Phylogenetic inference from binary sequences reduced by primary DNA sequences

Given a bi-classification of nucleotides, we can obtain a reduced binary sequence of a primary DNA sequence. This binary sequence will undoubtedly retain some biological information and lose the rest. Here we want to know what kind of and how much biological information an individual binary sequence carries. Three classifications of nucleotides are explored in the present article. Phylogenetic trees are built from these binary sequences by the Neighbor-Joining (NJ) method, with evolutionary distance evaluated on the basis of a symbolic sequence complexity. We find that, for all data sets studied, binary sequences reduced by the purine/pyrimidine classification give reliable phylogeny (almost the same as that from the primary sequences), while the other two result in discrepancies at different levels. Some possible reasons and a simple model of sequence evolutionary are introduced to interpret this phenomenon.     

Numerical characterization and similarity analysis of DNA sequences based on 2-D graphical representation of the characteristic sequences

Based on the classifications of the four nucleic acid bases, He and Wang reduced a DNA sequence to three binary sequences, which are called the characteristic sequences (J. Chem. Inf. Comput. Sci. 42 (2002) 1080). In this paper, we associate each characteristic sequence with a (b)L / (b)L matrix by giving a 2-D 'two horizontal lines' graphical representation, and thus obtain a 3-component vector with entries being the sums of the maximal and minimal eigenvalues of the (b)L / (b)L matrices. The introduced vector results in more simple characterizations and comparisons among the coding sequences of exon 1 of beta-globin gene of eleven different species.     

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.     

Similarity analysis of DNA sequences based on the weighted pseudo-entropy

A DNA primary sequence is a string consisting of letters on an alphabet Ω = {a, c, g, t}. Based on all of the 2-combinations of the set Ω, here the repetition is allowed, we transform a DNA primary sequence into a special sequence over a set with cardinality 10. With the 10-letter sequence, we associate 10 nonnegative numerical sequences and then derive a 10-component vector by means of a weighted pseudo-entropy, which can reflect the information on elements of a sequence and, especially, the order relation among them. The new quantitative characterization of DNA sequences is sensitive to substitution of the string elements. The examination of the relationship among β-globin genes of 15 species illustrates the utility of the proposed approach.     

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.     

The sieve ratio for characterization and similarity analysis of DNA sequences

A DNA sequence is a finite sequence of letters in the 4-letter DNA alphabet sigma = [A, C, G, T]. A set of condensed matrices was constructed to represent DNA sequences based on the sieve ratios of trinucleotide in sequence. Then, leading eigenvalues of these matrices were computed and considered as invariants for the DNA sequences. Similarity and dissimilarity analysis based on condensed matrices are given for eleven exon-1 genes of beta-globins of eleven species.     

A theoretical investigation on the interaction of a new gene vector with DNA

A new neutral gene vector, based on a lipopolythiourea N-(2-(3-[2-(2-(3-[2-(3-methyl-thioueido)-ethyl] -thioureido)-ethylamino)-ethyl]-thioureido)-ethyl)- N′, N′- ditetradecyl-succinamide (DTTU) has recently been synthetized but its behavior is difficult to study at the experimental level. Density functional theory (DFT) calculations have thus been performed to predict its interaction mode with B-DNA. Its acidic properties are first computed and suggest that DTTU should be non-charged when interacting with DNA. Different ways of DTTU/DNA associations based on hydrogen bonding–namely external and groove-binding interactions—are then investigated. Our calculations clearly point out that external interaction is preferred with respect to groove-binding, due to three bifurcated hydrogen bonds between DTTU thiourea groups and DNA phosphates. Such results can be explained by the absence of charged groups in groove-binding whereas the negative charge of DNA phosphates deeply strengthens hydrogen bonds.     

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.     

New invariant of DNA sequences

For a DNA sequence with n bases, one can always associate it with an n x n nonnegative real symmetric matrix whose diagonal entries are zero. Once the matrix is given, its leading eigenvalue is usually calculated and used as an invariant to characterize the DNA sequence. Let M be such a matrix, and lambda1 its leading eigenvalue. Then (1/n)//M//m1 and sqrt [(n-1)/n]//M//F are the lower and upper bounds of lambda1, respectively. Since their arithmetic average is an approximate value of lambda1 and simpler for calculation, we can use it as an alternative invariant to characterize the DNA sequence. The utility of the new parameter is illustrated on the DNA sequences of five species: human, chimpanzee, mouse, rat, and gallus.     

Metric representation of DNA sequences

A metric representation of DNA sequences is borrowed from symbolic dynamics. In view of this method, the pattern seen in the chaos game representation of DNA sequences is explained as the suppression of certain nucleotide strings in the DNA sequences. Frequencies of short nucleotide strings and suppression of the shortest ones in the DNA sequences can be determined by using the metric representation.     

