Probes for double helical DNA sequence information: molecular mechanics study of a proposed model

The biological activity of many molecules which bind to double helical DNA is related to the sequence specificity of their binding. The development of new substances of this type is challenging; a general solution to the problem does not exist. A new mechanism for small molecule-duplex DNA interaction termed intercalative displacement is proposed. The approach is promising for the design of new substances which will recognize sequence information on DNA. Molecular mechanics calculations in the absence of solvent and counterions predict that the proposed model is structurally and energetically closely related to the well known process of standard intercalation. The implications of these calculations for experimental studies are discussed.     

Molecular dynamic simulation and DFT study on the Drug-DNA interaction; Crocetin as an anti-cancer and DNA nanostructure model

In this research, the interaction of Crocetin as an anti-cancer drug and a Dickerson DNA has been investigated. 25 ns molecular dynamic simulations of Crocetin and DNA composed of 12 base pairs and a sequence of d(CGCGAATTCGCG)₂ were done in water. Three definite parts of the B-DNA were considered in analyzing the best interactive site from the thermodynamic point of view. Binding energy analysis showed that van der Waals interaction is the most important part related to the reciprocal O and H atoms of the Crocetin and DNA. Stabilizing interactions, obtained by ΔG calculations, showed that maximum and minimum interactions are related to the S1 and S3 regions, respectively. This means that the most probable van der Waals interaction site of the Dickerson B-DNA and Crocetin is located in the minor groove of DNA. Two sharp peaks at 2.55 and 1.75 Å in radial distribution functions of the PO?HO and NH?OC parts are related to new hydrogen bonds between the Crocetin and DNA in the complex which can be considered as the driving force of the anti-cancer mechanism of the Crocetin. Average values of 0.3 au and zero for the electron densities of the H?O bonds for DNA and complex, obtained by Quantum theory of atoms in molecules (QTAIM), means that the origin of DNA instability after complexation may be related to the H-bond denaturation by Crocetin. Finally, the evaluation of the dispersion interactions using the dispersion functional, -148.76 kcal.mol^?1, confirmed the importance of the dispersion interaction in drug-DNA complex.     

Thermodynamic Framework of the Interaction between Protein and Solvent Drives Protein Folding

Abstract

We use internal coordinate molecular mechanics calculations to study the impact of abasic sites on the conformation and the mechanics of the DNA double helix. Abasic sites, which are common mutagenic lesions, are shown to locally modify both the groove geometry and the curvature of DNA in a sequence dependent manner. By controlled twisting and bending, it is also shown that these lesions modify the deformability of the duplex, generally increasing its flexibility, but again to an extent which depends on the nature of the abasic site and on the surrounding base sequence. Both the conformational and mechanical influence of this type of DNA damage may be significant for recognition and repair mechanisms.     

An Iterative Approach to Placing Counterions Around DNA

Abstract

An iterative approach, in which the effect of placing counter ions around DNA influences the electrostatic potential that the other subsequently approaching ions feel, has been used to place sodium ions around polynucleotides. The main focus of this report is to study the sequence and structure dependence on the distribution of ions around DNA, particularly that of tightly bound ions. The interesting results of the calculations are that there is significant sequence dependence on the electrostatic potentials in the B form of DNA, whereas relatively less difference in A form. In the case of Z form, the cations bridge the inter-stand phosphates along the minor groove.     

A Theoretical Study of Formation of DNA Noncanonical Structures Under Negative Superhelical Stress

Abstract

The development of statistical mechanical models of the formation of noncanonical structures in circular DNA and the finding of the energy parameters for these models made it possible to predict the appearance of such structures in a DNA with any given sequence. It does not seem feasible, however, to perform such calculations for DNA sequences of considerable length by allowing for all the possible states. We propose a special algorithm for calculating the thermodynamic characteristics of various conformational rearrangements in DNA that occur under negative supercoilings, allowing for several possible states of each base pair in the chain. Calculations have been performed for a number of natural DNAs. According to these calculations, the most likely noncanonical structures in DNA under normal conditions are cruciform structures and the Z form. The results of the calculations are compared with the experimental data reported in the literature. State diagrams have been computed for a number of inserts in circular DNA that can adopt both the cruciform conformation and the left-handed helical Z form.     

