On the Similarity of DNA Primary Sequences Based on 5-D Representation

We propose a 5-D representation of DNA sequences based on the classifications of the four basic acid bases A,T,G, and C. The use of the 5-D representation is illustrated by constructing sequence invariants based on the entries in derived sequence matrices restricted to a selected width of a band along the main diagonal. As an application, we make a comparison for the first exon of β-globin gene sequences belonging to eleven different species based on the 5-D representation.     

A novel 2-D graphical representation of DNA sequences of low degeneracy

Some 2-D and 3-D graphical representations of DNA sequences have been given by Nandy, Leong and Mogenthaler, and Randic et al., which give visual characterizations of DNA sequences. In this Letter, we introduce a novel graphical representation of DNA sequences by taking four special vectors in 2-D space to represent the four nucleic acid bases in DNA sequences, so that a DNA sequence is denoted on a plane by a successive vector sequence, which is also a directed walk on the plane. It is showed that the novel graphical representation of DNA sequences has lower degeneracy and less overlapping.     

Some notes on 2-D graphical representation of DNA sequence

Some 2-D and 3-D graphical representations of DNA sequences have been given by Nandy, Leong and Mogenthaler, and Randic et al., which give visual characterizations of DNA sequences. In this paper, we presented a novel graphical representation of DNA sequences by taking four special vectors in 2-D Cartesian coordinate system to represent the four nucleic acid bases in DNA sequences, so that a DNA sequence is denoted on a plane by a directed walk. It is shown that the new graphical representation of DNA sequences has lower or nondegeneracy.     

On 3-D graphical representation of DNA primary sequences and their numerical characterization

In this article we (1) outline the construction of a 3-D "graphical" representation of DNA primary sequences, illustrated on a portion of the human beta globin gene; (2) describe a particular scheme that transforms the above 3-D spatial representation of DNA into a numerical matrix representation; (3) illustrate construction of matrix invariants for DNA sequences; and (4) suggest a data reduction based on statistical analysis of matrix invariants generated for DNA. Each of the four contributions represents a novel development that we hope will facilitate comparative studies of DNA and open new directions for representation and characterization of DNA primary sequences.     

A naturally logical representation for DNA primary sequences

In this paper, we (1) introduce a logical representation (LR) for DNA primary sequences; (2) show relations between LR and some other representations including the characteristic sequences of a DNA sequence, Randic's 2-D, 4-D representations, and Z-curve (a 3-D graphical representation); and (3) outline the constructions of the S/S matrix specific for a logical sequence and its 2*2 condensed matrix.     

On a 3-D representation of DNA primary sequences

We introduce a graphical representation of DNA primary sequences by taking four special vectors in a 3-D space to represent the four nucleic acid bases in DNA sequences, so that a DNA primary sequence is denoted in a 3-D space by a successive vector sequence which is a directed walk on the space. It is demonstrated that this representation has no overlap and intersection and allows numerical characterization.     

On a four-dimensional representation of DNA primary sequences

We consider a four-dimensional representation of DNA primary sequences by assigning to each of the four basic amino acids A, T, G, C directions along the four orthogonal coordinate axes. Advantages and limitations of the novel representation of DNA primary sequences are discussed, and the use of the 4-D representation is illustrated by constructing novel sequence invariants. Comparisons with the similarity/dissimilarity results based on 2-D and 3-D representations for a set of eight short DNA sequences corresponding to the first exon of beta globin in eight species, including human, are considered to illustrate the use of our novel sequence invariants based on the entries in derived sequence matrices restricted to a selected width of a band along the main diagonal.     

2-D Graphical representation of proteins based on virtual genetic code

We consider a novel 2-D graphical representation of proteins in which individual nucleic acids are represented as “spots” within a square frame distributed according to specific construction rules. The resulting “images” of proteins can not only serve to facilitate visual comparison of similarities and dissimilarities between lengthy protein sequences, but also offer a way for mathematical characterization of protein sequences, analogous to similar considerations for lengthy DNA sequences. Basically the approach is based on the concept of virtual genetic code, which is a hypothetical string of RNA nucleic acid bases, A, C, U and G, which generates reported protein sequences, without the knowledge of the actual genetic code that produces the protein.     

