Occurrence of DNA sequences specifically recognized by drugs in human promoters

Several DNA-binding drugs are being developed to create tailored molecules which can discriminate among the different sequences of the whole genome. By discriminating among specific sites in DNA, these molecules may provide optimal drug therapy. The complete sequencing of the human genome offers a wealth of DNA targets to be analyzed as potential drug-binding sites. To increase our understanding of DNA-drug interactions and their selectivity, we have studied the relative and absolute occurrence of CG-rich sequences, of various lengths, in human gene promoters. In several promoters, including those of oncogenes, cell cycle regulation factors, tumor suppressors and housekeeping genes, the presence of potential binding sites containing CpG steps (in which many drugs are known to intercalate) is variable, but in many cases these sites are not randomly distributed. Sequences 6-7 base pairs in length, like CGCCCG or CGCCCCG, occur only once in some promoters, thus they may be potentially specific therapeutic targets.     

Ancient flowering plants: DNA sequences and angiosperm classification

Phylogenetic analyses of gene sequences provide a clear pattern of which extant flowering plant genera diversified earliest. Combined with complete genomic sequences, these data will vastly improve understanding of the genetic basis of plant diversity.     

Vector space classification of DNA sequences

Revisiting the problem of intron-exon identification, we use a principal component analysis (PCA) to classify DNA sequences and present first results that validate our approach. Sequences are translated into document vectors that represent their word content; a principal component analysis then defines Gaussian-distributed sequence classes. The classification uses word content and variation of word usage to distinguish sequences. We test our approach with several data sets of genomic DNA and are able to classify introns and exons with an accuracy of up to 96%. We compare the method with the best traditional coding measure, the non-overlapping hexamer frequency count, and find that the PCA method produces better results. We also investigate the degree of cross-validation between different data sets of introns and exons and find evidence that the quality of a data set can be detected.     

How different DNA sequences are recognized by a DNA-binding protein: effects of partial proteolysis.

MDBP is a sequence-specific DNA-binding protein from mammals that recognizes a variety of DNA sequences, all of which show much homology to a partially palindromic 14 base-pair consensus sequence. MDBP subjected to limited proteolysis and then incubated with various specific oligonucleotide duplexes yielded two types of complexes. The relative concentrations of these complexes varied greatly depending on how closely the MDBP site matched the consensus sequence. No such DNA sequence-specific differences in the types of complexes formed were seen with intact MDBP. Partial proteolysis also changed the relative affinity of MDBP for several of its binding sites. The nature of the two types of complexes formed from fragmented MDBP and DNA was studied by DNA competition assays, protein titration, site-directed mutagenesis, and dimethyl sulfate and missing base interference assays. The results suggest that, for some specific DNA sequences, half-site interactions with one MDBP subunit predominate and for others, strong interaction of two subunits with both half-sites readily occur.     

Graphical classification of DNA sequences of HLA alleles by deep learning

Alleles of human leukocyte antigen (HLA)-A DNAs are classified and expressed graphically by using artificial intelligence “Deep Learning (Stacked autoencoder)”. Nucleotide sequence data corresponding to the length of 822 bp, collected from the Immuno Polymorphism Database, were compressed to 2-dimensional representation and were plotted. Profiles of the two-dimensional plots indicate that the alleles can be classified as clusters are formed. The two-dimensional plot of HLA-A DNAs gives a clear outlook for characterizing the various alleles.     

Cleavage of DNA adsorbed on the surface of phospholipid membranes by restrictases type II

Cleavage of phage lambda DNA by restriction endonucleases in the presence of model phosphatidylcholine membranes was studied. Bsp1, Pst1 and Bam H1 were found to cleave DNA under these conditions to a considerably decreased extent. This effect does not result from irreversible inactivation of the enzymes or their direct interaction with the membranes. The most probable explanation of the membrane inhibitory effect is the change of DNA substrate properties resulting from its Mg2+-mediated binding to the membranes.     

