Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
|---|
| gene sensors based on peptide nucleic acid (pna) probes: relationship between sensor sensitivity and probe/target duplex stability. | gene sensors based on peptide nucleic acid (pna) probes were prepared and the relationship between sensor sensitivity and the duplex stability of the probe pnas and target complementary dnas was studied using five synthesized pnas (10-, 15-, 17-, 20-, and 22-mers). it was found that the association constants for the probe pna/target dna pairs depend not only on the length but also on the base pair sequence, and that the trend in the sensor responses was the same as that in the association consta ... | 2005 | 16222367 |
| analysis of rna silencing in agroinfiltrated leaves of nicotiana benthamiana and nicotiana tabacum. | in this study we analyse several aspects of cytoplasmic rna silencing by agroinfiltration of dna constructs encoding single- and double-stranded rnas derived from a gfp transgene and from the endogenous virp1 gene. both types of inductors resulted after 2-4 days in much higher concentration of sirnas in the agroinfiltrated zone than normally seen during systemic silencing. more specifically, infiltration of two transgene hairpin constructs resulted in elevated levels of sirnas. however, differen ... | 2005 | 16244913 |
| recent highlights on photolithic oligonucleotide array in situ synthesis. | light directed synthesis of high-density oligonucleotide microarrays is currently performed using either ortho-nitro-benzyl-type [menpoc] (pease, a.c.; solas, d.; sullivan, e.j.; cronin, t.m.; holmes, c.p.; fodor, s.p.a. proc. natl. acad sci u.sa. 1994, 91, 6333.) or ortho-nitrophenylethyl-type [nppoc] (hasan, a.; stengele, k.p.; giegrich, h.; cornwell, p.; isham, k.r.; sachleben, r.a.; pfleiderer, w.; foote, r.s. tetrahedron 1997, 53, 424z) protecting groups as the 5'-o-carbonate ester of the p ... | 2005 | 16248056 |
| activation of natural killer-like yt-indy cells by oligodeoxynucleotides and binding by homologous pattern recognition proteins. | the present study was designed to examine the binding and signalling effects of single base and cpg dinucleotide phosphodiester (po) oligodeoxynucleotides (odn) on the human natural killer (nk)-like cell line (yt-indy). single base po odn composed of 20-mers of guanosine (dg20), adenosine (da20), cytosine (dc20) or thymidine (dt20) as well as 'conventional' po cpg odn were examined for their ability to bind and activate yt-indy cells. binding by dg20 and cpg odn to yt-indy cells was saturable an ... | 2005 | 16253123 |
| highly blue luminescent triazine-amine conjugated oligomers. | [reaction: see text]. the novel synthetic strategy and optical properties of highly fluorescent, triazine-amine conjugated oligomers are described herein. under basic conditions, aromatic dinitrile compounds, nc-c6h4-x-c6h4-cn (x = nme, o, ch2), underwent cyclic trimerization of the cyano groups at both ends to give a series of triazine-containing oligomers. the oligomers can be expressed as (2n + 1) mer, where n represents the number of triazine rings in the oligomer. the absorption maximum of ... | 2005 | 16268599 |
| gerstmann-sträussler-scheinker disease amyloid protein polymerizes according to the "dock-and-lock" model. | prion protein (prp) amyloid formation is a central feature of genetic and acquired prion diseases such as gerstmann-sträussler-scheinker disease (gss) and variant creutzfeldt-jakob disease. the major component of gss amyloid is a prp fragment spanning residues approximately 82-146, which when synthesized as a peptide, readily forms fibrils featuring gss amyloid. the present study employed surface plasmon resonance (spr) to characterize the binding events underlying prp82-146 oligomerization at t ... | 2006 | 16286452 |
| sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome. | we analyzed n-mers (n=3-8) in the local environment of 8,249,446 human snps and compared their distribution with that in the genome reference sequences. the results revealed that the short sequences, which contained at least one cpg dinucleotide, occurred more frequently in the local snp sequences than in the genome sequences. to exclude the hypermutability effect of the methylated cpg dinucleotides on the sequence context of snps, we examined the distribution patterns for each of the six catego ... | 2006 | 16314054 |
| sequence context analysis in the mouse genome: single nucleotide polymorphisms and cpg island sequences. | a genome-wide view of sequence mutability in mice is still limited, although biologists usually assume the same scenario for mice as for humans. in this study, we examined the sequence context in the local environment of 482,528 mouse single nucleotide polymorphisms (snps). we found that cpg-containing short sequences, in general, had more representation in the local sequences of snps compared to the genome sequences. the extent of this overrepresentation was stronger in mice than in humans, whi ... | 2006 | 16316740 |
| getting the right blood to the right patient: the contribution of near-miss event reporting and barrier analysis. | safety and reliability in blood transfusion are not static, but are dynamic non-events. since performance deviations continually occur in complex systems, their detection and correction must be accomplished over and over again. non-conformance must be detected early enough to allow for recovery or mitigation. near-miss events afford early detection of possible system weaknesses and provide an early chance at correction. national event reporting systems, both voluntary and involuntary, have begun ... | 2005 | 16316757 |
| a fast algorithm for the construction of universal footprinting templates in dna. | we introduce and give a complete description of a new graph to be used for dna sequencing questions. this graph has the advantage over the classical de bruijn graph that it fully accounts for the double stranded nature of dna, rather than dealing with single strands. technically, our graph may be thought of as the quotient of the de bruijn graph under the natural involution of sending a dna strand to its complementary strand. however, this involution has fixed points, and this complicates the st ... | 2006 | 16328479 |
| identification of gremmeniella abietina races with random amplified polymorphic dna markers. | seven random amplified polymorphic dna (rapd) markers amplified from four oligonucleotides (10-mers) by the polymerase chain reaction were used to distinguish between the north american and european races of gremmeniella abietina, the causal agent of scleroderris canker of conifers. forty-three isolates of the pathogen from 11 different host species originating from 11 countries, states, and provinces were tested; race designation was consistent with results from immunogenic and soluble-protein ... | 1993 | 16348951 |
| the discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. | we have developed several new methods to investigate transcriptional motifs in vertebrates. we developed a specific alignment tool appropriate for regions involved in transcription control, and exhaustively enumerated all possible 12-mers for involvement in transcription by virtue of their mammalian conservation. we then used deeper comparative analysis across vertebrates to identify the active instances of these motifs. we have shown experimentally in medaka fish that a subset of these predicti ... | 2005 | 16356267 |
