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Polynucleotides (3):
Recent article
Polynucleotides
Kidney International (78)10 2010
Abstract
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Kidney International (78)10 2010
Abstract
Kidney International (72) 2010
Abstract
Kidney International (78)10 2010
Abstract
Kidney International (78)10 2010
Abstract
Kidney International (78)10 2010
Abstract
Kidney International (78)10 2010
Abstract
Abstract
Molecular BioSystems (5)11 2009
Abstract
The binding of the known DNA intercalators methylene blue and quinacrine with four sequence specific polynucleotides, viz. poly(dG-dC).poly(dG-dC), poly(dG).poly(dC), poly(dA-dT).poly(dA-dT) and poly(dA).poly(dT), have been compared using absorbance, fluorescence, competition dialysi...
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PMID: 19823747
PDF is available here.
PDF is available here.
Abstract
Fe(II)/alpha-ketoglutarate-dependent hydroxylases uniformly possess a double-stranded beta-helix fold with two conserved histidines and one carboxylate coordinating their mononuclear ferrous ions. Oxidative decomposition of the alpha-keto acid is proposed to generate a ferryl-oxo intermediate capabl...
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PMID: 18813363
PDF is available here.
PDF is available here.
Abstract
The mechanism of the coupling step in polynucleotide synthesis using 5'-4,4'-dimethoxytritylthymidine-3'-beta-cyanoethyl-N,N-diisopropylphosphoramidite as the phosphitylating agent and catalysed by the salt of saccharin and N-methylimidazole in acetonitrile has been studied by (31)P NMR. Pre- and po...
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PMID: 18802632
PDF is available here.
PDF is available here.
ChemBioChem (9)13 2008
Abstract
In order to terminate the polymerase reaction at a desired position, a caged thymine derivative--4-O-[2-(2-nitrophenyl)propyl]thymine--was incorporated into PCR primers. In the PCR cycles, the elongation of the nascent strand (5'-->3' direction) by polymerase was site-selectively terminated at the 3...
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PMID: 18688827
PDF is available here.
PDF is available here.
Abstract
We evaluated the pre-immunization of mice with DNA-based vaccines subsequently challenged by the syngeneic Ph+ ALL cell line BM185. Ballistic transfer of minimalistic immunogenically defined gene expression (MIDGE) vectors encoding a BCR-ABLp185 fusion specific peptide or GM-CSF were used for in viv...
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PMID: 18639600
PDF is available here.
PDF is available here.
Abstract
Conventional lipid bilayer liposomes have similar inner and outer leaflet compositions; asymmetric liposomes have different lipid leaflet compositions. The goal of this work is to place cationic lipids in the inner leaflet to encapsulate negatively charged polynucleotides and to place neutral/anioni...
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PMID: 18597508
PDF is available here.
PDF is available here.
Abstract
We report on a replicative family B and a herpesvirus-encoded DNA Pol that possesses DNA lyase activity. We have discovered that the catalytic subunit of the HSV-1 DNA polymerase (Pol) (UL30) exhibits apurinic/apyrimidinic (AP) and 5'-deoxyribose phosphate (dRP) lyase activities. These activities ar...
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PMID: 18695225
PDF is available here.
PDF is available here.
Abstract
We proposed that Hoechst 33258 both monomers and dimers form complexes of the external type with poly(dG-dC).poly(dG-dC) from the side of the minor groove....
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PMID: 18533731
PDF is available here.
PDF is available here.
Immunology (124)4 2008
Abstract
I IFN production is dependent on IRF3 in brain astrocytes. These results suggest that brain inflammation, which produces inflammatory cytokines and type I IFNs, may enhance TLR3 expression in astrocytes. Additionally, upregulated TLR3 might modulate inflammatory processes by producing proinflammator...
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PMID: 18248388
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)24 2008
Abstract
One of the hallmarks of arthritis is swollen joints containing unusually high quantities of hyaluronan. Intact hyaluronan molecules facilitate cell migration by acting as ligands for CD44. Hyaluronan degradation products, readily formed at sites of inflammation, also fuel inflammatory processes. Irr...
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PMID: 18400745
PDF is available here.
PDF is available here.
Analytical Sciences (24)6 2008
Abstract
A fluorescent pyrazine derivative, 3,5-diamino-6-chloro-2-pyrazine carbonitrile (DCPC), is presented as a promising light-up ligand for single-nucleotide polymorphisms (SNPs) typing. In solutions buffered to pH 7.0 (I = 0.11 M, at 5 degrees C), DCPC can bind to thymine selectively over other nucleob...
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PMID: 18544854
PDF is available here.
PDF is available here.
