal structure, to include the sequence-dependent differences among base steps, in which values ranged from 20° to 50° per base step. However, in the solution simulations, not only did the average values of helical twist decrease to ∼30° per base step, but every base step was ∼30°, suggesting that the sequence-dependent information may be lost. This study reveals that MD simulations of the crystal environment complement solution simulations in validating the applicability of MD to the analysis of DNA structure.

Cloning and identification ofPHF2 cDNA and its alternatively spliced transcripts

Genes encoding proteins with PHD (plant homeodomain) finger motif (C4HC3) are highly conserved fromArabidopis toHomo sapiens. One of the major functions of these genes is regulating the expression of homeotic genes during the stage of embryonic development. They play a role in cell-cycle and cell differentiation and seem to be related with some human malignant diseases, such as leukemia. A human placenta cDNA library has been screened with cDNA probe amplified by PCR. The PCR primers have been designed according to theM96 (a mouse gene encoding a protein with PHD domain) homologous data in dbEST. A 2.1 kb insert fragment in a positive cDNA clone has been isolated and sequenced. This new full-length cDNA is namedPHF2 (GenBank Acc: AF052205). The putative protein composed of 567 aa has two typical PHD fingers at its N-terminus. Meanwhile it is identified that there are several alternatively spliced transcripts ofPHF2 in different human tissues through the PCR amplification, Northern blot hybridization and analysis of genomic DNA structure.

The effect of DNA phase structure on DNA walks

We have performed several kinds of DNA walks which often are the first steps for further analysis of DNA structure and long range correlations. The DNA walks analysing frequency of G+C versus A+T cannot indicate the coding strand while purine versus pyrimidine DNA walks or two-dimensional (A-T,G-C) DNA walks in some instances can indicate the coding strand but cannot resolve the coding frame. The modified two-dimensional (A-T,G-C) DNA walks respecting the three-nucleotide codon structure show very high correlation in nucleotide composition of DNA coding sequences. They can distinguish between coding and non-coding sequences and indicate the strand and the phase in which DNA is coding.

Switching of DNA Secondary Structure in Proenkephalin Transcriptional Regulation

Proper transcriptional regulation of the proenkephalin gene requires a switch between distinct factor binding sites that cannot exist at the same time. Each of the sites is formed from a nearly palindromic region that contains two functionally defined cAMP response elements. The region can switch between cruciform and linear duplex. Formation of the cruciform creates an alternative binding site for mediators of second messenger-directed transcription and abolishes the site present in the native duplex form. Use of the cruciform site has been shown to correlate with activated transcription. Analysis of DNA structure, protein binding, and gene expression from plasmids with mutant enhancers shows, however, that both sites are required for regulation of transcription. The two distinct structures form within the same enhancer. Shifting the balance between the two alters transcriptional response.

Identification and characterization of a predominant isoform of human MKK3

We have obtained a novel cDNA species of MKK3, termed MKK3b. MKK3b cDNA differs from its original form, MKK3, at the 5′-end, encoding 29 extra amino acids in the N-terminus. Analysis of MKK3 genomic DNA structure revealed that the MKK3b-unique 5′-end sequence is derived from an exon different from that of MKK3, and that they share identical sequences thereafter. This suggests that the two cDNA forms of MKK3 are either generated by differential splicing of the same gene or derived from differential promoter utilization. Northern blotting analysis showed that MKK3b mRNA is much more abundant than MKK3. Functional characterization based on the activation of p38 revealed that MKK3b is more efficient than MKK3 in mediating downstream signalling events. © 1997 Federation of European Biochemical Societies.

P-B1-01 A theoretical analysis of looped-out DNA structure during replication: Majumdar R 1, Thakur AR 2 1Biophysics Division, Saha Institute of Nuclear Physics, Calcutta (India), 2Dept of Biophysics, University of Calcutta (India)

P-B1-01 A theoretical analysis of looped-out DNA structure during replication: Majumdar R 1, Thakur AR 2 1Biophysics Division, Saha Institute of Nuclear Physics, Calcutta (India), 2Dept of Biophysics, University of Calcutta (India)

Visualization of site-specific recombination catalyzed by a recombinase from Zygosaccharomyces rouxii in Arabidopsis thaliana.