Nucleoside und Nucleotide. Teil 16. Verhalten von 1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)-pyrimidinon-5′-triphosphat, 1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)pyridinon-5′-triphosphat und 4-Amino-1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)-pyridinon-5′-triphosphat gegenüber DNA-Polymerase

Nucleosides and Nucleotides. Part 16. The Behaviour of 1-(2′-Deoxy-β-D -ribofuranosyl)-2(1H)-pyrimidinone-5′-triphosphate, 1-(2′-Deoxy-β-D -ribofuranosyl-2(1H))-pyridinone-5′-triphosphate and 4-Amino-1-(2′-desoxy-β-D -ribofuranosyl)-2(1H)-pyridinone-5′-triphosphate towards DNA Polymerase The behaviour of nucleotide base analogs in the DNA synthesis in vitro was studied. The investigated nucleoside-5′-triphosphates 1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyrimidinone-5′-triphosphate (pppM_d), 1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyridinone-5′-triphosphate (pppII_d) and 4-amino-1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyridinone-5′-triphosphate (pppZ_d) can be considered to be analogs of 2′-deoxy-cytidine-5′-triphosphate. However, their ability to undergo base pairing to the complementary guanine is decreased. When pppM_d, pppII_d or pppZ_d are substituted for pppC_d in the enzymatic synthesis of DNA by DNA polymerase no incorporation of these analogs is observed. They exhibit only a weak inhibition of the DNA synthesis. The mode of the inhibition is uncompetitive which shows that these nucleotide analogs cannot serve as substrates for the DNA polymerase.     

The 2-Amino Group of 8-Aza-7-deaza-7-bromopurine-2,6-diamine and Purine-2,6-diamine as Stabilizer for the Adenine–Thymine Base Pair in Heterochiral DNA with Strands in Anomeric Configuration

Stabilization of DNA is beneficial for many applications in the fields of DNA therapeutics, diagnostics, and materials science. Now, this phenomenon is studied on heterochiral DNA, an autonomous DNA recognition system with complementary strands in α-D and β-D configuration showing parallel strand orientation. The 12-mer heterochiral duplexes were constructed from anomeric (α/β-D) oligonucleotide single-strands. Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2′-deoxyribonucleosides having the capability to form tridentate base pairs with dT were used to strengthen the stability of the dA–dT base pair. T_m data and thermodynamic values obtained from UV melting profiles indicated that the 8-aza-7-deaza 2′-deoxyribonucleoside decorated with a bromo substituent is so far the most efficient stabilizer for heterochiral DNA. Compared with that, the stabilizing effect of the purine-2,6-diamine 2′-deoxyribonucleoside is low. Global changes of helix structures were identified by circular dichroism (CD) spectra during melting.     

A new mapping rule for RNA secondary structures with its applications

According to the characterization of RNA secondary structures, the RNA secondary structures are transformed into elementary sequences, namely characteristic sequences of RNA secondary structures, by representing A, U, G, C in A-U/ G-C pairs, as A′, U′, G′, C′. Based on the representation, three recurrences for mapping RNA secondary structures into 1-D graph, 2-D graph and 3-D graph are given, respectively. Furthermore, a frequency-based method for RNA secondary structures is given in terms of 1-D graph.     

Analysis of similarity/dissimilarity of DNA sequences based on nonoverlapping triplets of nucleotide bases

We consider a 6-D representation of triplets of nucleotide bases of DNA sequences. Based on this representation, we outline an approach by constructing a 3-component vector whose components are the normalized leading eigenvalues of the L/L matrices associated with the triplets derived from DNA sequences. The examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of different species illustrates the utility of the approach.     