The Journal of Chemical Physics (128)10 2008
Abstract
We have supplemented these calculations by the computation of correlation effects on the band structures of the base stacks by solving the inverse Dyson equation in its diagonal approximation taken for the self-energy the MP2 many body perturbation theory expression. In all cases the too large funda...
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PMID: 18345925
PDF is available here.
PDF is available here.
Abstract
We can conclude that self-assembling modes and gelation properties of nucleobase-appended organogelators are controllable by the addition of their complementary polynucleotide in organic solvents. We believe, therefore, that the present system can open the new paths to accelerate development of well...
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PMID: 18264571
PDF is available here.
PDF is available here.
Abstract
Transient species formed by photoexcitation (400 nm) of [Ru(dppz)(tap)2]2+ (1) (dppz = dipyrido[3,2-a:2',3'-c]phenazine; tap=1,4,5,8-tetraazaphenanthrene) in aqueous solution and when intercalated into a double-stranded synthetic polynucleotide, [poly(dG-dC)]2, have been observed on a picosecond tim...
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PMID: 17886324
PDF is available here.
PDF is available here.
Abstract
Water soluble homo-base polynucleotide analogues were synthesized in which polyvinyl alcohol and partially phosphonated polyvinyl alcohol constituted the backbones,onto which were grafted uracil or adenine via 1,3-dioxane spacers formed by acetal formation with the 1,3-diol moieties in PVA. The resu...
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PMID: 18463571
PDF is available here.
PDF is available here.
Abstract
It is shown that involvement of water in all these processes is mandatory, but the water must be of the simplified configuration in which there are only two strengths of water-water hydrogen bonds, and in which these two types of water coexist as microdomains throughout the liquid temperature range....
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PMID: 18183287
PDF is available here.
PDF is available here.
Abstract
Nieto et al.'s and Torres et al.'s metric space measures the relationships between polynucleotide chains incorrectly. Structurally highly different polynucleotide sequences are misclassified as highly similar ones, and completely different sequences are misclassified as identical ones. For this reas...
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PMID: 17614264
PDF is available here.
PDF is available here.
Immunology (122)1 2007
Abstract
Double-stranded RNA is produced during virus replication and, together with the viral antigen, is responsible for inducing host antivirus immunity. The hepatitis C virus (HCV) non-structural protein-3 (NS3) has been implicated in the immune evasion of HCV, and is one of the prime targets for inducin...
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PMID: 17451465
PDF is available here.
PDF is available here.
Abstract
Beta-1,3-glucans having carbohydrate-appendages (alpha-D-mannoside, N-acetyl-beta-D-glucosaminide and beta-lactoside) at the C6-position of every repeating unit can be readily prepared from curdlan (a linear beta-1,3-glucan) through regioselective bromination/azidation to afford 6-azido-6-deoxycurdl...
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PMID: 17637960
PDF is available here.
PDF is available here.
Abstract
The intercalation of fac-[(4,4'-bpy)Re(I)(CO)3(dppz)]+ (dppz = dipyridyl[3,2-a:2'3'-c]phenazine) in polynucleotides, poly[dAdT]2 and poly[dGdC]2, where A = adenine, G = guanine, C = cytosine and T = thymine, is a major cause of changes in the absorption and emission spectra of the complex. A strong...
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PMID: 17502935
PDF is available here.
PDF is available here.
Abstract
We show that disrupting the nucleosome over the core promoter of RNR3 is sufficient to drive preinitiation complex assembly and activate transcription in the absence of activating signals. Remodeling of chromatin over the RNR3 promoter requires the recruitment of the SWI/SNF complex by the general t...
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PMID: 17502614
PDF is available here.
PDF is available here.
Abstract
Luminescence intensity changes of a Pt(II) complex which is known to bind externally to DNA at low [DNA]/[complex] ratio and to intercalate at high [DNA]/[complex] ratio are studied in the presence of calf thymus DNA. External binding is demonstrated to induce luminescence enhancement whereas interc...
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PMID: 17404628
PDF is available here.
PDF is available here.
Abstract
We succeeded in the quantitative and selective introduction of an ammonium cationic group into the C6 position of Curdlan (CUR) by "Click Chemistry", and the obtained cationic Curdlan (CUR-N+) showed good solubility in water. ORD studies suggested that CUR-N+ adopts a single-stranded structure, diff...
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PMID: 17352476
PDF is available here.
PDF is available here.
Clinical Chemistry (53)3 2007
Abstract
Our method is an accurate, specific, and simple tool to characterize the 5T poly(TG) haplotype. Our results confirm the high frequency of 5T-12TG in CBAVD patients and do not preclude a potential effect also in pancreatitis. This assay can be useful in assessment of the disease risk in 5T carriers....
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PMID: 17234733
PDF is available here.
PDF is available here.