Periodic organisation of foldback sequences in Physarum polycephalum nuclear DNA.

Nuclear DNA from the slime mould Physarum polycephalum is shown to contain interspersed inverted repeat sequences, such that denatured fragments of DNA containing pairs of these sequences form intra-chain duplexes under appropriate conditions. The organisation and distribution of the nucleotide sequences responsible for the formation of foldback structures in Physarum DNA have been investigated using the electron microscope. The majority of foldback duplexes have sizes ranging up to 800 base pairs, and about 60-80% of DNA molecules 2.2 X 10(4) bases in length contain interspersed foldback elements. The size of individual foldback duplexes, and also the length of the intervening sequences which separate them, are non-random. The results can best be explained by a model in which separate foldback foci in Physarum DNA are spaced periodically at regular intervals. The regions containing foldback foci are thought to contain smaller, tandemly-arranged sequences of discrete sizes, in some cases related to other nucleotide sequences of a similar nature in the same locality in Physarum DNA.     

家牦牛线粒体DNA(mtDNA)遗传多样性及其分类

通过分析包括我国10个家牦牛品种(类群)在内共296个样本的mtDNA控制(D-loop)区部分序列的遗传变异,对我国家牦牛的遗传多样性、遗传分化、聚类关系和分类进行了研究.所测序列经比对后,共检测到61个变异位点,定义了77种单倍型.分析显示青海环湖牦牛的单倍型多样性最高,达0.9848±0.0403,而巴州牦牛单倍型多样性最低,为0.8000±0.0825;核苷酸多样性方面,斯布牦牛存在最为丰富的核苷酸序列变异,核苷酸多样性值为0.022582±0.011767,而巴州牦牛仅为0.006856±0.002476,表明我国家牦牛品种(类群)遗传多样性水平存在较大差异.总体上,我国家牦牛单倍型多样性、核苷酸多样性分别为0.9251±0.0095和0.015265±0.007757,呈现出丰富的遗传多样性.聚类分析显示我国家牦牛存在两个聚类簇--斯布牦牛独立为一类;其余9个品种(类群)聚为一类,表明家牦牛品种(类群)间遗传距离与地理分布无明显相关.分子变异分析(AMOVA)显示九龙、嘉黎、斯布牦牛构成的组与其余7个家牦牛品种(类群)构成的组之间存在极显著的遗传分化(?CT=0.05285,P<0.01),且其品种间/组内遗传分化不显著(?SC=0.00648,P>0.05),支持依据遗传分化程度将我国家牦牛划分为两大类型.AMOVA支持的分组在品种(类群)组成上与蔡立的研究结果相符,首次为我国家牦牛划分为横断高山型和青藏高原型两种类型提供了源自分子遗传学的证据.     

A two-stage evolutionary approach for effective classification of hypersensitive DNA sequences

Hypersensitive (HS) sites in genomic sequences are reliable markers of DNA regulatory regions that control gene expression. Annotation of regulatory regions is important in understanding phenotypical differences among cells and diseases linked to pathologies in protein expression. Several computational techniques are devoted to mapping out regulatory regions in DNA by initially identifying HS sequences. Statistical learning techniques like Support Vector Machines (SVM), for instance, are employed to classify DNA sequences as HS or non-HS. This paper proposes a method to automate the basic steps in designing an SVM that improves the accuracy of such classification. The method proceeds in two stages and makes use of evolutionary algorithms. An evolutionary algorithm first designs optimal sequence motifs to associate explicit discriminating feature vectors with input DNA sequences. A second evolutionary algorithm then designs SVM kernel functions and parameters that optimally separate the HS and non-HS classes. Results show that this two-stage method significantly improves SVM classification accuracy. The method promises to be generally useful in automating the analysis of biological sequences, and we post its source code on our website.     

