| effects of polycationic peptides on mucin release from airway goblet cells: relationship between polymer size and activity. | various sizes of poly-l-lysine (pll) and poly-l-arginine (pla) were tested for their possible effects on airway goblet cell mucin release using primary hamster tracheal surface epithelial (htse) cells in an attempt to identify the smallest size of the polycationic peptide to suppress mucin release without cytotoxicity. | 2002 | 12477077 |
| montmorillonite catalysis of 30-50 mer oligonucleotides: laboratory demonstration of potential steps in the origin of the rna world. | elongation of the primer 32pda(pda)8pa proceeds by the reaction of the 5'-phosphorimidazolides of adenosine and uridine in the presence of montmorillonite clay. daily addition of the activated nucleotides for up to 14 days results in the formation of 40-50 mers using the 5'-phosphorimidazolide of adenosine (impa) and 25-30 mers using the 5'-phosphorimidazolide of uridine (impu). the limitation on the lengths of the chains formed is not due to the inhibitors formed since the same chain lengths we ... | 2002 | 12458736 |
| all hierarchical levels are involved in conformational transitions of the 4 x 6-meric tarantula hemocyanin upon oxygenation. | the respiratory protein of the tarantula eurypelma californicum is a 4 x 6-meric hemocyanin that binds oxygen with high cooperativity. this requires the existence of different conformations which have been confirmed by small angle x-ray scattering (saxs). here we present reconstructed 3d-models of the oxy- and deoxy-forms of tarantula hemocyanins, as obtained by fitting small angle x-rays scattering curves on the basis of known x-ray structures and electron microscopy of related hemocyanins. for ... | 2002 | 12445474 |
| specificity of mammalian y-box binding protein p50 in interaction with ss and ds dna analyzed with generic oligonucleotide microchip. | p50 protein is a member of the y-box binding transcription factor family and is a counterpart of yb-1 protein. the generic microchip was used to analyze the sequence specificity of p50 binding to single (ss) and double-stranded (ds) oligodeoxyribonucleotides. the generic microchip contained 4,096 single-stranded octadeoxyribonucleotides in which all possible core 6-mers (4(6)=4,096) were flanked at their 3' and 5'-ends with degenerated nucleotides. the oligonucleotides were chemically immobilize ... | 2002 | 12421560 |
| cyclic and hairpin peptide complexes of heme. | we have synthesized and characterized a new class of heme-peptide complexes using disulfide-linked hairpin-turn and cyclic peptides and compared these to their linear analogues. the binding affinities, helicities, and mechanism of binding of linear, hairpin, and cyclic peptides to [feiii(coproporphyrin-i)]+ have been determined. in a minimalist approach, we utilize amphiphilic peptide sequences (15-mers), where a central histidine provides heme ligation, and the hydrophobic effect is used to opt ... | 2002 | 12381164 |
| reusable platforms for high-throughput on-chip temperature gradient assays. | this paper describes a reusable platform that can apply a linear temperature gradient to a lab-on-a-chip device. when a planar microfluidic device with a series of microchannels is placed on top of the platform with the channels perpendicular to the gradient, each channel is held at a discrete temperature. this allows temperature-dependent data for chemical or biochemical species flowed into the device to be obtained in a concurrent fashion. as a demonstration, a melting curve for dsdna is perfo ... | 2002 | 12380832 |
| the use of rapd and semi-random markers to verify somatic hybrids between diploid lines of solanum tuberosum l. | markers specific to diploid lines of cultivated potato were identified using the polymerase chain reaction (pcr), primed with arbitrary 10-mers generating rapds, or with semi-random primers targeting intron-exon semi-conservative sequences of plant genes. one hundred and fifty rapd primers and twelve semi-random primers were tested. selected primers were subsequently used for verification of putative somatic hybrids. | 2002 | 12378226 |
| a novel approach to a one-pot synthesis of unsubstituted oligo(alpha-thiophenes). | oligo(alpha-thiophenes) alpha-4t and alpha-8t were prepared by the following one-pot sequential conversions: thiophene (t) --> alpha-2t --> alpha-4t --> alpha-8t. pdcl(2)-induced coupling of a mono-alpha-mercuration derivative of each of the n-mers t, alpha-2t, and alpha-4t was applied in these conversions. | 2002 | 12375988 |
| synthesis and structural characterization of new stiff rod oligomeric domains by x-ray crystallography and nmr. | the monomers n,n'-dibenzylbenzene-1,4-diamine (1), n,n'-dibenzylnaphthalene-1,5-diamine (2), and n,n'-dibenzylanthracene-1,9-diamine (3) were reacted with phosgene in the presence of a base to produce the corresponding n,n'-dibenzyl-1,4-bis(chlorocarbonylamino)benzene (4), n,n'-dibenzyl-1,5-bis(chlorocarbonylamino)naphthalene (5), and n,n'-dibenzyl-9,10-bis(chlorocarbonylamino)anthracene (6). these monomers were used to create zigzag type stacks, in a stepwise fashion, of trimers and 9-mers of e ... | 2002 | 12375986 |
| monitoring the enzymatic polymerization of 4-phenylphenol by matrix-assisted laser desorption ionization time-of-flight mass spectrometry: a novel approach. | matrix-assisted laser desorption ionization time-of-flight (maldi-tof) mass spectrometry is a powerful tool for polymer characterization. it has been used to understand the enzymatic polymerization of 4-phenylphenol and to monitor number average molecular weight and weight average molecular weight of the polymer as a function of systematic addition of hydrogen peroxide (h(2)o(2)) in the reaction. a novel method, an introduction of internal standard for quantification of data, has been developed ... | 2013 | 12217031 |
| determining the electrophoretic mobility and translational diffusion coefficients of dna molecules in free solution. | the free solution mobility of dna molecules of different molecular weights, the sequence dependence of the mobility, and the diffusion coefficients of small single- and double-stranded dna (ss- and dsdna) molecules can be measured accurately by capillary zone electrophoresis, using coated capillaries to minimize the electroosmotic flow (eof) of the solvent. very small differences in mobility between various analytes can be quantified if a mobility marker is used to correct for small differences ... | 2002 | 12210184 |
| binding of radiolabeled folate and 5-methyltetrahydrofolate to cow's milk folate binding protein at ph 7.4 and 5.0. relationship to concentration and polymerization equilibrium of the purified protein. | binding of folate (pteroylglutamate) and 5-methyltetrahydrofolate, the major endogenous form of folate, to folate binding protein purified from cow's milk was studied at 7 degrees c to avoid degradation of 5-methyltetrahydrofolate. both folates dissociate rapidly from the protein at ph 3.5, but extremely slowly at ph 7.4, most likely due to drastic changes in protein conformation occurring after folate binding. dissociation of 5-methyltetrahydrofolate showed no increase at 37 degrees c suggestin ... | 2001 | 12166823 |
| chemistry of the 2-deoxyribonolactone lesion in oligonucleotides: cleavage kinetics and products analysis. | deoxyribonolactone in dna is an oxidized abasic site damage that is produced by a variety of physical and chemical agents such as gamma-irradiation and ene-diyne antibiotics. the extent and biological significance of the lesion are poorly documented due to the high lability of the damaged dna. the chemistry of degradation of deoxyribonolactone-containing dna was investigated using oligonucleotides of different length (5-, 11-, 23-, 34-mers) in which the lactone was photochemically generated, as ... | 2002 | 12149017 |