Abstract
Electroabsorption spectra were obtained for single-stranded polynucleotides poly(U), poly(C), poly(A), and poly(G) in glycerol/water glass at low temperature, and the differences in permanent dipole moment (Deltamu) and polarizability (Deltaalpha) were estimated for several spectral ranges covering...
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PMID: 17266277
PDF is available here.
PDF is available here.
Cancer Letters (246)1-2 2007
Abstract
We found a statistically significant correlation between levels of AP sites and age (rho=0.560, P<0.001). The results of this study demonstrated that levels of AP sites could predict survival in resected NSCLC patients. We postulate that an intact BER mechanism may reduce the accumulation of oxidati...
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PMID: 16519994
PDF is available here.
PDF is available here.
Abstract
We have discussed frequently used polymers, such as, polyethyleneimine, poly (lactide-co-glycolide), chitosan, as well as non-polymeric materials such as cationic lipids and metallic nanoparticles. The advantages and limitations of each system have been elaborated....
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PMID: 18019834
PDF is available here.
PDF is available here.
Abstract
We used thiobarbituric acid-reactivity assays and electrophoretic separation of DNA assays. The results showed no oxidative damage at the level of DNA degradation or strand break....
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PMID: 18028221
PDF is available here.
PDF is available here.
Abstract
The binding interactions of three naphthalimide derivatives with heteropoly nucleic acids have been evaluated using fluorescence, absorption and circular dichroism spectroscopies. Mono- and bifunctionalized naphthalimides exhibit sequence-dependent variations in their affinity toward DNA. The hetero...
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PMID: 17645660
PDF is available here.
PDF is available here.
Analytical Sciences (22)10 2006
Abstract
An ultra-sensitive colorimetric method to quantitate hundreds of polynucleotide molecules by gold nanoparticles with silver enhancement has been developed. The hybridization products from the target polynucleotides with biotin-labeled probes and gold nanoparticle-functioned oligonucleotides were imm...
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PMID: 17038778
PDF is available here.
PDF is available here.
Abstract
We evaluated the feasibility of inducing strong mucosal and systemic immune responses against both anthrax toxins and bacilli after nasal immunization using a synthetic double-stranded RNA (dsRNA), polyriboinosinic-polyribocytidylic acid (poly(I:C) or pI:C), as the adjuvant. We have shown that the c...
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PMID: 16828937
PDF is available here.
PDF is available here.
Journal of Chromatography A (1123)2 2006
Abstract
Abstract
We compare the efficacy of identical maternal immune stimulation induced by the exposure to polyriboinosinic-polyribocytidilic acid (Poly(I:C)) at a dose of 5mg/kg (i.v.) on distinct days of gestation (GD 6, 9, 13 or 17). The offspring derived were then compared to those collected from vehicle- and...
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PMID: 16378711
PDF is available here.
PDF is available here.
Journal of Cardiovascular Pharmacology (47)Supplement 2 2006
Abstract
Abstract
We generated mda-5-deficient mice and showed that mda-5 is the dominant receptor mediating type I IFN secretion in response to polyI:C in vitro and in vivo. Moreover, mda-5-/- mice exhibited a selectively impaired antiviral response to encephalomyocarditis picornavirus, indicating functional special...
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PMID: 16714379
PDF is available here.
PDF is available here.
Journal of Neuroscience (26)18 2006
Abstract
We demonstrate that the effects of maternal immune challenge between middle and late gestation periods in mice are dissociable in terms of fetal brain cytokine responses to maternal inflammation and the pathological consequences in brain and behavior. Specifically, the relative expression of pro- an...
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PMID: 16672647
PDF is available here.
PDF is available here.
Abstract
We examined the carbon chemical shift anisotropy (CSA) tensors of nucleobase adenine C2, pyrimidine C5 and C6, and purine C8. The differences between the measured RCSAs and the values back-calculated using three nucleobase carbon CSA sets [D. Stueber, D.M. Grant, 13C and 15N chemical shift tensors i...
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PMID: 16431143
PDF is available here.
PDF is available here.
Abstract
We extend the work concerning the Fuzzy Polynucleotide Space (FPS) introduced in Torres, A., Nieto, J.J., 2003. The fuzzy polynucleotide Space: Basic properties. Bioinformatics 19(5); 587-592 and Nieto, J.J., Torres, A., Vazquez-Trasande, M.M. 2003. A metric space to study differences between polynu...
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PMID: 16794951
PDF is available here.
PDF is available here.
Biopolymers (81)5 2006
Abstract
The binding of manganese(III)-tetra(4-N-methylpyridyl)porphyrin (MnTMpyP) with synthetic poly(dA-dT)2, poly(dI-dC)2, and poly(dG-dC)2 DNAs as well as calf thymus (CT) DNA has been quantitatively studied in detail using induced CD (circular dichroism) spectroscopy in the Soret absorption band. The CD...
