Search results for "nucleotides"
showing 10 items of 297 documents
Toward the understanding of DNA fluorescence: The singlet excimer of cytosine
2006
By using the multiconfigurational second-order perturbation method CASPT2, including corrections for the basis set superposition error, the lowest-singlet excited state of the face-to-face π-stacked cytosine homodimer is revealed to be bound by about half an eV, being the source of an emissive feature consistent with the observed redshifted fluorescence. Gloria.Olaso@uv.es Daniel.Roca@uv.es Luis.Serrano@uv.es Manuela.Merchan@uv.es
Template-Assembled Synthetic G-Quadruplex (TASQ): A Useful System for Investigating the Interactions of Ligands with Constrained Quadruplex Topologies
2010
A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular-like G-quadruplex motif 1 (parallel G-quadruplex conformation), an intramolecular G-quadruplex 2, and a duplex DNA 3 have been designed and developed. The method is based on the concept of template-assembled synthetic G-quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G-quadruplex conformation. Various known G-quadruplex ligands have been used to investigate the affinities of ligands for intermolecular…
Aryl-bis-(scorpiand)-aza receptors differentiate between nucleotide monophosphates by a combination of aromatic, hydrogen bond and electrostatic inte…
2014
Bis-polyaza pyridinophane scorpiands bind nucleotides in aqueous medium with 10–100 micromolar affinity, predominantly by electrostatic interactions between nucleotide phosphates and protonated aliphatic amines and assisted by aromatic stacking interactions. The pyridine-scorpiand receptor showed rare selectivity toward CMP with respect to other nucleotides, whereby two orders of magnitude affinity difference between CMP and UMP was the most appealing. The phenanthroline-scorpiand receptor revealed at pH 5 strong selectivity toward AMP with respect to other NMPs, based on the protonation of adenine heterocyclic N1. The results stress that the efficient recognition of small biomolecules with…
NMR study of hexanucleotide d(CCGCGG)2 containing two triplet repeats of fragile X syndrome
2003
Abstract Long repeated stretches of d(CCG) and tri-nucleotide are crucial mutations that cause hereditary forms of mental retardation (fragile X-syndrome). Moreover, the alternating (CG) di-nucleotide is one of the candidates for Z-DNA conformation. Solution NMR structure of d(CCGCGG) 2 has been solved and is discussed. The determined NMR solution structure is a distorted highly bent B-DNA conformation with increased flexibility in both terminal residues. This conformation differs significantly from the Z-DNA tetramer structure reported for the same hexamer in the crystal state at similar ionic strength by Malinina and co-workers. Crystal structure of d(CCGCGG) 2 at high salt concentration …
Oxaaza cyclophanes in the recognition of nucleotides. The role of oxygen and electron-rich aromatic rings
2007
Dioxapolyaza cyclophanes derived from resorcinol and different polyamine chains have been studied in aqueous solution as abiotic receptors for nucleotides. The presence of the additional ethyleneoxy subunits is reflected in a higher basicity and in a significant increase in the log K values for the interaction with nucleotides relative to that of related polyazacyclophanes.
The Role of Adenine Excimers in the Photophysics of Oligonucleotides
2009
Energies and structures of different arrangements of the stacked adenine homodimer have been computed at the ab initio CASPT2 level of theory in isolation and in an aqueous environment. Adenine dimers are shown to form excimer singlet states with different degrees of stacking and interaction. A model for a 2-fold decay dynamics of adenine oligomers can be supported in which, after initial excitation in the middle UV range, unstacked or slightly stacked pairs of nucleobases will relax by an ultrafast internal conversion to the ground state, localizing the excitation in the monomer and through the corresponding conical intersection with the ground state. On the other hand, long-lifetime intra…
Semiconductive and Magnetic One-Dimensional Coordination Polymers of Cu(II) with Modified Nucleobases
2013
Four new copper(II) coordination complexes, obtained by reaction of CuX2 (X = acetate or chloride) with thymine-1-acetic acid and uracil-1-propionic acid as ligands, of formulas [Cu(TAcO)2(H2O)4]·4H2O (1), [Cu(TAcO)2(H2O)2]n (2), [Cu3(TAcO)4(H2O)2(OH)2]n·4H2O (3), and [Cu3(UPrO)2Cl2(OH)2(H2O)2]n (4) (TAcOH = thymine-1-acetic acid, UPrOH = uracil-1-propionic acid) are described. While 1 is a discrete complex, 2-4 are one-dimensional coordination polymers. Complexes 2-4 present dc conductivity values between 10(-6) and 10(-9) S/cm(-1). The magnetic behavior of complex 2 is typical for almost isolated Cu(II) metal centers. Moderate-weak antiferromagnetic interactions have been found in complex…
Monoclonal antibody to a DNA-binding domain of p53 mimics charge structure of DNA: anti-idiotypes to the anti-p53 antibody are anti-DNA
2004
Antibodies to DNA are important markers of various autoimmune diseases and can be pathogenic; however, their generation is not understood. We previously reported that anti-DNA antibodies could be induced in mice by idiotypic immunization to PAb-421, an antibody to a DNA-binding domain of p53. We now report that two monoclonal antibodies of moderate affinity (K(D) asymptotically equal to 10(-7)), raised from PAb-421-immunized mice, specifically recognized both PAb-421 and DNA. These antibodies feature multiple arginine residues in the antigen-binding site, a unique characteristic of disease-associated anti-DNA antibodies; nevertheless, these anti-DNA antibodies show specific complementarity …
The membrane distal half of gp130 is responsible for the formation of a ternary complex with IL-6 and the IL-6 receptor
1995
AbstractGp130 is the signal transducing subunit of the interleukin-6 receptor. Signaling is initiated by the complex formation of gp130 with IL-6 bound to the IL-6 receptor (IL-6R). We have subdivided the extracellular domain of gp130 in two parts and expressed the mutant proteins as soluble IgG fusion proteins in COS-7 cells. By studying the formation of the ternary complex we show that the membrane distal half of gp130 which contains a cytokine receptor domain is responsible for the interaction with the IL-6/IL-6R complex. Interestingly this is the same region which is believed to be involved in specific recognition of the related cytokines LIF, OM, and probably also of CNTF and IL-11.
Assay for O6-alkylguanine-DNA-alkyltransferase using oligonucleotides containing O6-methylguanine in a BamHI recognition site as substrate
1992
Abstract Double-stranded oligonucleotides, 40 bases in length containing an O 6 -methylguanine in a Bam HI restriction site, were developed as substrates for the determination of human O 6 -alkylguanine-DNA-alkyltransferase (AGT). The assay proved highly sensitive and quantitative. After incubation of the 5′-end-labeled oligonucleotides with cell homogenates of peripheral blood lymphocytes, the DNA was digested with Bam HI. Cleavage with this restriction enzyme did not occur in the O 6 -methylguanine-containing oligonucleotide unless the fragment was repaired. The cleaved oligonucleotide was separated from the intact parent oligonucleotide by reverse-phase high-performance liquid chromatogr…