Bacterial classification with convolutional neural networks based on different data reduction layers

Abstract

For high accuracy classification of DNA sequences through Convolutional Neural Networks (CNNs), it is essential to use an efficient sequence representation that can accelerate similarity comparison between DNA sequences. In addition, CNN networks can be improved by avoiding the dimensionality problem associated with multi-layer CNN features. This paper presents a new approach for classification of bacterial DNA sequences based on a custom layer. A CNN is used with Frequency Chaos Game Representation (FCGR) of DNA. The FCGR is adopted as a sequence representation method with a suitable choice of the frequency k-lengthen words occurrence in DNA sequences. The DNA sequence is mapped using FCGR that produces an image of a gene sequence. This sequence displays both local and global patterns. A pre-trained CNN is built for image classification. First, the image is converted to feature maps through convolutional layers. This is sometimes followed by a down-sampling operation that reduces the spatial size of the feature map and removes redundant spatial information using the pooling layers. The Random Projection (RP) with an activation function, which carries data with a decent variety with some randomness, is suggested instead of the pooling layers. The feature reduction is achieved while keeping the high accuracy for classifying bacteria into taxonomic levels. The simulation results show that the proposed CNN based on RP has a trade-off between accuracy score and processing time.     

Structural and Molecular Biology of the eye Lens Membrane

Abstract

The DNA double helix exhibits local sequence-dependent polymorphism at the level of the single base pair and dinucleotide step. Curvature of the DNA molecule occurs in DNA regions with a specific type of nucleotide sequence periodicities. Negative supercoiling induces in vitro local nucleotide sequence-dependent DNA structures such as cruciforms, left-handed DNA, multistranded structures, etc. Techniques based on chemical probes have been proposed that make it possible to study DNA local structures in cells. Recent results suggest that the local DNA structures observed in vitro exist in the cell, but their occurrence and structural details are dependent on the DNA superhelical density in the cell and can be related to some cellular processes.     

西太平洋多金属结核区12个站位沉积物中可培养潜在腐殖质转化菌的多样性

【背景】海洋环境作为地球上最大的有机碳库贮藏着大量腐殖质,其中可能蕴藏着丰富的腐殖质转化菌。【目的】从深海沉积物环境中分离具有潜在腐殖质转化能力的细菌,为难降解天然有机多聚物的生物转化提供菌种资源。【方法】利用以腐殖质为唯一碳源的培养基,对西太平洋多金属结核区12个站位沉积物样品中的腐殖质转化菌进行富集培养和纯化,通过16S rRNA基因测序分析比对初步确定分离菌株的分类地位,并利用含苯胺蓝的培养基筛选潜在的腐殖质转化菌。【结果】从12个沉积物样品中共分离获得菌株276株,隶属于放线菌纲(Actinobacteria)、纤维粘网菌纲(Cytophagia)、黄杆菌纲(Flavobacteria)、 α变形菌纲(Alphaproteobacteria)和γ变形菌纲(Gammaproteobacteria)中的14个目37个属56个种(含1个潜在新属和2个新种),其中49个种呈现木质素修饰酶阳性。【结论】利用以腐殖质为唯一碳源和能源的培养基可以分离获得具有较高多样性的潜在腐殖质转化菌。     

New solvent-producing Clostridium sp. strains, hydrolyzing a wide range of polysaccharides, are closely related to Clostridium butyricum

Thirteen new Clostridium strains, previously isolated from soil and found to produce high amounts of solvents from glucose, hydrolyzed a great variety of α- and β-glycans, including raw starch, xylan, pectin, inulin and cellulose. The sequences of the PCR-amplified DNA fragments containing the variable 3′ part of one of the 16S rRNA genes were 99.5% identical. The macrorestriction pattern of two endonucleolytic digests of chromosomal DNA in the pulsed-field gel electrophoresis (PFGE) confirmed their high homogeneity on the DNA level. The complete 16S rRNA gene sequence of three selected strains was 99.8% identical to the 16S rRNA gene sequence from Clostridium butyricum and separates them from C. acetobutylicum. To the closely related four species of solventogenic clostridia a new group of strains has to be added, which has a great potential for the direct fermentation of biomass. Journal of Industrial Microbiology & Biotechnology (2001) 27, 329–335. Received 12 September 2000/ Accepted in revised form 25 July 2001     