| integrating genomic data to predict transcription factor binding. | transcription factor binding sites (tfbs) in gene promoter regions are often predicted by using position specific scoring matrices (pssms), which summarize sequence patterns of experimentally determined tf binding sites. although pssms are more reliable than simple consensus string matching in predicting a true binding site, they generally result in high numbers of false positive hits. this study attempts to reduce the number of false positive matches and generate new predictions by integrating ... | 2005 | 16362910 |
| structure and interaction in protein solutions as studied by small-angle neutron scattering. | small-angle neutron scattering (sans) measurements have been performed to compare the effect of the salts kf, kcl, and kbr on crystallization in aqueous solution of lysozyme protein. it is found that the propensity of the salt to crystallize protein follows the hoffmeister series (kf<kcl<kbr) with marked differences in the effect of these salts. in pure protein solution, lysozyme macromolecules are prolate ellipsoidal with semimajor and semiminor axes as 22 and 13.5 a, respectively. sans also gi ... | 2005 | 16383444 |
| nucleobase orientation and ordering in films of single-stranded dna on gold. | we demonstrate how the orientation and ordering of dna bases in ultrahigh vacuum (uhv) and ambient environments can be determined using complementary spectroscopic methods. near-edge x-ray absorption fine structure (nexafs) with fluorescence detection, x-ray photoelectron (xps), and fourier transform infrared (ftir) spectroscopies are used to quantify the coverage, chemical composition, orientation, and ordering of thymine bases in model self-assembled monolayers of thymine homo-oligonucleotides ... | 2006 | 16390092 |
| foldamer dynamics expressed via markov state models. i. explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water. | in this article, we analyze the folding dynamics of an all-atom model of a polyphenylacetylene (ppa) 12-mer in explicit solvent for four common organic and aqueous solvents: acetonitrile, chloroform, methanol, and water. the solvent quality has a dramatic effect on the time scales in which ppa 12-mers fold. acetonitrile was found to manifest ideal folding conditions as suggested by optimal folding times on the order of approximately 100-200 ns, depending on temperature. in contrast, chloroform a ... | 2005 | 16392592 |
| iwocs: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships. | lately the use of 16s-23s intergenic transcribed spacer (its) sequences for bacterial typing purposes has increased. the presence of conserved regions like trna genes or boxes together with hypervariable regions allows performing intraspecific discrimination of very close bacterial strains. on the other hand this mosaic of variability makes the its a sequence difficult to analyze and compare. | 2006 | 16403794 |
| tumor cells enhance their own cd44 cleavage and motility by generating hyaluronan fragments. | hyaluronan (ha) is an extracellular matrix glycosaminoglycan that interacts with cell-surface receptors, including cd44. although ha usually exists as a high molecular mass polymer, ha of a much lower molecular mass that shows a variety of biological activities can be detected under certain pathological conditions, particularly in tumors. we previously reported that low molecular weight has (lmw-has) of a certain size range induce the proteolytic cleavage of cd44 from the surface of tumor cells ... | 2006 | 16407205 |
| large-amplitude fast motions in double-stranded dna driven by solvent thermal fluctuations. | the nature of the internal dynamics of double-stranded dna in aqueous environment remains to be established. we consider the motions to stem from thermal fluctuations/dissipations of the harmonic modes of beads (bases and sugars) in a cylindrical geometry that are tracked through the stochastic langevin trajectories; these are characterized by parameters obtained from published data. the present approach has allowed a comparative study of the dynamics for dna lengths in the range of 20-600 base ... | 2006 | 16419073 |
| effect of estrogens on the interferon-gamma producing cell population of mouse splenocytes. | we examined the effect of 17beta-estradiol (e2) on the cytokine production by mouse splenocytes. the production of interferon-gamma (ifn-gamma) was enhanced by e2 stimulation. e2 increased the number of cells expressing ifn-gamma and the ifn-gamma mrna expression level in the cells. there were low- and high-level cells expressing ifn-gamma in the population. the natural killer (nk) cells and nkt cells were the low-level cells expressing ifn-gamma, and the number of these cells was increased by e ... | 2006 | 16428820 |
| substitution analog peptide derived from her-2 can efficiently induce her-2-specific, hla-a24 restricted ctls. | in order to broaden the possibility for anti-her-2/neu (her-2) immune targeting, it is important to identify hla-a24 restricted peptide epitopes derived from her-2, since hla-a24 is one of the most common alleles in japanese and asian people. in the present study, we have screened her-2-derived, hla-a24 binding peptides for cytotoxic t lymphocyte (ctl) epitopes. a panel of her-2-derived peptides with hla-a24 binding motifs and the corresponding analogs designed to enhance hla-a24 binding affinit ... | 2006 | 16435129 |
| group m-based hiv-1 gag peptides are frequently targeted by t cells in chronically infected us and zambian patients. | the enormous sequence diversity of hiv-1 has been a major obstacle in the development of a globally useful vaccine for aids. the consensus and ancestral sequence-based immunogens minimize the genetic distance between contemporary isolates and vaccine strains. hence these sequences may be promising candidates for hiv vaccines or serve as a universal reagent set for evaluating gag-specific responses. | 2006 | 16439868 |
| on optimizing distance-based similarity search for biological databases. | similarity search leveraging distance-based index structures is increasingly being used for both multimedia and biological database applications. we consider distance-based indexing for three important biological data types, protein k-mers with the metric pam model, dna k-mers with hamming distance and peptide fragmentation spectra with a pseudo-metric derived from cosine distance. to date, the primary driver of this research has been multimedia applications, where similarity functions are often ... | 2005 | 16447992 |
| profile-based string kernels for remote homology detection and motif extraction. | we introduce novel profile-based string kernels for use with support vector machines (svms) for the problems of protein classification and remote homology detection. these kernels use probabilistic profiles, such as those produced by the psi-blast algorithm, to define position-dependent mutation neighborhoods along protein sequences for inexact matching of k-length subsequences ("k-mers") in the data. by use of an efficient data structure, the kernels are fast to compute once the profiles have b ... | 2004 | 16448009 |
| dstho: database of sirnas targeted at human oncogenes: a statistical analysis. | existing treatments of human cancer, which is characterized by abnormal proliferation of cells often lead to fatal outcomes. sequence selective silencing of oncogene expression using sirna technology is emerging as a potential solution for cancer treatment. the exclusive selectivity and easy application to virtually any therapeutic target including intracellular factors and transcription factors renders sirna oligonucleotide applications very promising. however, synthesis of sirna having suffici ... | 2006 | 16448692 |