| clustering of nucleobases with alkali metals studied by electrospray ionization tandem mass spectrometry: implications for mechanisms of multistrand dna stabilization. | self-clustering of the five common nucleobases was investigated by electrospray ionization tandem mass spectrometry and shown to provide insight into the non-covalent interactions between identical bases. alkali and ammonium cations significantly increase self-aggregation of the nucleobases and lead to the formation of uniquely stable magic number clusters. sodium adducts of guanine, thymine and uracil preferentially take the form of tetrameric (quartet) clusters. this gas-phase result correlate ... | 2002 | 12125000 |
| large-scale preparation, purification, and characterization of hyaluronan oligosaccharides from 4-mers to 52-mers. | hyaluronan (ha) was depolymerized by partial digestion with testicular hyaluronidase and separated into size-uniform ha oligosaccharides from 4-mers to 52-mers by anion exchange chromatography after removal of the hyaluronidase. the purity and size of each ha oligosaccharide was confirmed by using hplc analyses, face, and esi-ms. (1)h and (13)c nmr assignments and elemental analyses were obtained for each ha oligosaccharide. endotoxins, proteins, and dna were absent or in trace amounts in these ... | 2002 | 12122023 |
| the free solution mobility of dna in tris-acetate-edta buffers of different concentrations, with and without added nacl. | the free solution mobility of a high-molecular-weight dna, linear puc19, and a 20-bp oligomer called dsa5 have been studied as a function of tris-acetate-edta (tae) buffer concentration, with and without added nacl. the two dnas migrate as separate peaks during capillary electrophoresis, because the mobility of linear puc19 is higher than that of the 20-bp oligomer. in tae buffers ranging from 10-400 mm in concentration, the migration times and peak areas of the two dnas are independent of wheth ... | 2002 | 12116139 |
| organization of model helical peptides in lipid bilayers: insight into the behavior of single-span protein transmembrane domains. | selectively deuterated transmembrane peptides comprising alternating leucine-alanine subunits were examined in fluid bilayer membranes by solid-state nuclear magnetic resonance (nmr) spectroscopy in an effort to gain insight into the behavior of membrane proteins. two groups of peptides were studied: 21-mers having a 17-amino-acid hydrophobic domain calculated to be close in length to the hydrophobic thickness of 1-palmitoyl-2-oleoyl phosphatidylcholine and 26-mers having a 22-amino-acid hydroph ... | 2002 | 12080125 |
| large scale sequencing by hybridization. | sequencing by hybridization is a method for reconstructing a dna sequence based on its k-mer content. this content, called the spectrum of the sequence, can be obtained from hybridization with a universal dna chip. however, even with a sequencing chip containing all 4(9) 9-mers and assuming no hybridization errors, only about 400-bases-long sequences can be reconstructed unambiguously. drmanac et al. (1989) suggested sequencing long dna targets by obtaining spectra of many short overlapping frag ... | 2002 | 12015890 |
| application of a chaperone-based refolding method to two- and three-dimensional off-lattice protein models. | a model of protein-chaperone interaction as a two-phase (unfolding/refolding) iterative annealing mechanism able to promote structural segregation of hydrophobic and hydrophilic monomers and thereby facilitate access to nativelike states has recently been applied successfully to two 22-mers of the honeycutt and thirumalai bln (hydrophobic, hydrophilic, neutral) heteropolymer model. this technique is here applied to a much wider data set: 94 8-mers of the off-lattice protein model originally pres ... | 2002 | 12012350 |
| mixed-phase hybridization of short oligodeoxyribonucleotides on microscopic polymer particles: effect of one-base mismatches on duplex stability. | hybridization of short oligonucleotides (10- and 11-mers) to complementary probes immobilized to microscopic polymer particles was quantified by a sandwich type mixed-phase hybridization assay based on a time-resolved fluorometric measurement of a photoluminescent europium(iii) chelate from the surface of a single particle. among the 54 sequences that were studied, 21 were fully complementary to the particle-bound probes, while 33 contained an internal one-base mismatch. the observed affinities ... | 2013 | 12009944 |
| site-resolved energetics in dna triple helices containing g*ta and t*cg triads. | recognition of specific sites in double-helical dna by triplex-forming oligonucleotides has been limited until recently to sites containing homopurine-homopyrimidine sequences. g*ta and t*cg triads, in which ta and cg base pairs are specifically recognized by guanine or by thymine, have now extended this recognition code to dna target sites of mixed base sequences. in the present work, we have obtained a characterization of the stabilities of g*ta and t*cg triads, and of the effects of these tri ... | 2002 | 11914088 |
| the elastic net algorithm and protein structure prediction. | predicting protein structures from their amino acid sequences is a problem of global optimization. global optima (native structures) are often sought using stochastic sampling methods such as monte carlo or molecular dynamics, but these methods are slow. in contrast, there are fast deterministic methods that find near-optimal solutions of well-known global optimization problems such as the traveling salesman problem (tsp). but fast tsp strategies have yet to be applied to protein folding, becaus ... | 2002 | 11913391 |
| charge effects for differentiation of oligodeoxynucleotide isomers containing 8-oxo-dg residues. | dissociation reactions of a series of multiply charged oligodeoxynucleotide (odn) 12-mer anions were studied using an ion trap mass spectrometer. these mixed nucleobase 12-mers fragment first by loss of a neutral nucleobase (a, g, c, and/or 5-methyl-cytosine) followed by cleavage at 3' c-o bond of the sugar from which the base is lost to produce the complementary sequence ions, i.e., [a - b] and w type of ions. no detectable loss of 8-oxo-guanine and/or thymine from these 12-mers is observed und ... | 2002 | 11908798 |
| evidence of a tendency to self-association of the transmembrane domain of erbb-2 in fluid phospholipid bilayers. | the transmembrane domains of receptor tyrosine kinases are single-span helical structures suggested to participate directly in the formation of side-to-side receptor homodimers/homooligomers that modulate signal transduction. transmembrane peptides from the class i receptor tyrosine kinase, erbb-2, were examined directly by 2h nmr spectroscopy as a means of following such phenomena under the dynamic conditions that characterize fluid, fully hydrated bilayers of natural phospholipids. appropriate ... | 2002 | 11841227 |
| number needed to treat in cardiac rehabilitation. | clinicians, patients, and health policy-makers must judge whether healthcare interventions are worth the side effects, inconvenience, and costs. the number needed to treat (nnt) provides an estimate of the number of patients who need to be treated to attain an additional favorable outcome, or to prevent an additional adverse outcome, and is the reciprocal of the absolute risk reduction. the closer the nnt is to 1.0-meaning that every patient who is treated achieves a benefit-the more effective t ... | 2009 | 11839993 |