Excision of a DNA segment can occur in Arabidopsis thaliana by reciprocal recombination between two specific recombination sites (RSs) when the recombinase gene (R) from Zygosaccharomyces rouxii is expressed in the plant. To monitor recombination events, we generated several lines of transgenic Arabidopsis plants that carried a cryptic beta-glucuronidase (GUS) reporter gene which was designed in such a way that expression of the reporter gene could be induced by R gene-mediated recombination. We also made several transgenic lines with an R gene linked to the 35S promoter of cauliflower mosaic virus. Each transgenic line carrying the cryptic reporter gene was crossed with each line carrying the R gene. Activity of GUS in F1 and F2 progeny was examined histochemically and recombination between two RSs was analyzed by Southern blotting and the polymerase chain reaction. In seedlings and plantlets of F1 progeny and most of the F2 progeny, a variety of patterns of activity of GUS, including sectorial chimerism in leaves, was observed. A small percentage of F2 individuals exhibited GUS activity in the entire plant. This pattern of expression was ascribed to germinal recombination in the F1 generation on the basis of an analysis of DNA structure by Southern blotting. These results indicate that R gene-mediated recombination can be induced in both somatic and germ cells of A. thaliana by cross-pollination of parental transgenic lines.

The role of a pentanucleotide repeat sequence, AGGGAAGGGA, in the regulation of JC virus DNA replication.

The human polyomavirus JCV differs from other papovaviruses in its narrow host range and tissue tropism for human glial cells. It is believed that the cell-specific tropism of JCV to glial cells rests, at least in part, in transcription of the viral early gene that encodes the large tumor antigen (T-antigen). The secondary stage, however, which restricts the replication cycle of JCV to primate cells, is controlled at the level of viral DNA replication. In this study, we demonstrate that a cis-acting transcription regulatory element encompassing the pentanucleotide repeat sequence AGGGAAGGGA (penta), which is located in close proximity to the origin of DNA replication, plays an important role in the replication of viral DNA mediated by the JCV T-antigen, but not T-antigen derived from SV40. Analysis of DNA structure by diethyl pyrocarbonate (DEPC) has revealed that mutations within the penta which affect DNA replication also alter the structure of the neighboring A+T-rich region. These results suggest that, in addition to the regulatory role in viral gene expression, the penta may function as a DNA structural element which is important for JCV DNA replication mediated by the JCV T-antigen.

Sequence dependent intrinsic deformability of the DNA base amino groups. An ab initio quantum chemical analysis

An accurate description of the interactions between DNA bases is of fundamental importance in the theoretical analysis of DNA structure, flexibility and dynamics. These base-base interactions are significantly influenced by the properties of the DNA base amino groups. In the present paper we show that, in constrast to the empirical force fields, ab initio calculations predict non-planar geometries for the DNA base amino groups. We compare the amino group non-planarity of cytosine, adenine, guanine, the guanine amino tautomer, 2-aminoadenine, 5-methylcytosine and the guanine formamidine hydrogen bonded complex, at the HF/6–31G(NH 2 ∗) level of theory. In addition, the geometry of cytosine is optimized at the MP2/6–31G ∗, MP2/6–31G(NH ∗ 2), HF/6–31G ∗, HF/4–21G(NH ∗ 2) and HF/6–31G levels of theory to estimate the role of electron correlation and polarization functions in the amino group geometry. It is shown that the gradient geometry optimization with inclusion of electron correlation significantly increases the non-planarity of the cytosine amino group compared to the HF level of calculations. The influence of non-planar DNA base amino groups on the conformational variability of DNA is briefly discussed.