| simultaneous rapid chemical synthesis of over one hundred oligonucleotides on a microscale. | an inexpensive, extremely rapid manual method for simultaneous synthesis of large numbers of oligodeoxyribonucleotides on 50 or 150 nanomole scale is described. the oligonucleotides are assembled in parallel by the phosphotriester method on small cellulose paper disks in a simple gas pressure-controlled continuous-flow system. for each addition of a nucleotide the disks are sorted into four sets which are placed in four columns for addition of a, c, g and t, respectively. during one 2-week perio ... | 1984 | 16453516 |
| attenuation of skeletal muscle reperfusion injury with intravenous 12 amino acid peptides that bind to pathogenic igm. | the injury sustained by reperfused skeletal muscle is inflammatory and is initiated by binding of pre-formed igm to involved tissue, followed by local complement activation and further inflammation. a clone of natural igm has been described that initiates this injury, suggesting that specific antigens are exposed on ischemic tissues that act as ligands for this pathogenic antibody. in these experiments, we examine the properties of short peptide sequences, and their homologues, that bind to the ... | 2006 | 16455333 |
| exploring transcription factor binding properties of several non-coding dna sequence elements in the human nf-il6 gene. | we examined several dna segments upstream of the transcription start site of the human nf-il6 gene to evaluate the predictions of two computational models developed to identify potential regulatory elements in the non-coding regions of genes. one model, comparative genomics, is based on the hypothesis that functional regulatory sequences can be localized in alignments of genomic dna from several species. the other model is based on the hypothesis that protein-binding sites in genomic dna may inc ... | 2006 | 16458921 |
| acrylic/cyclodextrin hydrogels with enhanced drug loading and sustained release capability. | the influence of the proportion of acrylamidomethyl-gamma-cyclodextrin (gamma-cd-nma) on loading and release of the hydrophobic triamcinolone acetonide (ta) and the hydrophilic propranolol (pr) by acrylic acid hydrogels was evaluated. gamma-cd-nma was synthesized by condensation of gamma-cyclodextrin (gamma-cd) with n-(hydroxymethyl) acrylamide. hydrogels were prepared with gamma-cd-nma and sodium acrylate (3 m or 4 m), using n,n'-methylen(bisacrylamide) (bis) as cross-linker, by free radical po ... | 2006 | 16464549 |
| identification of naturally processed peptides bound to the class i mhc molecule h-2kd of normal and tap-deficient cells. | this report details the biochemical features of natural peptides selected by the h-2kd class i mhc molecule. in normal cell lines, the length of the naturally processed peptides ranged from 8 to 18 amino acids, although the majority were 9-mers (16% were longer than nine residues). the binding motif for the 9-mer peptides was dominated by the presence of a tyrosine at p2 and an isoleucine/leucine at the p9 position. the p2 residue contributed most towards binding; and the short peptides bound be ... | 2006 | 16479539 |
| site-bond percolation of polyatomic species. | a generalization of the classical monomer site-bond percolation problem is studied in which linear k-uples of nearest neighbor sites (site k-mers) and linear k-uples of nearest neighbor bonds (bond k-mers) are independently occupied at random on a square lattice. we called this model the site-bond percolation of polyatomic species or k-mer site-bond percolation. motivated by considerations of cluster connectivity, we have used two distinct schemes (denoted as s intersection of b and s union of b ... | 2005 | 16486032 |
| protein folding dynamics via quantification of kinematic energy landscape. | we study folding dynamics of proteinlike sequences on a square lattice using a physical move set that exhausts all possible conformational changes. by analytically solving the master equation, we follow the time-dependent probabilities of occupancy of all 802 075 conformations of 16 mers over 7 orders of time span. we find that (i) folding rates of these proteinlike sequences of the same length can differ by 4 orders of magnitude, (ii) folding rates of sequences of the same conformation can diff ... | 2006 | 16487000 |
| frequency of rna-rna interaction in a model of the rna world. | the rna world model for prebiotic evolution posits the selection of catalytic/template rnas from random populations. the mechanisms by which these random populations could be generated de novo are unclear. non-enzymatic and rna-catalyzed nucleic acid polymerizations are poorly processive, which means that the resulting short-chain rna population could contain only limited diversity. nonreciprocal recombination of smaller rnas provides an alternative mechanism for the assembly of larger species w ... | 2006 | 16495233 |
| characterization of t cell epitopes in alphas1-casein in cow's milk allergic, atopic and non-atopic children. | one to two percent of infants suffer from ige-mediated allergic reactions against cow's milk proteins. most children develop clinical tolerance, but approximately 15% are still allergic by the age of 10 years. little is known about the t cell epitopes in individual cow's milk protein in relation to allergy and tolerance. | 2006 | 16499640 |
| feasibility of supercritical fluid chromatography/mass spectrometry of polypeptides with up to 40-mers. | supercritical fluid chromatography (sfc) provides a number of advantages over traditional hplc such as speed, practical use of longer columns, a normal-phase retention mechanism, and reduced use of organic solvents. yet, it has been a technique traditionally limited to relatively nonpolar compounds. the nature of sfc mobile and stationary phases did not allow the elution of ionic compounds or of peptides, except, in the latter case, for the most hydrophobic peptides. the characterization of pept ... | 2006 | 16503605 |
| crystallization and preliminary x-ray characterization of a ferritin from the hyperthermophilic archaeon and anaerobe pyrococcus furiosus. | crystals of the title protein have been produced and preliminary structural analysis has been carried out. the crystals belong to the orthorhombic space group c222(1), with unit-cell parameters a = 258.1, b = 340.1, c = 266.5 a. the protein forms a 24-mer of 20 kda subunits, which assemble with 432 non-crystallographic symmetry. a total of 36 monomers are found in the asymmetric unit, corresponding to one and a half 24-mers. | 2005 | 16511080 |
| selection of peptide inhibitors against the pseudomonas aeruginosa murd cell wall enzyme. | the purified pseudomonas aeruginosa cell wall biosynthesis murd amide ligase enzyme was used to screen c-7-c and 12 mers peptides from phage display libraries using competitive biopanning approaches with the specific substrates d-glutamate and atp. from the 60 phage-encoded peptides identified, dna was sequenced, deduced amino acid sequences aligned and two peptides were synthesized from consensus sequences identified. the udp-n-acetylmuramyl-l-alanine murd substrate was synthesized, purified an ... | 2006 | 16517013 |
| plasmid size up to 20 kbp does not limit effective in vivo lung gene transfer using compacted dna nanoparticles. | nanoparticles consisting of single molecules of dna condensed with polyethylene glycol-substituted lysine 30-mers efficiently transfect lung epithelium following intrapulmonary administration. nanoparticles formulated with lysine polymers having different counterions at the time of dna mixing have distinct geometric shapes: trifluoroacetate or acetate counterions produce ellipsoids or rods, respectively. based on intracytoplasmic microinjection studies, nanoparticle ellipsoids having a minimum d ... | 2006 | 16525478 |
