Isotherm of ligand adsorption on DNA at multiplicative noise

Fluctuations of the number of ligands adsorbed on macromolecules are considered in the case when the number of ligands in the solution fluctuates under the action of fluctuations of the external medium (external noise). For the case of small filling, the multiplicative type of stochastic differential equation is obtained, describing the time variation of the number of ligands adsorbed on macromolecules. The isotherm of adsorption of ligands on DNA is obtained. It is shown that at small ligand concentrations, for some relations between adsorption parameters and the intensity of the external noise, no macromolecule adsorption of ligands takes place.     

Tenascin-C: Its functions as an integrin ligand

This review summarizes the experimental evidence of tenascin-C/integrin interactions, emphasizing the identification of integrin binding sites and the effects of specific interactions on cell behavior. At least four integrins appear to bind to the third fibronectin-type 3 domain of tenascin-C: α9β1, αVβ3, α8β1 and αVβ6. The α9β1 integrin recognizes a highly conserved IDG motif in this domain, while the others recognize an RGD motif. There is also significant evidence that the collagen receptor α2β1 can bind to tenascin-C, but the interacting site is unknown. Tenascin-C interactions with α9β1 and αVβ3 can promote cell proliferation and interactions with αVβ3 can also inhibit apoptosis. Interactions with α7β1 integrin, which may bind to the alternatively spliced domain of tenascin-C, and α9β1 integrin are able to influence the differentiation of mesenchymal stem cells into the neuronal lineage. This illustrates the potential for using our knowledge of tenascins and their integrin receptors in stem cell-based therapies.     

Evolution of DNA base composition under no-strand-bias conditions when the substitution rates are not constant.

The evolution of DNA base composition evolution is simplified to a six-parameter model when there are no strand biases for mutation and selection. We analyzed the dynamics of this model with special attention to the influence of a change in substitution rates. The G + C content of the DNA sequence tends to an equilibrium value that is controlled by four parameters of the model. When the substitution rates are not constant, the G + C equilibrium position is not constant. The DNA sequence base frequencies always tend to a state in which A = T and G = C within a strand, regardless of substitution rates. This is true even when the substitution rates are not constant over time. This provides a simple way of rejecting the model from inspection of present-day DNA base composition.     

DNA microarray data and contextual analysis of correlation graphs

Background  

DNA microarrays are used to produce large sets of expression measurements from which specific biological information is sought. Their analysis requires efficient and reliable algorithms for dimensional reduction, classification and annotation.     

DNA barcoding: error rates based on comprehensive sampling

DNA barcoding has attracted attention with promises to aid in species identification and discovery; however, few well-sampled datasets are available to test its performance. We provide the first examination of barcoding performance in a comprehensively sampled, diverse group (cypraeid marine gastropods, or cowries). We utilize previous methods for testing performance and employ a novel phylogenetic approach to calculate intraspecific variation and interspecific divergence. Error rates are estimated for (1) identifying samples against a well-characterized phylogeny, and (2) assisting in species discovery for partially known groups. We find that the lowest overall error for species identification is 4%. In contrast, barcoding performs poorly in incompletely sampled groups. Here, species delineation relies on the use of thresholds, set to differentiate between intraspecific variation and interspecific divergence. Whereas proponents envision a “barcoding gap” between the two, we find substantial overlap, leading to minimal error rates of ~17% in cowries. Moreover, error rates double if only traditionally recognized species are analyzed. Thus, DNA barcoding holds promise for identification in taxonomically well-understood and thoroughly sampled clades. However, the use of thresholds does not bode well for delineating closely related species in taxonomically understudied groups. The promise of barcoding will be realized only if based on solid taxonomic foundations.     

Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA

A maximum likelihood method for independently estimating the relative rate of substitution at different nucleotide sites is presented. With this method, the evolution of DNA sequences can be analyzed without assuming a specific distribution of rates among sites. To investigate the pattern of correlation of rates among sites, the method was applied to a data set consisting of the protein-coding regions of the mitochondrial genome from 10 vertebrate species. Rates appear to be strongly correlated at distances up to 40 codons apart. Furthermore, there appears to be some higher order correlation of sites approximately 75 codons apart. The method of site-by-site estimation of the rate of substitution may also be applied to examine other aspects of rate variation along a DNA sequence and to assess the difference in the support of a tree along the sequence.     

Affinity adsorption of plasmid DNA

The development of a protein-mediated dual functional affinity adsorption of plasmid DNA is described in this work. The affinity ligand for the plasmid DNA comprises a fusion protein with glutathione-S-transferase (GST) as the fusion partner with a zinc finger protein. The protein ligand is first bound to the adsorbent by affinity interaction between the GST moeity and gluthathione that is covalently immobilized to the base matrix. The plasmid binding is then enabled via the zinc finger protein and a specific nucleotide sequence inserted into the DNA. At lower loadings, the binding of the DNA onto the Fractogel, Sepharose, and Streamline matrices was 0.0078 +/- 0.0013, 0.0095 +/- 0.0016, and 0.0080 +/- 0.0006 mg, respectively, to 50 microL of adsorbent. At a higher DNA challenge, the corresponding amounts were 0.0179 +/- 0.0043, 0.0219 +/- 0.0035, and 0.0190 +/- 0.0041 mg, respectively. The relatively constant amounts bound to the three adsorbents indicated that the large DNA molecule was unable to utilize the available zinc finger sites that were located in the internal pores and binding was largely a surface adsorption phenomenon. Utilization of the zinc finger binding sites was shown to be highest for the Fractogel adsorbent. The adsorbed material was eluted with reduced glutathione, and the eluted efficiency for the DNA was between 23% and 27%. The protein elution profile appeared to match the adsorption profiles with significantly higher recoveries of bound GST-zinc finger protein.     