Electrochemistry of a novel monoruthenated porphyrin and its interaction with DNA

Interactions of an anisomerous ruthenated porphyrin [Ru(MPyTPP)(bpy)₂Cl]⁺ (where bpy = 2,2′-bipyridine, MPyTPP = 5-pyridyl-10,15,20-triphenyl porphyrin) with calf thymus DNA are studied using a tin-doped indium oxide (ITO) electrode. The Ru^III/II redox reaction for the complex exhibits a surface-controlled electron transfer process in buffer solutions. There exists an obvious interaction of the adsorbed [Ru(MPyTPP)(bpy)₂Cl]⁺ on an ITO electrode with DNA in the buffer solutions. The formal potential for [Ru(MPyTPP)(bpy)₂Cl]^2+/+ redox reaction is found to shift negatively in the presence of DNA compared with that in the absence of DNA. However, the current signals of [Ru(bpy)₃]^3+/2+ reaction exhibits a distinct catalytic enhancement to DNA, in contrast to the interactions of [Ru(MPyTPP)(bpy)₂Cl]⁺with DNA.     

Sequence-selective DNA detection using multiple laminar streams: a novel microfluidic analysis method

On-site detection methods for DNA have been demanded in the pathophysiology field. Such analysis requires a simple and accurate method, rather than high-throughput. This report describes a novel microfluidic analysis method and its application for simple sequence-selective DNA detection. The method uses a microchannel device with a serpentine structure. Sequence-specific binding of probe DNA can be detected at one side of the microchannel. This method is capable of sequence-specific detection of DNA with high accuracy. Single base mutations can also be analyzed. Combination of laminar stream and laminar secondary flow in the microchannel enable specific detection of probe-bound DNA.     

Monovalent cation localization in DNA A-tracts with different sequences

The free solution mobilities of 26-base pair (bp) DNA oligomers containing A-tracts with and without internal ApT steps have been measured by capillary electrophoresis, using the mobility of a 26-bp random-sequence oligomer as a reference. The background electrolytes (BGEs) contained mixtures of Li⁺ and tetrapropylammonium (TPA⁺) ions, keeping the total cation concentration constant at 0.3 M. The mobility ratios equaled 1.00 in 0.3 M TPA⁺, indicating that the A-tract and reference oligomers had the same B-form conformation in this BGE. With increasing [Li⁺], the mobility ratio decreased as Li⁺ ions became localized in the A-tract minor groove, suggesting that the A-tract was now in the B* conformation. If the A-tract contained an internal ApT step and the oligomer contained less than ∼50% A + T, the mobility ratio reached a reduced plateau value that remained constant as the [Li⁺] increased to 0.3 M. However, for A-tracts without an internal ApT step and for A-tracts embedded in oligomers containing more than 50% A + T, the mobility ratios increased again at high [Li⁺], eventually reaching a plateau value of 1.00. Hence, DNA A-tracts in solution appear to exist as mixtures of the B and B* conformations, with the fractional concentration of each conformer depending on the [Li⁺], the A-tract sequence, and the total A + T content of the oligomer.     

Genomic data analysis using DNA structure: an analysis of conserved nongenic sequences and ultraconserved elements

Recent comparative studies of the human and mouse genomes have revealed sets of conserved nongenic sequences (CNGs) and sets of ultraconserved elements (UCEs). Both sets of sequences, which exhibit extremely high levels of conservation, extend over hundreds of bases and have no known function. Since there is no detectable sequence homology between paralogous CNGs or UCEs in either of the species, an alignment-free technique is needed for their analysis. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers, including information on stability, the minimum energy conformation, and flexibility. We have used Fourier techniques to analyze the UCEs and CNGs in terms of their octamer structural properties, to reveal structural correlations which may indicate possible functions for some of these sequences.     

Dynamical conductance of model DNA sequences

Using a tight binding model, we have investigated charge transport in model DNA sequences under external ac bias. The numerical results of emittance for several model DNA sequences are found to be well described by an analytical formula, especially when the dynamic response is inductivelike. This formula can be understood from general considerations of scattering matrix theory. The temperature dependence of emittance is also studied numerically within the tight binding model, and dynamic response of the model DNA sequences can change from inductivelike to capacitivelike as temperature is varied.     

Condensed representation of DNA primary sequences

With rapid reporting of DNA sequences derived from automated DNA sequencing techniques, the problem of reviewing and ordering such information has become acute. We have introduced a condensed representation of primary sequences of DNA that offers an alternative method of registering DNA. The advantage of the condensed codes for DNA is that it not only offers fast, qualitative comparisons of DNA but also allows quantitative comparisons of DNA from different sources. The approach is outlined for a particular human beta globin sequence extract. Using the condensed representation of the primary DNA sequences, comparisons are made between primary sequences for Exon 1 of human beta globin and seven other beta globins.     

Extended RCM-ROM sequences: a novel approach to polyunsaturated trisaccharides

The first examples of RCM-ROM-RCM-ROM-RCM sequences involving non-strained heterocyclic relays are described. The method can be used for the preparation of polyunsaturated trisaccharides.