| poly(adp-ribose) glycohydrolase silencing protects against h2o2-induced cell death. | par [poly(adp-ribose)] is a structural and regulatory component of multiprotein complexes in eukaryotic cells. par catabolism is accelerated under genotoxic stress conditions and this is largely attributable to the activity of a parg (par glycohydrolase). to overcome the early embryonic lethality of parg-knockout mice and gain more insights into the biological functions of parg, we used an rna interference approach. we found that as little as 10% of parg protein is sufficient to ensure basic cel ... | 2006 | 16526943 |
| evaluation of synthetic oligonucleotides as inhibitors of west nile virus replication. | a series of synthetic oligonucleotide phosphorothioate 15-mers were generated against specific sequences in the west nile virus rna genome. these antisense oligonucleotides targeted (1) conserved features of the west nile virus rna genome that may be expected to lead to inhibition of virus replication since such features play essential roles in the virus lifecycle; (2) g-quartet oligonucleotides with potential facilitated uptake properties and that also targeted conserved sequences among a range ... | 2006 | 16540182 |
| computer modeling demonstrates that electrostatic attraction of nucleosomal dna is mediated by histone tails. | we conducted molecular dynamics computer simulations of charged histone tail-dna interactions in systems mimicking nucleosome core particles (ncp) . in a coarse-grained model, the ncp is modeled as a negatively charged spherical particle with flexible polycationic histone tails attached to it in a dielectric continuum with explicit mobile counterions and added salt. the size, charge, and distribution of the tails relative to the core were built to mimick real ncp. in this way, we incorporate att ... | 2006 | 16565063 |
| dna hybridization detection on electrical microarrays using coulostatic pulse technique. | we demonstrated a novel application of transient coulostatic pulse technique for the detection of label free dna hybridization on nm-sized gold interdigitated ultramicroelectrode arrays (au-ida) made in silicon technology. the array consists of eight different positions with an au-ida pair at each position arranged on the si-based biochip. immobilization of capture probes onto the au-ida was accomplished by self-assembling of thiol-modified oligonucleotides. target hybridization was indicated by ... | 2006 | 16574397 |
| kinetic characterization of recombinant human acidic mammalian chitinase. | human acidic mammalian chitinase (amcase), a member of the family 18 glycosyl hydrolases, is one of the important proteins involved in th2-mediated inflammation and has been implicated in asthma and allergic diseases. inhibition of amcase results in decreased airway inflammation and airway hyper-responsiveness in a mouse asthma model, suggesting that the amcase activity is a part of the mechanism of th2 cytokine-driven inflammatory response in asthma. in this paper, we report the first detailed ... | 2006 | 16584180 |
| application of aptamers in therapeutics and for small-molecule detection. | nucleic acids that can bind with high affinity and specificity to target molecules are called "apta mers". aptamers recognise a large variety of different molecule classes. the main focus of this chapter is small molecules as targets. aptamers are applied complementarily to antibody technologies and can substitute antibodies or small molecules wherever their different properties, such as biochemical nature or highly discriminating capacities, are advantageous. examples of promising applications ... | 2006 | 16594625 |
| differentiation of escherichia coli pathotypes by oligonucleotide spotted array. | to accurately determine the pathotypes of escherichia coli strains, a comprehensive assessment of each strain that targets multiple genes is required. a new approach to the identification and characterization of e. coli pathotypes was developed by constructing gene-specific probes (70-mers) for not only the virulence genes associated with each e. coli pathotype but also the o157-, cft073-, and k-12-specific and common genes of each pathotype. analysis of oligonucleotide probes with reference and ... | 2006 | 16597882 |
| immobilization and afm of single 4 x 6-mer tarantula hemocyanin molecules. | the high molecular mass respiratory protein of the tarantula eurypelma californicum, a 4 x 6-mer hemocyanin, was investigated by atomic force microscopy (afm). various substrates and methods were evaluated for immobilization of individual hemocyanin molecules on a solid surface. samples were imaged after physisorption on mica and self-assembled monolayers, and after chemisorption on au(111) and n-hydroxy-succinimide (nhs) functionalized surfaces. afm measurements were carried out preferable in s ... | 2006 | 16632369 |
| cytotoxicity of albebetin oligomers depends on cross-beta-sheet formation. | prefibrillar cytotoxicity was suggested as a common amyloid characteristic. we showed two types of albebetin prefibrillar oligomers are formed during incubation at ph 7.3. initial round-shaped oligomers consist of 10-15 molecules determined by atomic force microscopy, do not bind thioflavin-t and do not affect viability of granular neurons and sh-sy5y cells. they are converted into ca. 30-40-mers possessing cross-beta-sheet and reducing viability of neuronal cells. neither monomers nor fibrils p ... | 2006 | 16638570 |
| dna and rna as new binding targets of green tea catechins. | the significance of catechins, the main constituent of green tea, is being increasingly recognized with regard to cancer prevention. catechins have been studied for interactions with various proteins, but the mechanisms of the various catechins are not yet elucidated. based on our previous observation that nucleic acids extracted from catechin-treated cells are colored, we studied whether catechins directly interact with nucleic acids using surface plasmon resonance assay (biacore) and cold spra ... | 2006 | 16641087 |
| polyribosomes from peas: ii. polyribosome metabolism during normal and hormone-induced growth. | polyribosomes as large as 10-mers (strands of messenger rna bearing 10 ribosomes) were isolated from etiolated pea (pisum sativum l. var. alaska) stem tissue during all stages of development when methods were used which essentially eliminated ribonuclease activity during extraction. actively growing tissue, harvested from the apical 10 mm, yielded many large polyribosomes and a low (<20%) proportion of monosomes. similar tissue, allowed to age by applying lanolin to decapitated apices, showed a ... | 1973 | 16658559 |
| differential repression of alternative transcripts: a screen for mirna targets. | alternative polyadenylation sites produce transcript isoforms with 3' untranslated regions (utrs) of different lengths. if a microrna (mirna) target is present in the utr, then only those target-containing isoforms should be sensitive to control by a cognate mirna. we carried out a systematic examination of 3' utrs containing multiple poly(a) sites and putative mirna targets. based on expressed sequence tag (est) counts and est library information, we observed that levels of isoforms containing ... | 2006 | 16699595 |