Determination of conjugation rates on solid surfaces

A cytometric method for the estimation of end-point conjugation rates is developed and adapted to surface conjugation. This method improves the through-put of conjugation assays based on replica-plating and results in less noisy experimental data. Although conjugation on solid surfaces deviates from ideal conditions in which cells are continuously mixed, results show that, within the limits of high initial population densities and short mating times, end-point estimates of the conjugation rates are robust measurements. They are independent of the donor/recipient ratios and, to some extent, of the sampling time. Remixing the mating population in the course of a conjugation experiment results in a boost in the frequency of transconjugants.     

Mechanistic analysis on the effects of salt concentration and pH on protein adsorption onto a mixed-mode adsorbent with cation ligand

Streamline Direct HST is a new kind of mixed-mode adsorbent with cation exchange ligand, especially developed for the expanded bed adsorption process, which can capture target protein directly from the moderate ionic strength feedstock without the need of dilution or other additives. In this study, the isotherm adsorption behaviors and the isocratic retention factors of bovine serum albumin (BSA) on Streamline Direct HST were measured, and the corresponding adsorption mechanisms were also described. The results indicated that Streamline Direct HST shows the typical property of salt-independent adsorption and the maximum binding capacity of BSA occurs near the isoelectric point of BSA. When there are some amounts of electrostatic repulsion protein-adsorbent interactions, the multilayer adsorption could be found, and high salt concentration does not favor the adsorption of protein. A patch-controlled adsorption process and an oriented adsorption model are proposed for describing the adsorption behaviors under electrostatic repulsion condition.     

Determination of binding constant of transcription factor AP-1 and DNA. Application of inhibitors.

The equilibrium binding and association kinetics of the fos-jun dimer (basic and leucine zipper domain) to the AP-1 DNA were studied using a quantitative assay. The basic-region and leucine zipper (bZip) domain of c-fos was expressed as a fusion protein with glutathione S-transferase, and it was bound to glutathione-agarose. The GST-fused fos bZip region was allowed to form a heterodimer with the bZip domain of c-jun, to which radiolabeled AP-1 nucleotides were added. After thorough washing, the gel-bound radioactivity was counted. The binding and dissociation rate constants (k(1) and k-(1)) of the fos-jun dimer and DNA could be obtained from a time-course experiment. The association binding constant (K(1)) was determined using both a thermodynamic equation and kinetic parameters. Nordihydroguaiaretic acid (NDGA), momordin I, natural product inhibitors of the fos-jun/DNA complex formation, was applied to this jun-GST-fused fos system and it was found to decrease the apparent equilibrium binding of dimer and DNA. The thermodynamic constant of dimer and inhibitor binding was also determined.     

Determination of mutation rates in bacteriophage T4 by unneighborly base pairs: Genetic analysis

Earlier studies showed that the 2-aminopurine-induced mutation rate at a particular base pair can be influenced by the base adjacent to, or one additional base-pair removed from, the measured site (Koch, 1971). The present study extends to 0.3 map unit (about 30 base pairs) the distance at which a single base-pair substitution can exert such an effect. A particular base-pair substitution (defined as a ts mutation in the rIIA gene of bacteriophage T4) reduces the spontaneous, 2-aminopurine-induced and nitrous acid-induced reversions of an rIIA amber mutation approximately threefold. The ts mutation also reduces the 2-aminopurine-induced conversion of the corresponding ochre codon to amber (UAA → UAG) about twofold and to opal (UAA → UGA) about eightfold. The 2-aminopurine-induced reversion of the ochre codon to a glutamine codon (UAA → CAA), however, is not affected. Control experiments demonstrate that these observed reductions in mutation frequency do not result from unacceptable pathways of reversion in the presence of the ts allele.     

The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy

Conformational fluctuations of single-stranded DNA (ssDNA) oligonucleotides were studied in aqueous solution by monitoring contact-induced fluorescence quenching of the oxazine fluorophore MR121 by intrinsic guanosine residues (dG). We applied fluorescence correlation spectroscopy as well as steady-state and time-resolved fluorescence spectroscopy to analyze kinetics of DNA hairpin folding. We first characterized the reporter system by investigating bimolecular quenching interactions between MR121 and guanosine monophosphate in aqueous solution estimating rate constants, efficiency and stability for formation of quenched complexes. We then studied the kinetics of complex formation between MR121 and dG residues site-specifically incorporated in DNA hairpins. To uncover the initial steps of DNA hairpin folding we investigated complex formation in ssDNA carrying one or two complementary base pairs (dC–dG pairs) that could hybridize to form a short stem. Our data show that incorporation of a single dC–dG pair leads to non-exponential decays for opening and closing kinetics and reduces rate constants by one to two orders of magnitude. We found positive activation enthalpies independent of the number of dC–dG pairs. These results imply that the rate limiting step of DNA hairpin folding is not determined by loop dynamics, or by mismatches in the stem, but rather by interactions between stem and loop nucleotides.