| peptides that mimic glycosaminoglycans: high-affinity ligands for a hyaluronan binding domain. | hyaluronan (ha) is a non-sulfated glycosaminoglycan (gag) that promotes motility, adhesion, and proliferation in mammalian cells, as mediated by cell-surface ha receptors. we sought to identify non-carbohydrate ligands that would bind to and activate cell-surface ha receptors. such analogs could have important therapeutic uses in the treatment of cancer, wound healing, and arthritis, since such ligands would be resistant to degradation by hyaluronidase (hase). | 2001 | 11731299 |
| highly enantioselective enone epoxidation catalyzed by short solid phase-bound peptides: dominant role of peptide helicity. | the series of l-leu 1-20-mers, peptides carrying 1-5 n-terminal gly residues, and oligomers of (s)-beta(3)-leu and (1r,2r)-2-aminocyclohexanecarboxylic acid were synthesized on tentagel s nh(2). five l-leu residues were found sufficient to catalyze the juliá-colonna epoxidation of chalcone with 96-98% ee. experiment and molecular modeling suggest that catalysis is effected by binding of the enone to the n-terminus, and the helicity of the peptide determines the epoxide configuration through face ... | 2001 | 11720549 |
| analysis of adp-ribose polymer sizes in intact cells. | poly(adp-ribose) is a polymer (padpr) that is synthesized by poly (adp-ribose) polymerases in response to dna damaging agents. for instance, chemical alkylating agents such as mnng or physical stimulation of cells by gamma-rays are well known to induce padpr synthesis. parps are members of a growing family of enzymes which includes parp-1, parp-2, s-parp-1, tankyrase and v-parp. the association of parp-1 and parp-2 in dna damage signaling pathways has been characterized, but tankyrase and v-parp ... | 2001 | 11693195 |
| reporting of near-miss events for transfusion medicine: improving transfusion safety. | half of the reported serious adverse events from transfusion are a consequence of medical error. a no-fault medical-event reporting system for transfusion medicine (mers-tm) was developed to capture and analyze both near-miss and actual transfusion-related errors. | 2001 | 11606817 |
| probing the lateral organization of membranes: fluorescence repercussions of pyrene probe distribution. | phospholipids pyrene labeled are widely used to investigate dynamics and organizations of membranes. we studied pyrene probe lateral distribution by analyzing the variations of the molar absorption coefficient (epsilon) versus probe concentrations, in small unilamellar vesicles (suv) made of phospholipids and/or glycolipids, with pyrene labeled phosphatidylcholine (pypc) or phosphatidylglycerol (pypg). the results were interpreted according to an infinite associative model. they indicated that a ... | 2001 | 11603845 |
| global minimization of an off-lattice potential energy function using a chaperone-based refolding method. | a global energy minimization method based on what is known about the mechanisms of the groel/groes chaperonin system is applied to two 22-mers of an off-lattice protein model whose native states are beta-hairpins and which have structural similarity to short peptides known to interact strongly with the groel substrate binding domain. these model substrates have been used by other workers to test the effectiveness of a number of global minimization techniques, and are regarded as providing a sign ... | 2001 | 11598876 |
| design, synthesis, and conformational study of biologically active photolabeled analogues of the main immunogenic region of the acetylcholine receptor. | photoaffinity labeling is a powerful tool for the characterization of the molecular basis of ligand binding to acceptor molecules, which provides important insights for mapping the bimolecular interfaces. the autoimmune disease myasthenia gravis is caused by autoantibodies against the acetylcholine receptor (achr). the majority of the anti-achr antibodies bind to the "main immunogenic region" (mir) of the achr. to identify the contact points between the complementarity determining regions of the ... | 2014 | 11582576 |
| solution structure of a dna double helix incorporating four consecutive non-watson-crick base-pairs. | a series of dna 21-mers containing a variety of the 4 x 4 internal loop sequence 5'-caag-3'/3'-acgt-5' were studied using nuclear magnetic resonance (nmr) methodology and distance geometry (dg)/molecular dynamics (md) approaches. such oligomers exhibit excellent resolution in the nmr spectra and reveal many unusual noes (nuclear overhauser effect) that allow for the detailed characterization of a dna hairpin incorporating a track of four different non-watson-crick base-pairs in the stem. these i ... | 2001 | 11575931 |
| oligonucleotides with isopolar phosphonate internucleotide linkage: a new perspective for antisense compounds? | several types of isopolar modified oligothymidylates and oligoadenylates (15 mers) with the phosphonate -o-p-ch2-o- internucleotide linkage were prepared. the modified oligonucleotides were subjected to the study of their hybridization properties, resistance against nucleases, and the ability to elicit rnase h activity. | 2013 | 11563123 |
| incorporation of positively charged deoxynucleic s-methylthiourea linkages into oligodeoxyribonucleotides. | oligodeoxyribonucleic acids (15- and 18-mers) containing both negatively charged phosphate and positively charged s-methyl thiourea internucleoside linkages (dnmt/dna chimera) have been synthesized. dna binding characteristics and nuclease resistance of dnmt/dna chimera have been evaluated. | 2001 | 11549438 |
| sequence dependent n-terminal rearrangement and degradation of peptide nucleic acid (pna) in aqueous solution. | the stability of the pna (peptide nucleic acid) thymine monomer ¿n-[2-(thymin-1-ylacetyl)]-n-(2-aminoaminoethyl)glycine¿ and those of various pna oligomers (5-8-mers) have been measured at room temperature (20 degrees c) as a function of ph. the thymine monomer undergoes n-acyl transfer rearrangement with a half-life of 34 days at ph 11 as analyzed by 1h nmr; and two reactions, the n-acyl transfer and a sequential degradation, are found by hplc analysis to occur at measurable rates for the oligo ... | 1998 | 11543609 |
| effect of dinucleoside pyrophosphates on the oligomerization of activated mononucleotides on na(+)-montmorillonite: reaction of 5'-phosphoro-4-(dimethylamino)pyridinium [4-(ch3)2npypa] with a5'ppa. | the oligomerization of adenosine 5'-phosphoro-4-(dimethylamino)pyridinium (4-(ch3)2-npypa) and diadenosine 5',5'-pyrophosphate (a5'ppa) (9:1) on na(+)-montmorillonite was studied. the oligomers were isolated and analyzed by selective enzymatic hydrolyses and the oligomeric composition and the percent of 3',5'-phosphodiester linkages present in each fraction was determined. the longest oligomers formed (11-mers) are slightly shorter than those produced in the absence of a5'ppa (12-mers). smaller ... | 1997 | 11536840 |
| selex selection of high-affinity oligonucleotides for bacteriophage ff gene 5 protein. | the ff gene 5 protein (g5p) is a cooperative ssdna-binding protein. selex was used to identify dna sequences favorable for g5p binding at physiological ionic strength (200 mm nacl) and 37 degrees c. sequences were selected from a library of 58-mers that contained a central variable segment of 26 nucleotides. dna sequences selected after eight rounds of selex were mostly g-rich, with multiple copies of cpuggpy, tpugggpy, and/or pypupugggpy motifs. this was unexpected, since g5p has higher binding ... | 2001 | 11478897 |