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PMID: 16358258
PDF is available here.
PDF is available here.
Biophysical Journal (90)4 2006
Abstract
We analyze here the adsorption mechanism via a self-consistent mean-field model that includes the pH effect on the surface-charge density and the interactions between divalent ions and surface groups. The adsorption is driven by the cooperative effect of divalent metal ion condensation along polynuc...
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PMID: 16449197
PDF is available here.
PDF is available here.
Abstract
Base excision repair (BER) is the main pathway for removal of endogenous DNA damage. This repair mechanism is initiated by a specific DNA glycosylase that recognizes and removes the damaged base through N-glycosylic bond hydrolysis. The generated apurinic/apyrimidinic (AP) site can be repaired in ma...
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PMID: 16673895
PDF is available here.
PDF is available here.
Abstract
We describe a method for analyzing the manner in which repair endonucleases differ in the way they create nicks in DNA and how to distinguish between them using cellular crude extracts....
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PMID: 16673893
PDF is available here.
PDF is available here.
Abstract
A rapid, convenient and safe in vitro assay system for base excision repair is described. Whole cell extracts are prepared by detergent-based cell lysis and provide a vigorous activity of AP site repair. A circular DNA substrate is used for detection of both DNA polymerase beta-dependent and prolife...
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PMID: 16673894
PDF is available here.
PDF is available here.
Abstract
We observed a decrease of spontaneous IgE levels in PBMC from high IgE producer of approximately 27% with both dSLIM-30L1 and lin-30L1. In addition, both molecules enhanced the production of IgA, IgM and IgG1/IgG2, but with a slightly different pattern. Both molecules stimulated the secretion of the...
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PMID: 16364157
PDF is available here.
PDF is available here.
Abstract
The new mixed ligand complex [Ru(5,6-dmp)2(dppz)]Cl2 [5,6-dmp = 5,6-dimethyl-1,10-phenanthroline, dppz = dipyrido[3,2-a:2',3'-c]phenazine] has been isolated and its DNA-binding properties studied by employing UV-visible (UV-Vis), steady-state and time-resolved emission and circular dichroism spectra...
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PMID: 16290058
PDF is available here.
PDF is available here.
Nucleic Acids Research (34)2 2006
Abstract
A simple method for the detection of sequence- and structural-selective ligand binding to nucleic acids is described. The method is based on the commonly used thermal denaturation method in which ligand binding is registered as an elevation in the nucleic acid melting temperature (T(m)). The method...
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PMID: 16432258
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (109)48 2005
Abstract
We show an experimental approach for directly observing the condensation of polynucleotides and their electrolyte counterions at a liquid/solid interface. X-ray standing waves (XSW) generated by Bragg diffraction from a d = 20 nm Si/Mo multilayer substrate are used to measure the distinct distributi...
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PMID: 16853997
PDF is available here.
PDF is available here.
Abstract
We find that nucleic acid simulations using NAMD give meaningful results and that the essential features of the resulting dynamics are similar to those arising from the AMBER package. This sets the stage for reliable large-scale simulations of nucleic acids using NAMD.
Copyright 2005 Wiley Periodica...
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PMID: 16170796
PDF is available here.
PDF is available here.
Journal of General Virology (86)Pt 12 2005
Abstract
I interferons (IFNs) to protection against infection with enterovirus 71 (EV71) was investigated using a murine model where the virus was administrated to neonatal Institute of Cancer Research (ICR) mice by either the intraperitoneal (i.p.) or the oral route. In i.p. inoculated mice, post-infection...
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PMID: 16298971
PDF is available here.
PDF is available here.
Abstract
It is fifty years since the first chemical synthesis of a dinucleoside phosphate and a dinucleotide with natural 3'-->5'-internucleotide linkages was reported. The main developments in the methodology of oligo- and poly-nucleotide synthesis that have taken place since are described.
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PMID: 16312051
PDF is available here.
PDF is available here.
Biophysical Journal (89)5 2005
Abstract
We solve the relevant kinetics equations simultaneously using Mathematica as a simulation language. Among the interesting results of this study are that, for certain circumstances, the relative ratio of incorrect to correct hybrids can change dramatically with time; that the relative abundances of t...
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PMID: 16126833
PDF is available here.
PDF is available here.
Abstract
Autolytic degradation of yeast RNA occurs in many foods and beverages and can impact on the sensory quality of the product, but the resulting complex mixture of nucleotides, nucleosides and nucleobases has not been properly characterised. In this study, yeast autolysis was induced by incubating cell...
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PMID: 16091942
PDF is available here.
PDF is available here.