Similarity analysis of DNA sequences based on the generalized LZ complexity of (0,1)-sequences

Based on the permutation of a binary alphabet, four generalized LZ complexities of a (0,1)-sequence are introduced. Since the logical representation of a DNA primary sequence includes four logical sequences, a DNA primary sequence can be characterized by a 16-D vector whose entries are the complexities corresponding to the logical sequences. The utility of the new quantitative characterization of DNA sequences is illustrated by an examination of the similarity among the full β-globin genes of 11 different species.     

Novel Nucleoside Analogues with Fluorophores Replacing the DNA Base

We describe the preparation and fluorescence properties of a set of new nucleosides in which a known hydrocarbon or oligothiophene fluorophore replaces the DNA base at C(1) of the deoxyribose moiety (see 3a – f ). These compounds are potentially useful as probes in the study of the structure and dynamics of nucleic acids and their complexes with proteins. In addition, they may find use as fluorescent labels for nucleic-acid-based biomedical diagnostics methods. The fluorophores conjugated to deoxyribose at C(1) in the α-D -form include terphenyl, stilbene, terthiophene, benzoterthiophene, and pyrene. Also included is a non-fluorescent spacer in which cyclohexene replaces the DNA base. The nucleosides are derived from brominated fluorophore precursors and Hoffer's 2-deoxy-3,5-di-O-(p-toluoyl)-D -ribofuranosyl chloride. The emission maxima of the free nucleosides range from 345 to 536 nm. Also described are the 5′-(dimethoxytrityl) 3′-O-phosphoramidite derivatives 5a – f , suitable for incorporation into oligonucleotides by automated synthesizers.     

Synthesis and structure of a 1-D copper(II) coordination polymer bridged both by oxamido and carboxylate: in vitro anticancer activity and reactivity toward DNA and protein BSA

A 1-D copper(II) coordination polymer formulated as {[Cu₂(bdpox)(dabt)](NO₃)·H₂O}_n, where H₃bdpox and dabt denote N-benzoate-N′-[3-(diethylamino)propyl]oxamide and 2,2′-diamino-4,4′-bithiazole, respectively, was synthesized and characterized by elemental analyses, molar conductance measurement, IR and electronic spectra studies, and single-crystal X-ray diffraction. The crystal structure analysis reveals that copper(II) ions are bridged by both cis-oxamido and carboxylato groups to form a 1-D coordination polymer with corresponding Cu···Cu separations of 5.2420(10) and 5.1551(8) Å. The endo- and exo-copper(II) ions of the cis-oxamido-bridge are located in distorted square-planar and square-pyramidal geometries, respectively. There is a 2-D hydrogen bonding network in the crystal. The in vitro anticancer activities suggest that the copper(II) complex is active against selected tumor cell lines. The reactivities toward herring sperm DNA and bovine serum albumin (BSA) reveal that the copper(II) complex can interact with DNA by intercalation and effectively quench the intrinsic fluorescence of BSA via a static mechanism. The influence of hydrophobicity of the substituents in bridging ligands on DNA and protein binding properties and the in vitro anticancer activities of such copper(II) polymers is discussed.     

The separation of acyl protection groups in alkali-sensitive glucosides. Synthesis of podophyllotoxin-beta-D-glucoside

The synthesis of podophyllotoxin-β-D -glucoside (III), an antimitotic lignan compound isolated from Podophyllum species, is reported. Reaction of podophyllotoxin (I) with tetra-O-acetyl-α-D -glucopyranosyl bromide in acetonitrile in the presence of Hg(CN)₂ yields tetra-O-acetyl-podophyllotoxin-α-D -glucoside (II), which is converted into podophyllotoxin-β-D -glucoside (III) by ZnCl₂-catalysed methanolysis. This transesterification is an advantageous method for the preparation of glycosides, sensitive to base and acid, from their corresponding acetyl derivatives. Scope and conditions of the reaction are discussed.     