| stabilization factors affecting duplex formation of peptide nucleic acid with dna. | peptide nucleic acid (pna) is an oligonucleotide analogue in which the sugar-phosphate backbone is replaced by an n-(2-aminoethyl)glycine unit to which the nucleobases are attached. we investigated the thermodynamic behavior of pna/dna hybrid duplexes with identical nearest neighbors but with different sequences and chain lengths (5, 6, 7, 8, 10, 12, and 16 mers) to reveal whether the nearest-neighbor model is valid for the pna/dna duplex stability. cd spectra of 6, 7, and 8 mer pna/dna duplexes ... | 2001 | 11456481 |
| multiplex sequencing by hybridization. | one of the limitations of classical sequencing by hybridization (sbh) is the inefficient use of probes in the "all k-mers" array. this limitation occurs due to the relatively short length (roughly the square root of c) of target that may be reconstructed by an array with c probes. we propose a new strategy, multiplex sequencing by hybridization, that greatly increases the efficiency of target reconstruction. in the typical multiplex sbh method, many different target sequences are simultaneously ... | 2001 | 11454302 |
| complete sequencing of mono-deprotonated peptide nucleic acids by sustained off-resonance irradiation collision-induced dissociation. | complete peptide nucleic acids (pnas) sequence information is obtained from the unimolecular decomposition of singly-charged pna oligomers in the negative-ion mode using electrospray ionization coupled with fourier transform ion cyclotron resonance mass spectrometry (esi-fticr-ms) and sustained off-resonance irradiation collision induced dissociation. the 4-mers, n-catt-c, n-agct-c, n-aact-c, and n-acetylated-aact-c and two 6-mers, n-aaaaaa-c and n-cccccc-c, were investigated to explore the unim ... | 2001 | 11444602 |
| dna binding mediated by the wheat hmga protein: a novel instance of selectivity against alternating gc sequence. | the high-mobility-group (hmg) chromosomal protein wheat hmga was purified to homogeneity and tested for its binding characteristics to double-stranded dna. wheat hmga was able to bind to p268, an a/t-rich fragment derived from the pea plastocyanin gene promoter, producing a small mobility shift in gel retardation assays where the bound complex was sensitive to addition of proteinase k but resistant to heat treatment of the protein, consistent with the identity of wheat hmga as a putative hmg-i/y ... | 2001 | 11442059 |
| comparative binding properties of metallobleomycins with dna 10-mers. | properties of the interaction of bleomycin (blm) and metallobleomycins [m = zn, cu(ii), fe(iii), and ho(2)-co(iii)] with site-specific and nonspecific dna oligomers, d(ggaagcttcc)(2) (i) and d(ggaaatttcc)(2) (ii), respectively, were investigated. with both 10-mers association constants increased in the series blm a(2), znblm a(2), cu(ii)blm a(2), fe(iii)blm a(2), and ho(2)-co(iii)blm a(2). generally, the metallobleomycins were bound with a modestly higher affinity to i. one-dimensional (1)h nmr ... | 2001 | 11412110 |
| identification and characterization of membrane estrogen receptor from mcf7 estrogen-target cells. | estrogens control the proliferation of estrogen-target cells through a receptor mediated pathway. we have recently presented evidence that estradiol cancels the proliferative inhibition exerted by albumin on estrogen-target cells (indirect-negative hypothesis). we postulate that this mechanism requires the presence of a membrane estrogen receptor (mer)-membrane albumin receptor complex. confirmation for meralpha in mcf7 cells is now made using both the c542 monoclonal and er-21 polyclonal antibo ... | 2001 | 11377974 |
| fragmentation mechanisms of oligodeoxynucleotides: effects of replacing phosphates with methylphosphonates and thymines with other bases in t-rich sequences. | this article reports another step in an ongoing effort to understand the fragmentation of t-rich oligodeoxynucleotides. we extended an earlier investigation of t-rich 4-mers to t-rich 6-mers, 8-mers and 10-mers by using four different tandem mass spectrometric methods. the methods include low-energy collisionally activated decomposition (cad) of electrospray ionization (esi)-produced ions, source-cad of esi-produced ions, post-source decay (psd), and cad of matrix assisted laser desorption ioniz ... | 2001 | 11349956 |
| sds-induced phenoloxidase activity of hemocyanins from limulus polyphemus, eurypelma californicum, and cancer magister. | phenoloxidase, widely distributed among animals, plants, and fungi, is involved in many biologically essential functions including sclerotization and host defense. in chelicerates, the oxygen carrier hemocyanin seems to function as the phenoloxidase. here, we show that hemocyanins from two ancient chelicerates, the horseshoe crab limulus polyphemus and the tarantula eurypelma californicum, exhibit o-diphenoloxidase activity induced by submicellar concentrations of sds, a reagent frequently used ... | 2001 | 11278677 |
| anginex, a designed peptide that inhibits angiogenesis. | novel beta-sheet-forming peptide 33-mers, betapep peptides, have been designed by using a combination approach employing basic folding principles and incorporating short sequences from the beta-sheet domains of anti-angiogenic proteins. one of these designed peptides (betapep-25), named anginex, was observed to be potently anti-angiogenic. anginex specifically inhibits vascular endothelial cell proliferation and induces apoptosis in these cells, as shown by flow-cytometric detection of sub-diplo ... | 2001 | 11171099 |
| preferential counterion binding to a-tract dna oligomers. | the free solution mobility of four 20 bp dna oligomers, with and without a-tracts, has been measured by capillary electrophoresis in tris-acetate buffer, to test the hypothesis that site-specific binding of monovalent counterions can occur in the narrow minor groove of a-tract dnas. preferential counterion binding has been proposed to cause a-tract bending because of asymmetric charge neutralization and collapse of the helix backbone toward the minor groove. preferential counterion binding in a- ... | 2001 | 11162111 |
| spectrum alignment: efficient resequencing by hybridization. | recent high-density microarray technologies allow, in principle, the determination of all k-mers that appear along a dna sequence, for k = 8 - 10 in a single experiment on a standard chip. the k-mer contents, also called the spectrum of the sequence, is not sufficient to uniquely reconstruct a sequence longer than a few hundred bases. we have devised a polynomial algorithm that reconstructs the sequence, given the spectrum and a homologous sequence. this situation occurs, for example, in the ide ... | 2000 | 10977087 |
| thermodynamic, spectroscopic, and equilibrium binding studies of dna sequence context effects in four 40 base pair deoxyoligonucleotides. | effects of different end sequences on melting, circular dichroism spectra (cd), and enzyme binding properties were investigated for four 40 base pair, non-self-complementary duplex dna oligomers. the center sequences of these oligoduplexes have either of two 22 base pair modules flanked on both sides by sequences differing in at content. temperature-induced melting transitions monitored by differential scanning calorimetry (dsc) and ultraviolet absorbance were measured for the six duplexes in bu ... | 2000 | 10869190 |
