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.     

A generalization of Lempel-Ziv complexity and its application to the comparison of protein sequences

In this paper, a complexity measure of symbolic sequences is proposed that generalizes the Lempel-Ziv complexity by taking into account a specific kind of the inexact copy in the text, and based on which, a new sequence distance measure for the similarity analysis is introduced. The utility of our approach is illustrated by an examination of the relationships among β-globin proteins of 13 species.     

Sequence classification of water channels and related proteins in view of functional predictions

We have worked with a classification method based upon a notion of probabilistic similarity or “likelihood of similarity” between aligned sequences. One important parameter, among others, affecting the sequence similarities and hence the classification results is the amino acid similarity matrix. We present a method for choosing the most adapted matrix to classify protein sequences. This method has been applied to the transmembrane channels of the major intrinsic protein (MIP) family. At present, two functional subgroups have been well characterized in this family: (1) specific water transport by the aquaporins and (2) small neutral solutes transport. The aim of the present study is to show the usefulness of the classification method in the prediction of sequence segments important for substrate selectivity. Moreover, we show that this method can also be used to predict the function of undetermined MIP proteins. The method could be applied to other protein families as well. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Label-free detection of nucleic acids by turn-on and turn-off G-quadruplex-mediated fluorescence

In this study we have used two fluorescent probes, tetrakis(diisopropylguanidino)-zinc-phthalocyanine (Zn-DIGP) and N-methylmesoporphyrin IX (NMM), to monitor the reassembly of “split” G-quadruplex probes on hybridization with an arbitrary “target” DNA. According to this approach, each split probe is designed to contain half of a G-quadruplex-forming sequence fused to a variable sequence that is complementary to the target DNA. Upon mixing the individual components, both base-pairing interactions and G-quadruplex fragment reassembly result in a duplex–quadruplex three-way junction that can bind to fluorescent dyes in a G-quadruplex-specific way. The overall fluorescence intensities of the resulting complexes were dependent on the formation of proper base-pairing interactions in the duplex regions, and on the exact identity of the fluorescent probe. Compared with samples lacking any “target” DNA, the fluorescence intensities of Zn-DIGP-containing samples were lower, and the fluorescence intensities of NMM-containing samples were higher on addition of the target DNA. The resulting biosensors based on Zn-DIGP are therefore termed “turn-off” whereas the biosensors containing NMM are defined as “turn-on”. Both of these biosensors can detect target DNAs with a limit of detection in the nanomolar range, and can discriminate mismatched from perfectly matched target DNAs. In contrast with previous biosensors based on the peroxidase activity of heme-bound split G-quadruplex probes, the use of fluorescent dyes eliminates the need for unstable sensing components (H₂O₂, hemin, and ABTS). Our approach is direct, easy to conduct, and fully compatible with the detection of specific DNA sequences in biological fluids. Having two different types of probe was highly valuable in the context of applied studies, because Zn-DIGP was found to be compatible with samples containing both serum and urine whereas NMM was compatible with urine, but not with serum-containing samples.     

Related matrices of DNA primary sequences based on triplets of nucleic acid bases

We considered constructing three 8-component vectors for a DNA primary sequence using triplets of nucleic acid bases. For two DNA sequences, using the corresponding vectors, we constructed a set of 3 × 3 matrices called the related matrix. The normalized leading eigenvalues from the constructed matrices were selected as invariants to characterize the degree of similarity between the two DNA sequences. Construction of similarity/dissimilarity tables based on this invariant for sequences of DNA of the first exon of the β-globin gene from 11 species illustrates the utility of the newly formulated matrices for DNA.     

Differences in electrostatic potential around DNA fragments containing guanine and 8-oxo-guanine

Changes of electrostatic potential (EP) around the DNA molecule resulting from chemical modifications of nucleotides may play a role in enzymatic recognition of damaged sites. Effects of chemical modifications of nucleotides on the structure of DNA have been characterized through large-scale density functional theory computations. Quantum mechanical structural optimizations of DNA fragments with three pairs of nucleotides and accompanying counteractions were performed with a B3LYP exchange-correlation functional and 6–31G** basis sets. The “intact” DNA fragment contained guanine in the middle layer, while the “damaged” fragment had the guanine replaced with 8-oxo-guanine. The electrostatic potential around these DNA fragments was projected on a surface around the double helix. The 2D maps of EP of intact and damaged DNA fragments were analyzed to identify these modifications of EP that result from the occurrence of 8-oxo-guanine. It was found that distortions of the phosphate groups and displacements of the accompanying countercations are clearly reflected in the EP maps. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Preparative isolation of oligodeoxynucleotides