| olanzapine treatment is associated with reduced high molecular weight adiponectin in serum: a potential mechanism for olanzapine-induced insulin resistance in patients with schizophrenia. | treatment of schizophrenia with olanzapine and other atypical antipsychotic agents is associated with insulin resistance and diabetes mellitus. the mechanism for this is not understood. adiponectin is an insulin-sensitizing cytokine secreted by adipocytes. it is present in serum in multimers of varying size. trimers and hexamers are referred to as low molecular weight (lmw) adiponectin. larger multimers (12-, 18-, and 24-mers) have been designated high molecular weight (hmw) adiponectin and seem ... | 2006 | 16702887 |
| a technique for minimally altering anatomically based subthalamic electrode targeting by microelectrode recording. | implantation of a subthalamic nucleus (stn) deep brain stimulation (dbs) electrode is increasingly recognized as an effective treatment for advanced parkinson disease (pd). despite widespread use of microelectrode recording (mer) to delineate the boundaries of the stn prior to stimulator implantation, it remains unclear to what extent mer improves the clinical efficacy of this procedure. in this report, the authors analyze a series of patients who were treated at one surgical center to determine ... | 2006 | 16711665 |
| intron gain and loss in segmentally duplicated genes in rice. | introns are under less selection pressure than exons, and consequently, intronic sequences have a higher rate of gain and loss than exons. in a number of plant species, a large portion of the genome has been segmentally duplicated, giving rise to a large set of duplicated genes. the recent completion of the rice genome in which segmental duplication has been documented has allowed us to investigate intron evolution within rice, a diploid monocotyledonous species. | 2006 | 16719932 |
| intermediate amyloid oligomers of lysozyme: is their cytotoxicity a particular case or general rule for amyloid? | in the current study we investigated the molecular mechanisms of cytotoxicity of amyloid oligomers of horse milk lysozyme. we have shown that lysozyme forms soluble amyloid oligomers and protofibrils during incubation at ph 2.0 and 4.5 and 57 degrees c. these structures bind the amyloid-specific dyes thioflavin t and congo red, and their morphology and size were analyzed by atomic force microscopy. monomeric lysozyme and its fibrils did not affect the viability of three cell types used in our ex ... | 2006 | 16732728 |
| unrestricted hybridization of oligonucleotides to structure-free dna. | the existence of secondary structure in long single-stranded dna and rna is a serious obstacle to the practical use of short oligonucleotide probes (<20-mers). here, we show that replication of a highly structured dna in the presence of a unique set of dntp analogues leads to synthesis of daughter dna with a significantly reduced level of secondary structure. this replicated dna, composed of 2-aminoadenine, 2-thiothymine, 7-deazaguanine, and cytosine bases, was readily accessible to tiled 8-mer ... | 2006 | 16734433 |
| thermal decomposition of multiply charged t-rich oligonucleotide anions in the gas phase. influence of internal solvation on the arrhenius parameters for neutral base loss. | arrhenius activation parameters (e(a), a) for the loss of neutral nucleobases from a series of t-rich, doubly and triply deprotonated 15- and 20-mer oligodeoxynucleotides (odn) containing a single reactive base (x = a or c) with the sequence, xt14, xt19 and t19x, have been determined using the blackbody infrared radiative dissociation technique. the a-containing anions are significantly more reactive (> or =3000 times) than the c-containing ions over the temperature range investigated. important ... | 2006 | 16782356 |
| robust expansion of viral antigen-specific cd4+ and cd8+ t cells for adoptive t cell therapy using gene-modified activated t cells as antigen presenting cells. | cytomegalovirus (cmv) reactivation after stem cell transplantation can be treated with cmv-specific t cells, but current in vitro techniques using dendritic cells as antigen-presenting cells are time-consuming and expensive. to simplify the production of clinical grade cmv-specific t cells, we evaluated gene-modified activated t cells [antigen presenting t cells (t-apcs)] as a reliable and easily produced source of apcs to boost cd4+ and cd8+ t-cell responses against the immunodominant cmv antig ... | 2006 | 16799339 |
| heparan sulfate-related oligosaccharides in ternary complex formation with fibroblast growth factors 1 and 2 and their receptors. | biosynthesis of heparan sulfate (hs) is strictly regulated to yield products with cell/tissue-specific composition. interactions between hs and a variety of proteins, including growth factors and morphogens, are essential for embryonic development and for homeostasis in the adult. fibroblast growth factors (fgfs) and their various receptors (frs) form ternary complexes with hs, as required for receptor signaling. libraries of hs-related, radiolabeled oligosaccharides were generated by chemo-enzy ... | 2006 | 16807244 |
| maldi analysis of oligonucleotides directly from montmorillonite. | oligonucleotides synthesized on a montmorillonite catalyst were analyzed directly. by mixing the catalyst with a matrix (2,4,6-trihydroxyacetophenone or 6-aza-2-thiothymine) and dibasic ammonium citrate, higher molecular weight products were detected compared with "classical" methods such as gel electrophoresis and hplc with uv as a detector. the oligomers (30-mers and higher) were detected by mass spectrometry even though their concentration was less than 10(-4)% of the total content of the rna ... | 2006 | 16809045 |
| single-based resolution for oligodeoxynucleotides and their phosphorothioate modifications by replaceable capillary gel electrophoresis. | a replaceable capillary gel electrophoretic (replaceable cge) method was developed for the separation of two sets of model compounds of single-stranded oligodeoxynucleotide mixtures (18-20 mers), phosphodiester oligodeoxynucleotides (po-odns) and their phosphorothioate modifications (ps-odns), with equal sequences differing in a single base. polyethylene glycol (peg) 35000 was chosen as the sieving matrix. it was confirmed that peg polymer solution less influenced resolutions of the ps-odns comp ... | 2006 | 16809077 |
| interactions of cationic ligands and proteins with small nucleic acids: analytic treatment of the large coulombic end effect on binding free energy as a function of salt concentration. | for nonspecific binding of oligopeptides and other cationic ligands, including proteins, to nucleic acid oligomers, we develop a model capable of quantifying and predicting the salt concentration dependence of the binding free energy (deltag(o)obs) by way of an analytic treatment of the coulombic end effect (cee). ligands, nucleic acids, and their complexes (species j of valence zj) are modeled as finite lattices with absolute value(zj) charged residues; the cee is quantified by its characterist ... | 2006 | 16819840 |
| one-step, regioselective synthesis of up to 50-mers of rna oligomers by montmorillonite catalysis. | 5'-nucleotides of a and u with the phosphate activated with 1-methyladenine generate rna oligomers containing 40-50 monomers in 1 day in reactions catalyzed by montmorillonite. the corresponding monomers of c give oligomers that are 20-25-mers in length after a 9-day reaction. it was not possible to determine the chain lengths of the oligomers of g since they did not give well-defined bands on gel electrophoresis. co-oligomers of a and u as well as a, u, g, and c were also prepared. the oligo(a) ... | 2006 | 16819887 |