| from small charged molecules to oligomers: a semiempirical approach to the modeling of actual mobility in free solution. | according to stokes' treatment, the ionic mobility of particles, which are small with respect to debye length, is usually considered to be proportional to the nominal charge and inversely proportional to the hydrodynamic radius. experimentally, it is well known, however, that the ionic mobility of a small multicharged molecule does not depend linearly on its nominal charge in a wide range. this behavior can be accounted for by a condensation of the charge or a modification of the friction coeffi ... | 2000 | 10832879 |
| dna homo as a new landmark for nucleic acid properties. ab initio calculations and experimental mapping. | of the non-covalent binding forces in dna-drug or dna-protein interaction, electrostatic interaction, stacking interaction, hydrogen bonds and hydrophobic effect have been well established. however, only a few homo-lumo interaction in dna have been reported. we examined the ab initio calculations of b-dna duplex 5-mers. based on the calculated results, we investigated the mapping of homo experimentally and found that dna cleavage patterns with co(ii) and bpo (benzoyl peroxide) were in good agree ... | 1999 | 10780408 |
| synthesis of oligonucleotides containing the oxidatively modified kappab site: unique binding affinity to the nfkappab p50 homodimer. | synthesis of oligonucleotide 26-mers including single 5-formyl-2'-deoxyuridine (1) or 5-formyl-2'-o-methyluridine (2) in place of thymidine at the kappab site has been accomplished. one of the 26-mers with 1 was critically discriminated by the nfkappab p50 homodimer in binding. | 1999 | 10780365 |
| benzo[a]pyrene diol epoxide adducts in dna are potent suppressors of a normal topoisomerase i cleavage site and powerful inducers of other topoisomerase i cleavages. | the catalytic intermediates of dna topoisomerase i (top1) are cleavage complexes that can relax dna supercoiling (intramolecular reaction) or mediate recombinations (intermolecular religation). we report here that dna adducts formed from benzo[a]pyrene bay-region diol epoxides can markedly affect top1 activity. four oligonucleotide 22-mers of the same sequence were synthesized, each of which contained a stereoisomerically unique benzo[a]pyrene 7, 8-diol 9,10-epoxide adduct at the 2-amino group o ... | 2000 | 10688881 |
| introduction of 6-formylcytidine into a myb binding sequence. | single 6-formylcytidine was introduced into a oligonucleotide duplex (23 mers) as a substitute for thymidine in the myb binding sequence of 3'-ttgac-5'. the modified duplex showed tm of 67 degrees c, which was six degrees lower than the tm of the native duplex. binding affinity of the 23-mers to the myb protein was estimated by electrophoretic mobility shift assays, and the binding was almost completely abolished. | 2013 | 10639756 |
| stabilization of double stranded homologous poly(da)·poly(dt) by taxol. | abstract the nucleic acid activity of taxol and paclitaxel was investigated with synthetic and natural oligo- and polynucleotides. the polynucleotides poly(da)·poly(dt), poly(dg)·poly(dc), poly [d(a-t)]·poly[d(a-t)], poly[d(g-c)]·poly[d(g-c)] and calf thymus dna were used. the oligonucleotides are 24-mers with d(purine)(24)·d(pyrimidine)(24) strands, as well as d[(purine)(x)-(pyrimidine)(x)]·d[(purine)(x)-(pyrimidine)(x)] sequences. the study was performed with spectroscopic and calorimetric met ... | 2000 | 22607443 |
| bridging the prebiotic and rna worlds: prebiotic rna synthesis on clay. | abstract progress towards the laboratory demonstration of the steps in the prebiotic origin of the rna world is reviewed. montmorillonite clay catalyzes the formation of rnas containing 6-14 monomer units from the activated mononucleotides of a, c, g, i and u. the rnas formed have 3', 5'- and 2', 5'-links, pyrophosphate links and have both linear and cyclic chains. the purine oligonucleotides have more 3', 5'- links while the pyrimidine nucleotides have more 2', 5'-linkages. template-directed sy ... | 2000 | 22607426 |
| abasic sites in duplex dna: molecular modeling of sequence-dependent effects on conformation. | molecular modeling calculations using junction minimization of nucleic acids (jumna) have been used to study sequence effects on the conformation of abasic sites within duplex dna. we have considered lesions leading to all possible unpaired bases (x), adenine, guanine, cytosine, or thymine contained within two distinct sequence contexts, cxc and gxg. calculations were carried out on dna 11-mers using extensive conformational search techniques to locate the most stable abasic conformations and us ... | 1999 | 10585943 |
| observation of daunomycin and nogalamycin complexes with duplex dna using electrospray ionisation mass spectrometry. | the noncovalent binding of the antitumour drugs daunomycin and nogalamycin to duplex dna has been studied using electrospray ionisation mass spectrometry (esi-ms). the conditions for the preparation of drug/duplex dna complexes and for their detection by esi-ms have been optimised. ions corresponding to these complexes were most abundant relative to free dna when prepared in the ph range 8-9, and using gentle esi interface conditions. self-complementary oligonucleotides, 5'-d(ggctagcc)-3' or 5'- ... | 1999 | 10589098 |
| lattice-fluid model for gas-liquid chromatography. | lattice-fluid models describe molecular ensembles in terms of the number of lattice sites occupied by molecular species (r-mers) and the interactions between neighboring molecules. the lattice-fluid model proposed by sanchez and lacombe (macromolecules, 1978;11:1145-1156) was used to model specific retention volume data for a series of n-alkane solutes with n-alkane, polystyrene, and poly(dimethylsiloxane) stationary liquid phases. theoretical equations were derived for the specific retention vo ... | 1999 | 10588340 |
| a novel strategy to generate biologically active neo-glycosaminoglycan conjugates. | heparin and heparan sulfate are structurally related polysaccharides with a variety of biological effects/functions. most of these effects are due to interactions, of varying specificity, between the negatively charged polysaccharide chains and proteins. while such interactions generally involve a single saccharide domain of decasaccharide size or less, ternary complexes of two protein molecules binding to separate domains on a single polysaccharide chain are known to occur. to facilitate studie ... | 1999 | 10561458 |
| trans-(nh3)(2)pt(ii)-modified deoxyoligonucleotides as potential antisense agents: cross-linking reactions between two 12-mers. | an approach is presented which probes the possible use of trans-[(nh3)(2)ptcl](+)-modified deoxyoligonucleotides in the antisense strategy. it consists of (1) the selective platination of an oligonucleotide containing 11 pyrimidine (t, c) bases as well as a single guanine (g) as a pt-anchoring group at the 5'-end to give trans-[(nh3)(2)pt¿5'-d(g(n7)t(2)c(2)t(2)c(2)t(2)c¿cl](10-) 1 ("antisense strand") and (2) subsequent hybridization with the purine 12-mer 5'-d(ga(2)g(2)a(2)g(2)a(2)g)(11-) ("sen ... | 1999 | 10550694 |
| electrochemical polymerization of aniline investigated using on-line electrochemistry/electrospray mass spectrometry. | a thin-layer electrochemical flow cell coupled on-line with electrospray mass spectrometry (ec/es-ms) was used to investigate the soluble products from the controlled-potential anodic polymerization of aniline in h(2)o and h(2)o/ch(3)oh (1/1 v/v) with ammonium acetate and acetic acid or ammonium hydroxide as electrolytes (ph 4, 6.5, or 9). at a working electrode (glassy carbon) potential of 1.0 v versus ag/agcl, singly protonated aniline oligomers containing as many as 10 aniline units (10-mer) ... | 1999 | 21662856 |