Characterization of a full-length petunia cDNA encoding a polypeptide of the light-harvesting complex associated with photosystem I

We have isolated and characterized a full-length cDNA clone (LHCI-15) which specifies a new chlorophyll-binding protein. This protein is associated with the light-harvesting complex of photosystem I (LHCI). The DNA sequence predicts a precursor protein of 270 amino acids, which shares significant homology with the amino acid sequence of another chlorophyll-binding protein; the chlorophyll a/b-binding (Cab) protein of the photosystem II light-harvesting complex (LHCII). There are two extensive regions of homology (at least 45 residues each) which have approximately 50% amino acid sequence identity. These regions coincide with two of the proposed membrane-spanning alpha helices in the Cab proteins of the LHCII and probably include conserved chlorophyll-binding sites. The LHCI-15 cDNA hybridizes to at least 7 genomic EcoRI DNA fragments, which are very closely related at the nucleotide sequence level.     

Conformations of DNA Duplexes Containing 8-Oxoguanine

Abstract

As a step towards elucidating the mechanisms of mutagenesis induced by irradiation and oxidation, we study the incorporation of 8-oxoguanine (OG) into duplex DNA. Molecular modelling is used to reveal changes in DNA conformational parameters due to mispairs within the sequences d(A₅XA₅) · d(T₅YT₅) and d(G₅XG₅) · d(C₅YC₅) where one of the bases of the bases of the central X:Y pair is OG and the other A T, G or C. The G:C to OG:C replacements in DNA duplexes produce only minor conformational changes, similar to normal base sequence effects. The calculations suggest that both OG(syn): G and OG(syn): A mispairs can also be introduced without drastic distortion of sugar-phosphate backbone. The distortions produced by OG-containing mispairs are also found to be sequence dependent Overall these calculations suggest that the G→OG conversion could be an important factor in the irradiative or oxidative damage of DNA.     

Free Energy Calculations Predict Sequence Specificity in DNA-Drug Complexes

Abstract

Molecular dynamics simulations of DNA-netropsin complexes in water were performed using the thermodynamic cycle-perturbation method to calculate the free energy difference between complexes with an adenine-containing binding site and corresponding complexes where adenines are replaced by 2,6-diaminopurines (dap). The calculations predict a free energy difference of 3.7±0.9 kcal/mol (at 300K) in favour of netropsin binding to an (AATT)₂ DNA sequence compared to a (dapdapTT)₂ sequence.     

A Theoretical Consideration of the Influence of Selective Binding of Small Ligands on DNA Helix-Coil Transition

Abstract

The influence of small ligands on DNA helix-coil transition is considered theoretically. The ligands are supposed to interact with DNA base pairs reversibly and selectively. The long-range ligand-ligand interactions are taken into account. Simple formulae are derived for calculation of melting curve alteration induced by ligand binding. The proposed theoretical approach requires neither knowledge of nucleotide sequence nor long computation time.     

Dna Analysis by Mass Spectrometry: Applications in Dna Sequencing And Dna Diagnostics

Abstract

Use of mass spectrometry to detect PCR amplified DNA from individuals infected with hepatitis B virus, to derive DNA sequence information through exo-nuclease based degradation or Sanger sequencing and a new format (PROBE) for the efficient determination of mutations is described.     

Carbohydrate-based heteronuclear complexes as topoisomerase Iα inhibitor: approach toward anticancer chemotherapeutics