| comparative genomics of drosophila and human core promoters. | the core promoter region plays a critical role in the regulation of eukaryotic gene expression. we have determined the non-random distribution of dna sequences relative to the transcriptional start site in drosophila melanogaster promoters to identify sequences that may be biologically significant. we compare these results with those obtained for human promoters. | 2006 | 16827941 |
| rna interference in vitro and in vivo using a novel chitosan/sirna nanoparticle system. | this work introduces a novel chitosan-based sirna nanoparticle delivery system for rna interference in vitro and in vivo. the formation of interpolyelectrolyte complexes between sirna duplexes (21-mers) and chitosan polymer into nanoparticles, ranging from 40 to 600 nm, was shown using atomic force microscopy and photon correlation spectroscopy. rapid uptake (1 h) of cy5-labeled nanoparticles into nih 3t3 cells, followed by accumulation over a 24 h period, was visualized using fluorescence micro ... | 2006 | 16829204 |
| remote homology detection based on oligomer distances. | remote homology detection is among the most intensively researched problems in bioinformatics. currently discriminative approaches, especially kernel-based methods, provide the most accurate results. however, kernel methods also show several drawbacks: in many cases prediction of new sequences is computationally expensive, often kernels lack an interpretable model for analysis of characteristic sequence features, and finally most approaches make use of so-called hyperparameters which complicate ... | 2006 | 16837522 |
| interpolated variable order motifs for identification of horizontally acquired dna: revisiting the salmonella pathogenicity islands. | there is a growing literature on the detection of horizontal gene transfer (hgt) events by means of parametric, non-comparative methods. such approaches rely only on sequence information and utilize different low and high order indices to capture compositional deviation from the genome backbone; the superiority of the latter over the former has been shown elsewhere. however even high order k-mers may be poor estimators of hgt, when insufficient information is available, e.g. in short sliding win ... | 2006 | 16837528 |
| critical factors in the development of fluorescence polarization-based peptide binding assays: an equilibrium study monitoring specific peptide binding to soluble hla-a*0201. | there is currently a significant interest in the identification and validation of hla-restricted ctl epitopes, which are thought to have important implications for the development of preventive and/or therapeutic applications in bacterial or viral infections, autoimmune diseases, and cancer. to better facilitate epitope discovery and validation, we present a cell- and radioisotope-free hla-a*0201 assay system which relies upon fluorescence polarization. the assay has the advantage of allowing re ... | 2006 | 16844138 |
| effect of the range of interactions on the properties of fluids. 2. structure and phase behavior of acetonitrile, hydrogen fluoride, and formic acid. | to complete the study on the effect of the long-range part of coulombic interactions on properties of complex polar and associating fluids, we have investigated in detail three compounds with extreme features: acetonitrile for its unusually large dipole moment, hydrogen fluoride with very strong hydrogen bonding, and formic acid for its potential formation of different n-mers in liquid and gaseous phases. the effect of the long-range coulombic interactions on both the structure and thermodynamic ... | 2005 | 16852173 |
| long-lived conformational isomerism of protein dimers: the role of the free energy of subunit association. | the association of protein subunits to form n-mers (n >or= 3) does not follow the dependence on the law of mass action predicted by the classical thermodynamic description used for the equilibrium of association of small molecules. for those anomalous cases, a so-called deterministic model has been previously proposed. the latter model was based on the empirical observation that the dynamics of subunit exchange between protein oligomers can be very slow, leading to the existence of long-lived co ... | 2006 | 16861278 |
| motifcut: regulatory motifs finding with maximum density subgraphs. | dna motif finding is one of the core problems in computational biology, for which several probabilistic and discrete approaches have been developed. most existing methods formulate motif finding as an intractable optimization problem and rely either on expectation maximization (em) or on local heuristic searches. another challenge is the choice of motif model: simpler models such as the position-specific scoring matrix (pssm) impose biologically unrealistic assumptions such as independence of th ... | 2006 | 16873465 |
| efficient identification of dna hybridization partners in a sequence database. | the specific hybridization of complementary dna molecules underlies many widely used molecular biology assays, including the polymerase chain reaction and various types of microarray analysis. in order for such an assay to work well, the primer or probe must bind to its intended target, without also binding to additional sequences in the reaction mixture. for any given probe or primer, potential non-specific binding partners can be identified using state-of-the-art models of dna binding stabilit ... | 2006 | 16873493 |
| a database of 9-mers from promoter regions of human protein-coding genes. | discovery of lexical characteristics of specific sequence motifs in human genomic dna can help with predicting and classifying regulatory cis elements according to the genes they control. in lexical models, some "words" may serve as downstream targets of signaling systems, whereas other "words" may specify sequences that selectively control the expression of a subset of genes to produce the various cell types and tissues. to discover lexical features of potential regulatory "words," we have crea ... | 2006 | 16888355 |
| a program toolkit for the analysis of regulatory regions of genes. | a major challenge in systems biology is to discover and reconstruct the cis-regulatory networks through which the expression of genes is controlled. even though a variety of sequences have been shown to interact with the transcription factors that bind dna, extensive work is needed to discover and classify regulatory "codes" and to elucidate the role played by the sequence context of genomic dna in the regulation of genes. databases of sequence elements extracted from regulatory regions may faci ... | 2006 | 16888356 |
| interpreting oligonucleotide microarray data to determine rna secondary structure: application to the 3' end of bombyx mori r2 rna. | a method to deduce rna secondary structure on the basis of data from microarrays of 2'-o-methyl rna 9-mers immobilized in agarose film on glass slides is tested with a 249 nucleotide rna from the 3' end of the r2 retrotransposon from bombyx mori. various algorithms incorporating binding data and free-energy minimization calculations were compared for interpreting the data to provide possible secondary structures. two different methods give structures with 100 and 87% of the base pairs determined ... | 2006 | 16893182 |
| elastogenic effects of exogenous hyaluronan oligosaccharides on vascular smooth muscle cells. | prior studies suggest that hyaluronan (ha), a glycosaminoglycan, may upregulate innately poor elastin matrix synthesis by adult vascular smooth muscle cells (smcs). ha scaffolds could thus be useful to regenerate damaged vascular elastin. in an earlier study, we established that the elastogenic effects of non-oligomeric ha are fragment size- and/or dose-specific. we currently investigate the pro-elastogenic effects of exogenous ha oligomers on rat aortic smooth muscle cells (rasmcs). rasmcs were ... | 2006 | 16899292 |