| sequence specific hybridization properties of methylphosphonate oligodeoxynucleotides. | methylphosphonate oligodeoxynucleotides (mpo's) with isomerically pure rp-configurated methylphosphonates (mp's) were synthesized by block coupling of apt and tpa dinucleoside methylphosphonates (dmp's, p indicating mp-linkage). oligonucleotide duplexes (20 mers) with these rp-mp's showed almost the same melting temperatures (tm) as those with phosphorodiester bonds. further a dependence of the duplex stability from the nucleosides (bases) adjacent to the mp moiety was observed. for the first ti ... | 1999 | 10447202 |
| electrospray quadrupole mass spectrometry analysis of model oligonucleotides and polymerase chain reaction products: determination of base substitutions, nucleotide additions/deletions, and chemical modifications. | esi fticr mass spectrometry is the only technique currently used for accurate molecular weight analysis of pcr products above 100 bp in size. this is important in demonstrating the potential for ms in making major contributions in the molecular biology and genomics areas. in the near future, it is more likely that less expensive, more user friendly ms techniques will be used for high-throughput analyses (including maldi tof and esi quadrupole). there have been numerous reports on the use of mald ... | 1999 | 10424176 |
| the role of linkers in the reassembly of the 3.6 mda hexagonal bilayer hemoglobin from lumbricus terrestris. | the extent and kinetics of reassembly of the four groups of linkers l1-l4 with 213 kda subassemblies of twelve globin chains d, (bac)3(d)3, isolated from the approximately 3.6 mda hexagonal bilayer (hbl) hemoglobin (hb) of lumbricus terrestris, was investigated using gel filtration. the reassembled hbl's were characterized by scanning transmission electron microscopic (stem) mass mapping and their subunit content determined by reversed-phase chromatography. in reassembly by method (a), the linke ... | 1999 | 10373372 |
| hybridization of complementary strand and single-base mutated oligonucleotides detected with an on-line acoustic wave sensor. | the hybridization of a biotinylated 25-mer oligonucleotide probe with complementary, non-complementary and single-base mutated 25-mer targets at the liquid-solid (neutravidin-modified) interface of a thickness-shear mode acoustic wave device was studied. the sensor was incorporated into an on-line configuration capable of both variable flow and stop-flow experiments. under ambient temperature conditions different signals were obtained for the complementary and non-complementary cases. at higher ... | 1998 | 10209884 |
| dr (mhc class ii) ligands: an approach to rheumatoid arthritis therapeutics. | the presentation of peptide antigens to t-cells by mhc class ii proteins is a central process in cellular and humoral immune responses. blockade of this presentation event via synthetic ligands that bind to disease-associated mhcs (such as dr1 and dr4) may be useful for the treatment of autoimmune diseases such as rheumatoid arthritis, type 1 diabetes, multiple sclerosis, lupus erthymatosis and graves disease. recently reported synthetic ligands for dr1 and dr4 are short modified peptides (2-7 m ... | 1998 | 10197051 |
| low-energy (5-25 ev) electron damage to homo-oligonucleotides. | radiation-induced damage to homo-oligonucleotides is investigated by electron-stimulated desorption of neutral fragments from chemisorbed organic films. six and 12 mers of cytidine phosphate (poly dcs) and thymidine phosphate (poly dts) are chemisorbed from various solutions onto a crystalline gold substrate by a thiol modification at the 3' end and are irradiated under ultra-high vacuum conditions with 5-25 ev electrons. the mass selected neutral desorption yields consist mainly of fragments of ... | 1999 | 10073671 |
| in vitro evaluation of the haemostatic value of the lfb-von willebrand factor concentrate. | the structural and functional studies of the concentrate of von willebrand factor (vwf) manufactured by lfb have been first performed as part of the preclinical development of this product specially intended for the treatment of von willebrand disease. the electrophoretic analyses showed the high purity of lfb-vwf concentrate (specific activity of 100 iu of ristocetin cofactor activity per milligram of protein) and the multimeric pattern attesting the presence of high molecular weight multimeter ... | 1998 | 10028317 |
| triplex formation by oligonucleotides containing 5-(1-propynyl)-2'-deoxyuridine: decreased magnesium dependence and improved intracellular gene targeting. | oligonucleotides capable of sequence-specific triple helix formation have been proposed as dna binding ligands useful for modulation of gene expression and for directed genome modification. however, the effectiveness of such triplex-forming oligonucleotides (tfos) depends on their ability to bind to their target sites within cells, and this can be limited under physiologic conditions. in particular, triplex formation in the pyrimidine motif is favored by unphysiologically low ph and high magnesi ... | 1999 | 10026270 |
| the importance of coulombic end effects: experimental characterization of the effects of oligonucleotide flanking charges on the strength and salt dependence of oligocation (l8+) binding to single-stranded dna oligomers. | binding constants kobs, expressed per site and evaluated in the limit of zero binding density, are quantified as functions of salt (sodium acetate) concentration for the interactions of the oligopeptide ligand kwk6nh2 (designated l8+, with zl = 8 charges) with three single-stranded dna oligomers (ss dt-mers, with |zd| = 15, 39, and 69 charges). these results provide the first systematic experimental information about the effect of changing |zd| on the strength and salt dependence of oligocation- ... | 1999 | 9916032 |
| oligonucleotides bearing 5-formyl-2'-o-methyluridine: preference in binding affinity to the nf-kappa b (p50)2 homo- and p50/p65 heterodimers. | 5-formyl-2'-o-methyluridine was incorporated into the various positions of oligonucleotide 26-mers containing the nf-kappa b binding sequence. some of them showed binding selectivity toward the homo- and heterodimers of subunits of nf-kappa b. | 1998 | 9873704 |
| identification and classification of the causes of events in transfusion medicine. | transfusion medicine lacks a standard method for the systematic collection and analysis of event reports. review of event reports from the food and drug administration (fda) showed a relative paucity of information on event causation. thus, a causal analysis method was developed as part of a prototype medical event reporting system for transfusion medicine (mers-tm). | 2007 | 9838940 |
| kinetic steps for alpha-helix formation. | the kinetics of alpha-helix formation in polyalanine and polyglycine eicosamers (20-mers) were examined using torsional-coordinate molecular dynamics (md). of one hundred fifty-five md experiments on extended (ala)20 carried out for 0.5 ns each, 129 (83%) formed a persistent alpha-helix. in contrast, the extended state of (gly)20 only formed a right-handed alpha-helix in two of the 20 md experiments (10%), and these helices were not as long or as persistent as those of polyalanine. these simulat ... | 1998 | 9829694 |
| blackbody infrared radiative dissociation of oligonucleotide anions. | the dissociation kinetics of a series of doubly deprotonated oligonucleotide 7-mers [d(a)7(2-), d(aattaat)2-, d(ttaatta)2-, and d(ccggccg)2-] were measured using blackbody infrared radiative dissociation in a fourier-transform mass spectrometer. the oligonucleotides dissociate first by cleavage at the glycosidic bond leading to the loss of a neutral nucleobase, followed by cleavage at the adjacent (5') phosphodiester bond to produce structurally informative a-base and w type ions. from the tempe ... | 1998 | 9794082 |