Summary DNA can be degradated on a preparative scale to mixtures of oligonucleotides by various chemical methods. The resulting highly complex oligonucleotide mixture can be almost completely separated by liquid chromatography. The separation procedures are demonstrated by the isolation of pyrimidine oligonucleotides from a partial hydrolysate of herring sperm DNA. The partial hydrolysate is fractionated into oligonucleotide mixtures of defined compositions by a separation route in which ion exchangers are used at different pH-values. From the resulting mixtures of sequence isomers pyrimidine oligonucleotides of defined sequences are obtained by ion exchange and/or reversed phase HPLC. Oligonucleotides which can not be isolated by this separation route are obtained from the preseparated partial hydrolysate by template chromatography using the specificity of the base-pairing mechanism. Purity and sequence of the isolated oligonucleotides are determined by the “fingerprint” method. Presented at the 15th International Symposium on Chromatography, Nürnberg, October 1984     

Molecular genetics ofPhanerochaete chrysosporium

InPhanerochaete chrysosporium ME446 lignin degradation is a secondary metabolic event triggered by carbon and nitrogen limitation. It is therefore possible to study lignin degradation at the level of gene expression by comparing mRNA populations produced during primary and secondary growth in both wild-type strains and in strains mutant in lignin degradation. We have isolated mutants deficient in phenol oxidase activity. These mutants fall into three phenotypic categories with respect to lignin degradation: (1) negative, (2) delayed onset after nitrogen starvation, (3) enhanced. Polyacrylamide gel electrophoresis of rabbit reticulocyte polypeptide translation products ofPhanerochaete mRNA shows differences between populations from primary and secondary growth. Differences in the range of polypeptides (and therefore of mRNA) have also been demonstrated between a mutant and its wild-type progenitor under identical conditions. A gene bank has been prepared from P.chrysosporium strain ME446 genomic DNA using a bacteriophage λ vector. This gene bank is being screened with labeled mRNA from secondary growth mycelium in the presence of excess competing cold RNA from primary growth mycelium. Using this method (and/or using labeled cDNA probes), we hope to isolate clones carrying sequences expressed only during lignin degradation. A gene bank has also been constructed fromSporotrichum pulverulentum (Novobranova), which is on morphological criteria considered to be the imperfect form ofP. chrysosporium. DNA probes from randomly chosen clones of both gene banks have been hybridized to restricted and electrophoresed total DNA of the two “gene bank” strains and of two other isolates ofP. chrysosporium on Southern blots. We found very strong DNA homology between the two “gene bank” strains, but far less homology between these two strains and the two others. These degrees of relationships were supported by the analysis of mitochondrial DNA from the four strains. We thank the Agricultural Research Council and the British Petroleum Venture Research Unit for support.     

Danube River Water Data Modelling by Multivariate Data Analysis

 A data set (48×19) consisting of Danube river water analytical data collected at Galati site, Romania, during a four-year period has been treated by principal components analysis (PCA). The PCA indicated that seven latent factors (“hardness”, “biochemical”, “waste inlets”, “turbidity”, “acidity”, “soil extracts” and “organic wastes”) are responsible for the data structure and explain over 80 % of the total variance of the system. Its complexity is further proved by the application of multiple linear regression analysis on the absolute principal components scores (APCS) where the contribution of each natural or anthropogenic sources in the factor formation is shown. The apportioning makes clear that each variable participates to a different extent to each source and, in this way, no pure natural or pure anthropogenic influence could be determined. No specific seasonality for the variables in consideration is found. Received January 24, 2001. Revision July 6, 2001.     

Similarity analysis of protein sequences based on the normalized relative-entropy

Based on the classification of 20 amino acids, we reduce a protein primary sequence to six (0,1) sequences. For each of them, two so-called normalized relative-entropies are calculated and thus a 12-D vector is constructed to describe the protein primary sequence. The examination of similarities/dissimilarities among eight different proteins illustrates the utility of the approach.     

An advanced multivariate statistical approach to study coastal sediment data

The present paper deals with the application of classical and fuzzy principal components analysis to a large data set from coastal sediment analysis. Altogether 126 sampling sites from the Atlantic Coast of the USA are considered and at each site 16 chemical parameters are measured. It is found that four latent factors are responsible for the data structure (“natural”, “anthropogenic”, “bioorganic”, and “organic anthropogenic”). Additionally, estimating the scatter plots for factor scores revealed the similarity between the sampling sites. Geographical and urban factors are found to contribute to the sediment chemical composition. It is shown that the use of fuzzy PCA helps for better data interpretation especially in case of outliers.     