| total carbo-mer of benzene, its carbo-trannulene form, and the zigzag nanotube thereof. | the total carbo-mer of benzene, hexaethynyl carbo-benzene c30h6, has been calculated at the b3pw91/6-31g** level. its geometrical and magnetic characteristics are compared with those of the c18h6 partial carbo-mers, unsubstituted carbo-benzene, and hexaethynylbenzene. the carbo-[6]trannulene isomer is found to exist as a minimum on the singlet spin state potential energy surface (pes) and is 65.6 kcal.mol(-1) higher in energy than hexaethynyl-carbo-benzene. in the former, a strong cyclic electro ... | 2006 | 16901111 |
| antisense inhibition of rnase p: mechanistic aspects and application to live bacteria. | we explored bacterial rnase p as a drug target using antisense oligomers against the p15 loop region of escherichia coli rnase p rna. an rna 14-mer, or locked nucleic acid (lna) and peptide nucleic acid (pna) versions thereof, disrupted local secondary structure in the catalytic core, forming hybrid duplexes over their entire length. binding of the pna and lna 14-mers to rnase p rna in vitro was essentially irreversible and even resisted denaturing page. association rates for the rna, lna, and p ... | 2006 | 16901906 |
| dna stability in the gas versus solution phases: a systematic study of thirty-one duplexes with varying length, sequence, and charge level. | we report herein a systematic mass spectrometric study of a series of thirty-one non-self-complementary, matched, dna duplexes ranging in size from 5- to 12-mers. the purpose of this work is threefold: (1) to establish the viability of using mass spectrometry as a tool for examining solution phase stabilities of dna duplexes; (2) to systematically assess gas-phase stabilities of dna duplexes; and (3) to compare gas and solution phase stabilities in an effort to understand how media affects dna s ... | 2006 | 16914323 |
| synthesis and pairing properties of alpha-tricyclo-dna. | we describe the synthesis of the phosphoramidite building blocks of alpha-tricyclo-dna (alpha-tc-dna) covering all four natural bases, starting from the already known corresponding alpha-tc-nucleosides. these building blocks were used for the preparation of three alpha-tc-oligonucleotide 10-mers representing a homopurine, a homopyrimidine, and a mixed purine/pyrimidine base sequence. the base-pairing properties with complementary parallel and antiparallel oriented dna and rna were studied by uv- ... | 2006 | 16915595 |
| effect of electrostatic interactions on binding and retention of dna oligomers to pna liposomes assessed by fret measurements. | a fret-based method is used to observe the desorption of di-alkyl peptide nucleic acid amphiphiles (pnaa) from liposomes occurring on binding of complementary dna oligomers. pna liposomes were prepared containing fluorescein-labeled pnaa and rhodamine-labeled dipalmitoylphosphoethanolamine (dppe). these liposomes showed efficient energy transfer from the fluorescein to rhodamine, with an average donor-to-acceptor distance of 5.91nm. in low-ionic-strength buffer (50mm tris-hcl, ph 8.0), the fret ... | 2006 | 16934441 |
| scaling and the smoluchowski equations. | the smoluchowski equations, which describe coalescence growth, take into account combination reactions between a j-mer and a k-mer to form a (j+k)-mer, but not breakup of larger clusters to smaller ones. all combination reactions are assumed to be second order, with rate constants k(jk). the k(jk) are said to scale if k(lambda j,gamma k) = lambda(mu)gamma(nu)k(jk) for j < or = k. it can then be shown that, for large k, the number density or population of k-mers is given by ak(a)e(-bk), where a i ... | 2006 | 16942336 |
| determinants for prediction of malignant potential by metalloproteinase:e-cadherin ratio in prostate core needle biopsy. | according to a good correlation between in situ hybridization-based metalloproteinase-2/9:e-cadherin ratio (mer) and the pathological stage of prostate cancer, we set the cutoff line of mer at 6.0 (mer>6) to distinguish between organ-confined (pt2) and advanced diseases (pt3a-b/n1). in this study, we looked at the factors affecting mer and leading to a misprediction of the pathological stage. we examined mer in 39 paired specimens of prostate core needle biopsy and prostatectomy from the same pa ... | 2006 | 16943690 |
| selection of cc chemokine receptor 5-binding peptide from a phage display peptide library. | human cc chemokine receptor (ccr) 5 is a g protein-coupled receptor involved in a broad range of human diseases that mediates hiv-1 viral entry into cells. certain small molecule receptor antagonists to ccr5 have been useful in therapy for these diseases. in this study, ccr5-expressing cho cells (cho/ccr5 cells) were used to select ccr5-binding peptides from a phage-displayed 12-mers peptide library. all of the 30 clones selected from the library showed specific binding to cho/ccr5 cells by enzy ... | 2006 | 16960395 |
| serum ige reactive against small myelin protein-derived peptides is increased in multiple sclerosis patients. | though independent findings suggest roles for the allergic arm of the immune system and myelin-reactive antibodies in ms, myelin-reactive ige has not been investigated. we have developed a radioimmunoassay that measures reactive ige, igg and iga against short (5-6-mers) myelin protein-derived peptides bearing little to no sequence identity with other human proteins, and which might therefore be targets of a cns-specific autoimmune attack. here we show that, irrespective of clinical subtype, ms p ... | 2006 | 16996143 |
| compact, universal dna microarrays to comprehensively determine transcription-factor binding site specificities. | transcription factors (tfs) interact with specific dna regulatory sequences to control gene expression throughout myriad cellular processes. however, the dna binding specificities of only a small fraction of tfs are sufficiently characterized to predict the sequences that they can and cannot bind. we present a maximally compact, synthetic dna sequence design for protein binding microarray (pbm) experiments that represents all possible dna sequence variants of a given length k (that is, all 'k-me ... | 2006 | 16998473 |
| detection of oligosaccharide ligands for hepatocyte growth factor/scatter factor (hgf/sf), keratinocyte growth factor (kgf/fgf-7), rantes and heparin cofactor ii by neoglycolipid microarrays of glycosaminoglycan-derived oligosaccharide fragments. | neoglycolipid technology is eminently adaptable for microarray design for high-throughput detection and specificity assignments of carbohydrate-protein interactions. dermatan sulfate (ds) is known to play an important role because of its ability to bind growth factors as well as chemokines and to modulate their biological activities during inflammation and response to injury. we prepared various iduronic acid-rich fragments from ds by complete digestion with chondroitinase aci, and investigated ... | 2006 | 17006643 |
| genetic variation in opisthorchis viverrini (trematoda: opisthorchiidae) from northeast thailand and laos pdr based on random amplified polymorphic dna analyses. | genetic variation in opisthorchis viverrini adults originating from different locations in northeast thailand and laos, people's democratic republic (pdr), was examined using random amplified polymorphic dna (rapd) analyses. in an initial analysis, the genomic dna of one fluke from each of ten localities was amplified using 15 random primers (10-mers); however, genetic variation among o. viverrini specimens was detected reliably for only four primers. a more detailed rapd analysis using these fo ... | 2007 | 17016722 |