Docking macromolecules with flexible segments

We address a major obstacle to macromolecular docking algorithms by presenting a new method that takes into account the induced conformational adjustment of flexible loops situated at a protein/macromolecule interface. The method, MC2, is based on a multiple copy representation of the loops, coupled with a Monte Carlo conformational search of the relative position of the macromolecules and their side chain conformations. The selection of optimal loop conformations takes place during Monte Carlo cycling by the iterative adjustment of the weight of each copy. We describe here the parameterization of the method and trials on a protein-DNA complex of known 3-D structure, involving the Drosophila prd paired domain protein and its target oligonucleotide Wenqing, X. et al., Cell 1995, 80, 639. We demonstrate that our algorithm can correctly configure and position this protein, despite its relatively complex interactions with both grooves of DNA.     

A 2D graphical representation of DNA sequence based on dual nucleotides and its application

From the perspective of the neighboring dual nucleotides, we introduce a novel 2D graphical representation of DNA sequences based on the magic circle, which correspond to 16 dual nucleotides. So, we can reduce a DNA sequence into a plot set in two‐dimensional space and get a two‐component vector relatively to the introduced covariance matrix. The utility of our approach can be illustrated by the examination of similarities/dissimilarities among the complete coding sequences of β‐globin gene belonging to 11 species. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

On 3-D graphical representation of proteomics maps and their numerical characterization

We consider numerical characterization of proteomics maps by representing a map as a three-dimensional graphical object based on x, y coordinates of the spots and using their relative abundance as the z coordinate. In our representation the protein spots are first ordered based on their relative abundance and labeled accordingly. In the next step a 3-D path is constructed connecting spots having adjacent labels. Finally a matrix is constructed by assigning to each pairs of labels (i, j) matrix element, the numerical value of which is based on the quotients of the Euclidean distance and the distance along the 3-D zigzag between the two points. The approach has been illustrated on a fragment of a proteomics map and compared with 2-D graphical representation of proteomics maps.     

New results for the OH (nu = 0,j = 0) + CO (nu = 0,j = 0) --> H + CO2 reaction: Five- and full-dimensional quantum dynamical study on several potential energy surfaces

Full- [six-dimensional (6-D)] and reduced-dimensional [five-dimensional (5-D)] quantum wave packet calculations have been performed for the title reaction to obtain reaction probabilities deriving from the ground rovibrational states of OH and CO with total angular momentum J = 0. Three potential energy surfaces (PES) are studied, namely, those of Bradley and Schatz (BS), Yu, Muckerman, and Sears (YMS), and Lakin, Troya, Schatz, and Harding (LTSH). 6-D calculations are performed only for the BS PES, while 5-D results are reported for all three PES'. The 6-D results obtained in the present work improve on those previously reported, since a larger vibrational basis and a better representation of the OH and CO bonds has been introduced. In particular, we now employ a generalized Lanczos-Morse discrete variable representation for both the OH and CO vibrations. In a further improvement, the generalized discrete variable representation of the CO vibration is based on different CO intramolecular potentials for the asymptotic and product grids employed in our projection formalism. This new treatment of the vibrational bases allows for a large reduction in computation time with respect to our previous implementation of the wave packet method, for a given level of accuracy. As a result, we have been able to extend the range of collision energies for which we can obtain converged 6-D results to a higher energy (0.8 eV) than was possible before (0.5 eV). The comparison of the new 6-D and previous 5-D results for the BS PES shows good agreement of the general trend in the reaction probabilities over all collision energies considered (0.1-0.8 eV), while our previous 6-D calculation showed reaction probabilities that differed from the 5-D results by up to 10% between 0.5 and 0.8 eV. The 5-D reaction probabilities reveal interesting trends for the different PES'. In particular, at low energies (< 0.2 eV) the LTSH PES gives rise to much larger reactivity than the other PES', while at high energies (> 0.3 eV) its reaction probability decreases with respect to the BS and YMS PES', being more than a factor of 2 smaller at 0.8 eV. A 5-D calculation on a modified version of the LTSH surface shows that the van der Waals interaction in the entrance channel, which is not correctly described in the other PES' is largely responsible for its larger reactivity at low energies. The large difference between the 5-D reaction probabilities for the YMS and LTSH PES' serves to emphasize the importance of the van der Waals interaction for the reactivity at low energies, because most of the stationary point energies on the YMS and LTSH PES are rather similar, being in line with high-level ab initio information.