Evaluation of World Anti-Doping Agency criteria for anabolic agent analysis by using comprehensive two-dimensional gas chromatography–mass spectrometry

This work presents the validation study of the comprehensive two-dimensional gas chromatography (GC×GC)–time-of-flight mass spectrometry method performance in the analysis of the key World Anti-Doping Agency (WADA) anabolic agents in doping control. The relative abundance ratio, retention time, identification and other method performance criteria have been tested in the GC×GC format to confirm that they comply with those set by WADA. Furthermore, tens of other components were identified with an average similarity of >920 (on the 0–999 scale), including 10 other endogenous sterols, and full mass spectra of 5,000+ compounds were retained. The testosterone/epitestosterone ratio was obtained from the same run. A new dimension in doping analysis has been implemented by addressing separation improvement. Instead of increasing the method sensitivity, which is accompanied by making the detector increasingly “blind” to the matrix (as represented by selected ion monitoring mode, high-resolution mass spectrometry (MS) and tandem MS), the method capabilities have been improved by adding a new “separation” dimension while retaining full mass spectral scan information. Apart from the requirement for the mass spectral domain that a minimum of three diagnostic ions with relative abundance of 5% or higher in the MS spectra, all other WADA criteria are satisfied by GC×GC operation. The minimum of three diagnostic ions arises from the need to add some degree of specificity to the acquired mass spectrometry data; however, under the proposed full MS scan method, the high MS similarity to the reference compounds offers more than the required three diagnostic ions for an unambiguous identification. This should be viewed as an extension of the present criteria to a full-scan MS method.     

Toward hybridization assays without PCR using universal nanoamplicons

An innovative scheme for signal amplification using random tetramer-modified gold nanoparticles, termed “nanoamplicons,” has been developed for hybridization assay without PCR. Large numbers of nanoamplicons could be integrated onto one target, providing much greater amplification than the larger nanoparticles usually adopted. Using M13mp18 single-strand DNA as a target, this concept is shown to be a feasible approach to detecting 0.17 amol L⁻¹ DNA without target amplification, based on microgravimetric detection of the adsorption of the probe–target–nanoamplicons complex via thiol–gold binding. To our knowledge, this method has a sensitivity that is close to that of PCR and superior to those of nanoparticle-based methods reported previously. Additionally, this novel nanoamplicon could be prepared in the same way and used for all diagnostic tests; such universality would make the nanoamplicons highly advantageous for the generalization and standardization of bioassays, and when applying this new technology in clinical laboratories. Figure A novel signal amplification method for DNA detection with subattomolarsensitivity has been developed using random tetramer-modified gold nanoparticlesas nanoamplicons, which are easily prepared with high uniformity and can be universally adaptedto any sequences     

Phylogenetic analysis of DNA sequences with a novel characteristic vector

In the basic biological research, one of major tasks is to compare biological sequences to infer evolutionary relations among sequences. In this paper, considering both the positions and numbers of a k-word and the random background, a novel characteristic vector of a DNA sequence is proposed to serve for genetic sequences comparison and phylogenetic analysis. The vector is composed of elements which characterize the relative difference of a DNA sequence from a sequence generated by a (k − 2)th order Markov process. Finally, we reconstruct the phylogenetic trees of 48 HEV (Hepatitis E virus) and 20 Eutherian mammals. The results show that this new method provides more information about k-word and improves the efficiency of sequence comparison.     

Synthesis of a “memory tripeptide” (Arg—Glu—Arg,RER) and the Kabachnik—Fields reaction with di- and tripeptides as a method for the synthesis of phosphorus-containing peptide analogs

Methods for the synthesis of potential “twin-drugs” containing fragments of the glutamate receptor antagonist and cognitive function enhancing oligopeptides were developed. The “memory tripeptide” Arg—Glu—Arg (RER) containing the tripeptide sequence of a protein APP_328–330, a gB-amyloid precursor, was synthesized. A method for the synthesis of gA-aminophosphonates with oligopeptides as the amine component of the one-pot three-component Kabachnik—Fields reaction was developed. A method for the synthesis of phosphonopeptides by the introduction of gA-aminophosphonates into the peptide chain was proposed.     