| clinical implications of p53 autoantibodies in the sera of patients with non-small-cell lung cancer. | the presence of autoantibodies to p53 protein has been associated with the presence of p53 (also known as tp53) gene mutations in primary tumors and with poor prognosis. this study was undertaken to determine the clinical significance of p53 autoantibodies in patients with non-small-cell lung cancer (nsclc). | 1998 | 9790550 |
| cellular and molecular characterization of a major soybean allergen. | soybean proteins share a large number of cross-reacting allergens with other members of the legume family; however, soy-allergic patients rarely react clinically to other members of the legume family. gly m bd 30k, an ige-binding protein with a molecular weight of 30 kd, was identified in soybean extracts by western ige-immunoblot analysis. this monomeric allergen was shown to have an n-terminal amino acid sequence and amino acid composition identical to that of the seed 34-kd protein, p34, a th ... | 1998 | 9751845 |
| synthesis, biophysical properties, and nuclease resistance properties of mixed backbone oligodeoxynucleotides containing cationic internucleoside guanidinium linkages: deoxynucleic guanidine/dna chimeras. | the synthesis of mixed backbone oligodeoxynucleotides (18-mers) consisting of positively charged guanidinium linkages along with negatively charged phosphodiester linkages is carried out. the use of a base labile-protecting group for guanidinium linkage offers a synthetic strategy similar to standard oligonucleotide synthesis. the nuclease resistance of the oligodeoxyribonucleotides capped with guanidinium linkages at 5' and 3' ends are reported. the hybridization properties and sequence specifi ... | 1998 | 9736687 |
| the detection of oligonucleotide n3'-->p5' phosphoramidate/rna duplexes with capillary gel electrophoresis. | oligonucleotide n3'-->p5' phosphoramidates (3'-phosphoramidates) are dna analogs that are presently under investigation as potential therapeutic agents. these compounds may also hold promise as a diagnostic tool. here, we describe a rapid method for the analysis of single-stranded rna fragments utilizing 3'-phosphoramidate oligonucleotides as probes in conjunction with capillary gel electrophoresis (cge). 3'-phosphoramidate 9-mers were mixed with complimentary rna, and cge was used to monitor du ... | 1998 | 9694262 |
| identification, composition, and asymmetric formation mechanism of glycidyl methacrylate/butyl methacrylate copolymers up to 7000 da from electrospray ionization ultrahigh-resolution fourier transform ion cyclotron resonance mass spectrometry. | glycidyl methacrylate (gma) and butyl methacrylate (bma) have the same nominal mass (142 da) but differ in exact mass by 0.036 da (ch(4) vs o). therefore, copolymers formed from the two isobaric monomers exhibit a characteristic isobaric distribution due to different monomer compositions. here, we show that electrospray ionization ft-icr mass spectrometry at 9.4 t resolves the isobaric components of copolymers as large as 7000 da with a resolving power (m/δm(50%)) of ∼500 000 in a gel permeation ... | 1998 | 21644659 |
| mermade: an oligodeoxyribonucleotide synthesizer for high throughput oligonucleotide production in dual 96-well plates. | we have designed and constructed a machine that synthesizes two standard 96-well plates of oligonucleotides in a single run using standard phosphoramidite chemistry. the machine is capable of making a combination of standard, degenerate, or modified oligos in a single plate. the run time is typically 17 hr for two plates of 20-mers and a reaction scale of 40 nm. the reaction vessel is a standard polypropylene 96-well plate with a hole drilled in the bottom of each well. the two plates are placed ... | 1998 | 9685322 |
| effect of single benzo[a]pyrene diol epoxide-deoxyguanosine adducts on the action of dna polymerases in vitro. | neither sequenase 2.0 nor klenow fragment were able to extend 12-mer primers using the eight templates (16-mers) derived by placing each of the four isomeric benzo[a]pyrene diol epoxide-deoxyguanosine adducts at the 13th nucleotide from the 3'-end of two different sequence contexts. using an 11-mer primer to get a running start did not overcome the adduct induced block of primer extension except for the klenow fragment and one of the two sequence contexts, indicating primer extension is dependen ... | 1998 | 9664121 |
| enhancement of insect antifreeze protein activity by solutes of low molecular mass. | antifreeze proteins (afps) lower the non-equilibrium freezing point of water (in the presence of ice) below the melting point, thereby producing a difference between the freezing and melting points that has been termed thermal hysteresis. in general, the magnitude of the thermal hysteresis depends upon the specific activity and concentration of the afp. this study describes several low-molecular-mass solutes that enhance the thermal hysteresis activity of an afp from overwintering larvae of the ... | 1998 | 9662495 |
| in vitro inhibition of ras-raf association by short peptides. | seven amino acid peptides were tested as in vitro inhibitors of oncogenic ras-raf association. the sequences of these peptides were derived from the h-ras effector region (amino acids 25 to 51) and the ras binding domain of raf-1 (amino acids 64 to 105). eleven out of the twenty-one ras 7-mers tested inhibited formation of the ras-raf complex by at least 20% at 100 microm. the most potent of these inhibitory peptides contained the effector residues 32 to 37 or 40 to 45. of the raf-1 peptides tes ... | 1998 | 9636675 |
| bacteriophage p2 and p4 morphogenesis: structure and function of the connector. | the connector, the structure located between the bacteriophage capsid and tail, is interesting from several points of view. the connector is in many cases involved in the initiation of the capsid assembly process, functions as a gate for dna transport in and out of the capsid, and is, as implied by the name, the structure connecting a tail to the capsid. occupying a position on a 5-fold axis in the capsid and connected to a coaxial 6-fold tail, it mediates a symmetry mismatch between the two. to ... | 1998 | 9614863 |
| molecular characterization and sequencing of antifreeze proteins from larvae of the beetle dendroides canadensis. | the deduced amino acid sequences of antifreeze proteins (afps) from larvae of the beetle dendroides canadensis were determined from both complementary dnas (cdnas) and from peptide sequencing. these consisted of proteins with a 25-residue signal peptide and mature proteins 83 (dendroides antifreeze protein; dafp-1) or 84 (dafp-2) amino acids in length which differed at only two positions. peptide sequencing yielded sequences which overlapped exactly with those of the deduced cdna sequences of da ... | 1998 | 9591363 |
| sequence dependence and characteristics of bends induced by site-specific polynuclear aromatic carcinogen-deoxyguanosine lesions in oligonucleotides. | the tumorigenic metabolite of benzo[a]pyrene, the (+)-7r,8s,9s,10r enantiomer, and the nontumorigenic mirror-image isomer, (-)-7s,8r,9r, 10s, of r7,t8-dihydroxy-t9,10-epoxy-7,8,9, 10-tetrahydrobenzo[a]pyrene (anti-bpde) bind covalently to the exocyclic amino group of deoxyguanosine (n2-dg) in native dna. these adducts can cause structural perturbations such as dna bends, which in turn may influence the cellular processing of these lesions. the characteristics of bends in site-specifically modifi ... | 1998 | 9538018 |