| structural characterization of beta-sheeted oligomers formed on the pathway of oxidative prion protein aggregation in vitro. | the pathology of transmissible spongiform encephalopathies (tses) is strongly associated with the structural conversion of the cellular prion protein (prpc) into a misfolded isoform (prpsc) that assembles into amyloid fibrils. since increased levels of oxidative stress have been linked to prion diseases, we investigated the metal-induced oxidation of human prp (90-231). a novel in vitro conversion assay based on aerobic incubation of prp in the presence of elemental copper pellets at ph 5 was es ... | 2007 | 17023178 |
| a peptide inhibitor of mura udp-n-acetylglucosamine enolpyruvyl transferase: the first committed step in peptidoglycan biosynthesis. | the mura enzyme from pseudomonas aeruginosa was purified to homogeneity and found to be biologically active as a udp-n-acetylglucosamine (unag) enolpyruvyl transferase in a coupled enzyme assay where atpase activity was measured by the release of inorganic phosphate. a microtiter plate assay coupled to competitive biopanning using the udp-n-acetylglucosamine was used to screen 10(9) c-7-c and 12-mers peptides from phage display libraries. from 60 phage-encoded peptides identified after the fourt ... | 2006 | 17030076 |
| a graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites. | given a set of known binding sites for a specific transcription factor, it is possible to build a model of the transcription factor binding site, usually called a motif model, and use this model to search for other sites that bind the same transcription factor. typically, this search is performed using a position-specific scoring matrix (pssm), also known as a position weight matrix. in this paper we analyze a set of eukaryotic transcription factor binding sites and show that there is extensive ... | 2006 | 17041233 |
| array-based identification of species of the genera abiotrophia, enterococcus, granulicatella, and streptococcus. | some species of enterococci and streptococci are difficult to differentiate by phenotypic traits. the feasibility of using an oligonucleotide array for identification of 11 viridans group streptococci was previously established. the aim of this study was to expand the array to identify species of abiotrophia (1 species), enterococcus (18 species), granulicatella (3 species), and streptococcus (31 species and 6 subspecies). the method consisted of pcr amplification of the ribosomal dna intergenic ... | 2006 | 17065265 |
| interactions of bovine serum albumin with aluminum polyoxocations and aluminum hydroxide. | interactions of aqueous solutions of aluminum polyoxocations (al13-mers and al30-mers) and aluminum hydroxide suspensions of varying particle sizes (26, 55, and 82 nm) with a model protein, bovine serum albumin (bsa), have been investigated using potentiometry, conductometry, viscometry, 27al solution nmr, uv-vis spectroscopy, dynamic light scattering, zeta-potential measurements, thermogravimetry, x-ray diffraction, and scanning electron microscopy. increasing amounts of bsa partially convert a ... | 2006 | 17107003 |
| chemoenzymatic synthesis of stable isotope labeled udp-n-[2h]-acetyl-glucosamine and [2h]-acetyl-chitooligosaccharides. | labeled udp-glcnac and chitooligosaccharides should be powerful tools for studies of n-acetylglucosaminyltransferase such as chitin synthases. we describe here a rapid, inexpensive and a common strategie for the chemoenzymatic synthesis of uridine 5'-diphospho-n-[(2)h]-acetyl-glucosamine and the chemical preparation of n-[(2)h]-acetyl chitooligosaccharides (from 2 to 5 mers). deuterated udp-glcnac analogue was tested as chitin synthase substrate and it exhibited an incorporation level in chitin ... | 2006 | 17123165 |
| percolation of polyatomic species with the presence of impurities. | in this paper, the percolation of (a) linear segments of size k and (b) k-mers of different structures and forms deposited on a square lattice contaminated with previously adsorbed impurities have been studied. the contaminated or diluted lattice is built by randomly selecting a fraction of the elements of the lattice (either bonds or sites) which are considered forbidden for deposition. results are obtained by extensive use of finite size scaling theory. thus, in order to test the universality ... | 2006 | 17144718 |
| statistical mechanics of dna-mediated colloidal aggregation. | we present a statistical mechanical model of aggregation in colloidal systems with dna-mediated interactions. we obtain a general result for the two-particle binding energy in terms of the hybridization free energy deltag of dna and two model-dependent properties: the average number of available dna bridges <n> and the effective dna concentration c(eff). we calculate these parameters for a particular dna bridging scheme. the fraction of all the n-mers, including the infinite aggregate, are shown ... | 2006 | 17155058 |
| filling of the one-dimensional lattice by k-mers proceeds via fast power-law-like kinetics. | during the filling of a one-dimensional lattice by k-site-long hard particles, we find that after initial "jamming" a power-law-like decay of the density of interparticle gaps occurs, described by a much larger exponent than that expected from mean-field theory. we show that this effect dominates post-jamming filling for large k and should be observable, e.g., during the binding of proteins along a long, stretched dna molecule. | 2006 | 17155065 |
| selectivity of montmorillonite catalyzed prebiotic reactions of d, l-nucleotides. | the montmorillonite-catalyzed reactions of the 5'-phosphorimidazolides of d, l-adenosine (d, l-impa) (figure 1a. n = a, r = h) and d, l-uridine (figure 1a., n = u, r = h) yields oligomers that were as long as 7 mers and 6 mers, respectively. the reactions of dilute solutions of d-impa and d-impu under the same conditions gave oligomers as long as 9 and 8 mers respectively. this demonstrated that oligomer formation is only partially inhibited by incorporation of both the d- and l-enantiomers. the ... | 2007 | 17160436 |
| from macrocyclic oligo-acetylenes to aromatic ring carbo-mers. | 2006 | 17165690 | |
| antitumor effects of cationic synthetic peptides derived from lys49 phospholipase a2 homologues of snake venoms. | the effects of two cationic synthetic peptides, derived from the c-terminal region of lys49 phospholipase a2 homologues from snake venoms, upon various murine tumor cell lines (b16 melanoma, emt6 mammary carcinoma, s-180 sarcoma, p3x myeloma, tend endothelial cells) were evaluated. the peptides are 13-mers derived from agkistrodon piscivorus piscivorus lys49 pla2 (p-appk: kkykayfklkckk) and bothrops asper lys49 myotoxin ii (pem-2[d]: kkwrwwlkalakk), respectively, in the latter case with slight m ... | 2007 | 17178238 |
| the first total synthesis of the peptaibol hypomurocin a1 and its conformation analysis: an application of the 'azirine/oxazolone method'. | the first total synthesis of hypomurocin a1 (hm a1) in solution phase is described. as members of the peptaibol family, hypomurocins are constituted by two groups of peptides: six undecapeptides (undecamers) in the hm a group and six octadecapeptides (18-mers) in the hm b group. the synthesis presented has been successfully achieved by the 'azirine/oxazolone method' to introduce the two aib-pro sequences included in this undecapeptaibol in one step with methyl 2,2-dimethyl-2h-azirine-3-prolinate ... | 2005 | 17193196 |