“Topohydrophobic positions” as key markers of globular protein folds

The positions of a given fold always occupied by strong hydrophobic amino acids (V, I, L, F, M, Y, W), which we call “topohydrophobic positions”, were detected and their properties demonstrated within 153 non-redundant families of homologous domains, through 3D structural alignments. Sets of divergent sequences possessing at least four to five members appear to be as informative as larger sets, provided that their mean pairwise sequence identity is low. Amino acids in topohydrophobic positions exhibit several interesting features: they are much more buried than their equivalents in non-topohydrophobic positions, their side chains are far less dispersed; and they often constitute a lattice of close contacts in the inner core of globular domains. In most cases, each regular secondary structure possesses one to three topohydrophobic positions, which cluster in the domain core. Moreover, using sensitive alignment processes such as hydrophobic cluster analysis (HCA), it is possible to identify topohydrophobic positions from only a small set of divergent sequences. Amino acids in topohydrophobic positions, which can be identified directly from sequences, constitute key markers of protein folds, define long-range structural constraints, which, together with secondary structure predictions, limit the number of possible conformations for a given fold. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 16 November 1998     

Urine dry reagent strip “error” rates using different reading methods

 The need for “quality” in near patient testing (NPT) has been acknowledged since the mid 1980s. The commonest biochemical NPT device is the dry reagent strip or “dipstick” for urinalysis. Dipsticks may be read in three ways, against the color chart printed along the side of the bottle, using a benchreader (the color chart printed on a flat card) or using an electronic reader. This report uses the results of a urinalysis quality assurance (QA) program, over 1998, to evaluate the “error” rates which occur using the three different reading methods. The QA samples are buffered aqueous solutions which are “spiked” to give concentrations midway between two color blocks for each analyte. Results are scored as ±1 if a color block adjacent to the target value, ±2 for results two color blocks (defined as “error”) and ±3 for results three color blocks (defined as “gross error”) from the target value. Analysis of the results show that the error rates are similar reading visually by either method, but greatly reduced when read electronically. Some persisting errors when using the electronic reader are explained by observation studies. The study highlights the value of a urinalysis QA program for NPT urinalysis in understanding the error rates of this simple but ubiquitous test. Received: 10 July 2000 / Accepted: 10 July 2000     

Quantum-Chemical Study of “Hydride” Mobility in the Molecules of Chalcogenopyrans

An approach is proposed for the quantum-chemical investigation of “hydride ion” transfer based on analysis of the similarity of the order of variation in the ionization potentials, enthalpies, and free energies of affinity to the hydride ion, the hydrogen atom, and the proton in the substrate molecules and also the derivatives of their cations, radicals, and ions to the experimentally established “hydride” series. It was established that the experimental “hydride” mobility series of six chalcogenopyrans based on “semicyclic” 1,5-diketones agrees with the quantum-chemically calculated ionization potentials of the molecules and with the affinity of the respective radicals to the hydrogen atom participating in the transfer. It was found that direct removal of a hydride ion and initial deprotonation of the substrates followed by the removal of two electrons are unlikely. “Hydride” shift mechanisms, in which the first stage is transfer of an electron or hydrogen atom from the chalcogenopyran molecules, are feasible. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1305–1311, September, 2005.     

Multivariate analysis of HT/GC-(IT)MS chromatographic profiles of triacylglycerol for classification of olive oil varieties

The ability of multivariate analysis methods such as hierarchical cluster analysis, principal component analysis and partial least squares-discriminant analysis (PLS-DA) to achieve olive oil classification based on the olive fruit varieties from their triacylglycerols profile, have been investigated. The variations in the raw chromatographic data sets of 56 olive oil samples were studied by high-temperature gas chromatography with (ion trap) mass spectrometry detection. The olive oil samples were of four different categories (“extra-virgin olive oil”, “virgin olive oil”, “olive oil” and “olive-pomace” oil), and for the “extra-virgin” category, six different well-identified olive oil varieties (“hojiblanca”, “manzanilla”, “picual”, “cornicabra”, “arbequina” and “frantoio”) and some blends of unidentified varieties. Moreover, by pre-processing methods of chemometric (to linearise the response of the variables) such as peak-shifting, baseline (weighted least squares) and mean centering, it was possible to improve the model and grouping between different varieties of olive oils. By using the first three principal components, it was possible to account for 79.50% of the information on the original data. The fitted PLS-DA model succeeded in classifying the samples. Correct classification rates were assessed by cross-validation.