| mapping of the interleukin-10/interleukin-10 receptor combining site. | the discontinuous interleukin-10(il-10)/interleukin-10 receptor (il-10r) combining site was mapped using sets of overlapping peptides derived from both binding partners bound to continuous cellulose membranes. low affinity binding of single regions of the discontinuous contact sites on il-10 and il-10r could be identified due to (1) high peptide density on the membrane support, (2) incubation with high protein concentrations, (3) indirect immunodetection of the ligates after electrotransfer onto ... | 1998 | 9568901 |
| conformations of nicked and gapped dna structures by nmr and molecular dynamic simulations in water. | we have analyzed and compared the molecular structures and dynamics of dna duplexes containing a nick or a gap of one nucleotide where the base in front of the gap is a guanine. the continuous strand has the sequence 5'(cagagtcxctggctc) where the residue x is absent for the nick, 14-mer, and where it is a g residue for the gap. duplexes were formed with the two corresponding 7-mers. neither of these is phosphorylated adjacent at the nick site, but it is a good model for a single strand break. fo ... | 1998 | 9521727 |
| spectroscopic studies of single-stranded dna ligands and oxazole yellow dyes. | interactions between short single-stranded dna ligands and fluorescent dna indicator dyes were used to investigate binding selectivity of the ligands. conformational differences among four dna ligands of different sequence and structure, including two that form a g-quartet and two that do not, were confirmed by circular dichroism spectroscopy. their interactions with indicator dyes yo-pro-1 iodide (yo) and yoyo-1 iodide (yoyo) were probed using measurements of dye absorbance; induced circular di ... | 1998 | 9547012 |
| oxazole yellow dye interactions with short dna oligomers of homogeneous base composition and their hybrids. | interactions between short single-stranded dna oligomers of homogeneous base composition and the fluorescent probes oxazole yellow (yo) and its homodimer yoyo are described. the oligomers included 15-mers and 30-mers of polyda, polydt, polydg, and polydc. interactions between the dyes and dna hybrids formed from complementary homogeneous strands of equal length were also investigated. no interactions were observed between the dyes and the monomeric monophosphate nucleosides a, g, t, or c. the dy ... | 1998 | 9547011 |
| genetic and alkaloid analysis of papaver species and their f1 hybrid by rapd, hplc and elisa. | total dna was extracted from the leaves of a f1 hybrid and its parents, papaver bracteatum lindle and p. pseudo-orientale medw. analysis of random-amplified polymorphic dna (rapd) using ten arbitrary oligonucleotide 10-mers, showed that f1 hybrid was confirmed to be genetically intermediate of both parental plants compared with the genetic distance between f1 hybrid and individual parents. furthermore, the comparison of the band patterns between a f1 hybrid, p. bracteatum and p. pseudo-orientale ... | 1998 | 9530831 |
| comparison of mass spectrometric techniques for generating molecular weight information on a class of ethoxylated oligomers. | the results of fast atom bombardment (fab), time-of-flight secondary ion mass spectrometry (tof-sims), matrix-assisted laser desorption/ionization (mald/i), electrospray ionization (esi), and field desorption (fd) analyses of ethoxylated oligomers of 2,4,7,9-tetramethyl-5-decyne-4,7-diol (surfynol(®) 104) were compared.each of these desorption mass spectrometry (ms) techniques can produce spectra of unfragmented cationized oligomers. from the observed ion series we calculate average molecular we ... | 1998 | 27518863 |
| separation of oligonucleotides of identical size, but different base composition, by free zone capillary electrophoresis in strongly acidic, isoelectric buffers. | a novel method for analyzing oligonucleotides of the same length, but bearing a single base substitution, is reported, based on free zone capillary electrophoresis (cze) under rather acidic ph values. for this purpose, a set of four 18-mers of fairly random base composition has been synthesized, bearing, in nucleotide 9, the following bases: t, c, g or a. theoretical predictions, based on titration curves of single free nucleotides, allowed us to predict that the simultaneous separation of a mix ... | 1997 | 9504830 |
| a free energy analysis by unfolding applied to 125-mers on a cubic lattice. | a common approach to the protein folding problem involves computer simulation of folding using lattice models of amino acid sequences. key factors for good performance in such models are the correct choice of the temperature and the average interaction energy between residues. in order to push the lattice approach to its limit it is important to have a method to adjust these parameters for optimal folding that is not limited by our ability to successfully simulate folding in a reasonable time. | 1998 | 9502320 |
| [synthesis of modified oligodeoxyribonucleotides containing 9-(2'-amino-2'-deoxy-beta-d-arabinofuranosyl)adenine]. | a method for preparing a modified derivative of 2'-amino-2'-deoxy-arabino-adenosine ready for directed insertion into an oligonucleotide chain during solid-phase synthesis was elaborated. a series of the title oligonucleotides (6-25-mers) containing a 2'-amino-2'-deoxy-arabino-adenosine fragment were prepared. a high reactivity of the 2'-amino group during the acylation with carboxylic acid anhydrides was demonstrated. it was shown that the insertion of the modified fragments into oligonucleotid ... | 1997 | 9490617 |
| molecular modeling study of adsorption of poly-l-lysine onto silica glass. | a research program was initiated with both experimental and computational chemistry based molecular modeling components to investigate specific amino acid-surface interactions. the experimental portion of this study, with details reported elsewhere, investigated the adsorption of selected molecular weights of poly(l-lysine) onto silica glass microspheres with the adsorption enthalpy per adsorbed mer determined to be -0.23 +/- 0.13 kcal/mol (mean +/- 95% confidence interval). molecular modeling o ... | 1997 | 9407308 |
| the use of ketamine or etomidate to supplement sufentanil/n2o anesthesia does not disrupt monitoring of myogenic transcranial motor evoked responses. | intraoperative monitoring of myogenic transcranial motor evoked responses (tc-mers) requires an anesthetic technique that minimally depresses response amplitudes. acceptable results have been obtained during opioid/n2o anesthesia, provided that the concentration of n2o does not exceed 50%. however, this technique may necessitate supplementation with additional agents to achieve adequate depth of anesthesia. etomidate and ketamine have been reported anecdotally or in nonsurgical situations to pro ... | 1997 | 9239584 |
| sequence analysis by hybridization with oligonucleotide microchip: identification of beta-thalassemia mutations. | diagnostics for genetic diseases were run and sequence analysis of dna was carried out by hybridization of rna transcripts with oligonucleotide array microchips. polyacrylamide gel pads (100 x 100 x 20 microm) were fixed on a glass slide of the microchip and contained allele-specific immobilized oligonucleotides (10-mers). the rna transcripts of pcr-amplified genomic dna were fluorescently labeled by enzymatic or chemical methods and hybridized with the microchips. the simultaneous measurement i ... | 1997 | 9099858 |