Organisation and properties of repeated DNA sequences in rice genome

Reassociation of high molecular weight rice DNA has revealed the occurrence of long stretches of repeated DNA which are not interrupted by single copy DNA even at a fragment length as high as 20 kilo base pairs (kbp). Majority of these repeated sequences are unusually G + C rich and show significant variations in their thermal stability. Homology studies indicate that short repeats may have evolved from long repeats in total repetitive DNA while they may be of different origin in highly repetitive DNA fraction. Restriction enzyme analysis shows the occurrence of Ava I and EcoR V repeat families.     

Identification of the sequences recognized by the Bacillus subtilis response regulator YclJ

The Bacillus subtilis yclJ gene encodes an OmpR-type response regulator of a two-component regulatory system with unknown function. A previous DNA microarray experiment suggested that multicopy yclJ greatly enhances the expression of several operons in a cognate kinase (YclK)-deficient strain. To confirm this, lacZ fusion analysis was performed in the yclK background with overexpressed yclJ. As a result, yclHI, ykcBC, and yngABC were indeed positively regulated by YclJ. Gel retardation and DNase I footprint analyses revealed that YclJ binds to the promoter regions of yclHI, ykcBC, and yngABC. Nucleotide sequence analysis of the binding regions suggested that YclJ recognizes a direct repeat of the consensus sequence TTCATANTTT, the upstream half of which has close similarity to the consensus binding sequence of the other OmpR family response regulator PhoP. LacZ fusion analysis of the control region of yngA with deletion or point mutation confirmed that the YclJ-binding sequence is required for the YclJ-mediated activation of yngA. Furthermore, we identified two more YclJ-regulated genes, yycA and yfjR, using bioinformatic analysis of the B. subtilis genome, and it was shown that YclJ binds to those promoters and controls the expression of those genes.     

Thermodynamic properties of DNA sequences: characteristic values for the human genome

MOTIVATION: Central to many molecular biology techniques as ubiquitous as PCR and Southern blotting is the design of oligonucleotide (oligo) probes and/or primers possessing specific thermodynamic properties. Here, we use validated theoretical methods to generate distributions of predicted thermodynamic properties for DNA oligos of various lengths. These distributions facilitate immediate appreciation of typical thermodynamic values for oligos of various lengths. RESULTS: Distributions of melting temperature (Tm), free energy (DeltaG(T)o), and fraction hybridized or fraction bound (Fb), are presented for oligos of length 10-50 bases sampled from the human genome. The effects of changing temperature, oligo and salt concentrations, constraining G+C content, and introducing mismatches are exemplified. Our results provide the first survey of typical and limiting thermodynamic values evaluated on a genomic scale. Described numbers comprise useful 'rules of thumb' that are applicable to most technologies dependent upon DNA oligo design.     

The nucleotide sequences recognized by endonucleases AvaI and AvaII from Anabaena variabilis.

Determination of the 5'-terminal sequences flanking all the individual cleavage sites for endonuclease AvaI in bacteriophage-lambda DNA has shown that this enzyme recognizes the hexanucleotide sequences: (Formula: see text), This sequence is cut as shown by the arrows to give single-stranded 5'-tetranucleotide protrusions (cohesive ends). Endonucleases SmaI, XhoI and XmaI recognize different symmetrical subsets of this sequence and provide independent evidence for the occurrence of these subsets at particular endonuclease-AvaI cleavage sites in the bacteriophage-lambda genome. Further evidence for this structure came from the demonstration that DNA fragments generated by endonuclease AvaI can be ligated to form a discrete set of larger molecules and from nearest-neighbor analysis which showed that cytosine residues occurred at the 3'-side of cleavage points. The observation that endonuclease AvaII recognized a subset of the sites recognized by AsuI [Hughes, Bruce & Murray (1979) Biochem. J. 185, 59-63[ led to the deduction that AvaII recognize the pentanucleotide sequence: (Formula: see text), and breaks internucleotide bonds at the positions indicated by the arrows.