Due to the critical role of cellular enzymes necessary for cell proliferation by deciphering topological hurdles in the process of DNA replication, topoisomerases have been one of the major targets in the anticancer drug development area. A need, therefore, arises for new metallodrugs that specifically recognizes DNA and inhibits the activity of topoisomerase enzymes, herein, we report the synthesis and characterization of new metal-based glycoconjugate entities containing heterobimetallic core Cu^II–Sn^IV (1) and Ni^II–Sn^IV (2) derived from N-glycoside ligand (L). The optimized structure of complex 1 and other significant vibrational modes have been explained using dispersion corrected B3LYP/DFT calculations. In vitro DNA binding profile of the L and both the complexes 1 and 2 were done by various biophysical studies. Complex 1 breaks pBR322 DNA via a hydrolytic means which was validated by T4 DNA enzymatic assay. To get a mechanistic insight of mode of action topoisomerase I (Topo I) inhibition assay was carried out. Also, we have taken the help of molecular modeling studies in accordance with experimental findings. In vitro cytotoxicity of the complex 1 was evaluated against a panel of cancer cells which exhibited remarkably good anticancer activity (GI₅₀ values <10 μg/ml). Moreover, intracellular localization of the complex 1 was visualized by confocal microscopy against HeLa cells.     

The Accurate Detection of One Point Mutations by Ligation of Short Oligonucleotides

Abstract

A new approach which is based on the selective ligation of the cooperative tandem of three short oligonucleotides (octa-, tetra- and octamers) is proposed to reveal a point mutation in DNA. The ligation product is registered only when the correct complex of the tandem and DNA is formed. If there is one substitution base in the binding site of tetranucleotide in DNA, no product of ligation is observed.

     

Polyphasic analysis in the description of Sulfitobacter salinus sp. nov., a marine alphaproteobacterium isolated from seawater

Purpose

A polyphasic analysis was performed on a novel bacterium, designated strain KMU-143^T, which was isolated from seawater collected in the Republic of Korea.

Methods

A novel marine bacterium KMU-143^T was analyzed and described using a polyphasic taxonomic method including 16S rRNA gene sequence analysis, DNA–DNA hybridization, and physiological, biochemical, and chemotaxonomic analyses.

Results

Strain KMU-143^T was Gram-stain-negative, strictly aerobic, oval-shaped, non-motile, and chemoorganoheterotrophic. Phylogenetic analysis based on the 16S rRNA gene sequence demonstrated that the novel marine bacterium belongs to the family Rhodobacteraceae, of the class Alphaproteobacteria, and that it possessed the highest (97.1%) sequence similarity with Sulfitobacter pontiacus ChLG 10^T and Sulfitobacter undariae W-BA2^T. DNA–DNA relatedness values between strains KMU-143^T, S. pontiacus JCM 21789^T, and S. undariae KCTC 42200^T were less than 70%. The major isoprenoid quinone of the novel isolate was ubiquinone-10 (Q-10) and the major (> 10%) cellular fatty acids were C16:0 and C18:1 ω7c. The genomic DNA G+C content of strain KMU-143^T was 56.1 mol%. The polar lipid profile of the strain KMU-143^T was found to consist of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, and two unidentified lipids.

Conclusion

Based on the discriminative phylogenetic position and combination of genotypic and phenotypic properties, the strain is considered to represent a new species of the genus Sulfitobacter for which the name Sulfitobacter salinus sp. nov. is proposed. The type strain of S. salinus sp. nov. is KMU-143^T (= KCCM 90322^T = NBRC 113459^T).

     

Detecting genomic deletions from high-throughput sequence data with unsupervised learning

Background

Structural variation (SV), which ranges from 50 bp to \(\sim\) 3 Mb in size, is an important type of genetic variations. Deletion is a type of SV in which a part of a chromosome or a sequence of DNA is lost during DNA replication. Three types of signals, including discordant read-pairs, reads depth and split reads, are commonly used for SV detection from high-throughput sequence data. Many tools have been developed for detecting SVs by using one or multiple of these signals.

Results

In this paper, we develop a new method called EigenDel for detecting the germline submicroscopic genomic deletions. EigenDel first takes advantage of discordant read-pairs and clipped reads to get initial deletion candidates, and then it clusters similar candidates by using unsupervised learning methods. After that, EigenDel uses a carefully designed approach for calling true deletions from each cluster. We conduct various experiments to evaluate the performance of EigenDel on low coverage sequence data.

Conclusions

Our results show that EigenDel outperforms other major methods in terms of improving capability of balancing accuracy and sensitivity as well as reducing bias. EigenDel can be downloaded from https://github.com/lxwgcool/EigenDel.