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Thymine
Terms modified by Thymine Selected AbstractsGenotyping single nucleotide polymorphisms using intact polymerase chain reaction products by electrospray quadrupole mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 18 2001James J. Walters Both single nucleotide polymorphisms (SNPs) and mutations are commonly observed in the gene encoding the tumor suppressor protein, p53. SNPs occur at specific locations within genes whereas mutations may be distributed across large regions of genes. When determining nucleotide differences, mass spectrometry is the only method other than Sanger sequencing which offers direct structural information. Electrospray ionization (ESI) quadrupole mass spectrometry (MS) analysis of intact polymerase chain reaction (PCR) products was performed following a simple purification and on-line heating to limit ion adduction. The PCR products were amplified directly from genomic DNA rather than plasmids, as in our previous work. Two known polymorphisms of the p53 gene were genotyped. A cytosine (C) or guanine (G) transversion, designated C,,,G (G,,,C on the opposite strand), were each detected by a 40.0,Da change upon ESI quadrupole MS analysis. Using known PCR products as standards, the genotypes determined for 10 human samples corresponded with restriction fragment length polymorphism (RFLP) analysis. Cytosine/thymine (T) transitions, designated C,,,T (G,,,A on the opposite strand), were also genotyped by ESI-MS. This SNP is discriminated by a 15.0,Da change on one strand (C,,,T) and a 16.0,Da change on the other (G,,,A). Appropriate sample preparation and instrumental configuration (including heated sample inlet syringe and MS source), to limit adducts, are both vital for successful ESI quadrupole MS analysis of intact PCR products. Copyright © 2001 John Wiley & Sons, Ltd. [source] Pyrrolidino DNA with Bases Corresponding to the 2-Oxo Deletion Mutants of Thymine and Cytosine: Synthesis and Triplex-Forming PropertiesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 24 2007Alain Mayer Abstract The dual recognition properties of pyrrolidino DNA species as parallel triplex-forming oligonucleotides were previously found to be strongly dependent upon the nature of the pyrimidine bases. In the structure,activity study presented here we were able to exclude this differential binding being due to their 2-oxo function. We had previously reported on the incorporation of pyrrolidino C -nucleosides into triplex-forming 2,-deoxyoligonucleotides (TFOs). The basic nitrogen atom that replaces the 4,-oxygen atom of the 2,-deoxysugar in such modified units introduces a positive charge in the third strand, and this is able to produce favourable electrostatic interaction with the negatively charged DNA target duplex. A first series of pyrrolidino pseudonucleosides with the bases isocytosine and uracil proved successful for GC base-pair recognition, but was unsuccessful for AT base-pair recognition within the parallel triplex binding motif. Here we report on the synthesis of the two novel 2,-deoxypyrrolidino nucleosides carrying the bases pyridin-2-one and 2-aminopyridine, their phosphoramidite building blocks and theirincorporation into TFOs. Pyrrolidinylpyridin-2-one (dp2P) and -2-aminopyridine (dp2AP), prepared as part of a structure,activity profiling of pyrrolidino DNA in triplex binding, are deletion mutants of T and C, respectively. We found by Tm measurements that neither modification increased triplex binding efficiency relative to the iso-C- and -U-containing pyrrolidino TFOs. These experiments clearly show that the C4 carbonyl function, although important for triplex binding through indirect contributions in general, is not responsible for the differential binding of the latter two aminonucleosides and suggest that TFO conformation is more important. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] Molecular Beacon Probes of Photodamage in Thymine and Uracil Oligonucleotides,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 2 2005Soujanya Yarasi ABSTRACT Molecular beacons (MB) are becoming more common as sequence-selective detectors of nucleic acids. Although they can easily detect single-base mismatches, they have never been used to directly detect DNA or RNA damage. To measure the degree of ultraviolet (UV) light damage in oligonucleotides, we report a novel MB approach for general detection of photoproducts in UV-irradiated rU17 and dT17 oligonucleotides. With monochromatic UV light irradiation at ca 280 nm under anoxic conditions, the oligonucleotide absorption decays with a single-exponential time constant of 123 ± 1 min for rU17 and with double-exponential time constants of 78 ± 0.5 min (99%) and 180 ± 5 min (0.05%) for dT17 oligonucleotides. Under the same conditions, the MB fluorescence decays more quickly, with single-exponential time constants of 19 ± 2 and 26 ± 3 min for rU17 and dT17, respectively. Similar kinetics were observed with broadband UV light irradiation of oligonucleotides. The differences in the UV damage kinetics of dT17 and rU17 and their detection by absorption and fluorescence techniques will be discussed in the context of differential instabilities introduced in the nucleic acid-MB duplex by the different photoproducts formed. [source] Infrared Spectra of Protonated Uracil, Thymine and CytosineCHEMPHYSCHEM, Issue 15 2007Jean-Yves Salpin Dr. Abstract The gas-phase structures of protonated uracil, thymine, and cytosine are probed by using mid-infrared multiple-photon dissociation (IRMPD) spectroscopy performed at the Free Electron Laser facility of the Centre Laser Infrarouge d,Orsay (CLIO), France. Experimental infrared (IR) spectra are recorded for ions that were generated by electrospray ionization, isolated, and then irradiated in a quadrupole ion trap; the results are compared to the calculated infrared absorption spectra of the different low-lying isomers (computed at the B3LYP/6-31++G(d,p) level). For each protonated base, the global energy minimum corresponds to an enolic tautomer, whose infrared absorption spectrum matched very well with the experimental IRMPD spectrum, with the exception of a very weak IRMPD signal observed at about 1800 cm,1 in the case of the three protonated bases. This signal is likely to be the signature of the second-energy-lying oxo tautomer. We thus conclude that within our experimental conditions, two tautomeric ions are formed which coexist in the quadrupole ion trap. [source] Etched succinate-functionalized silica hydride stationary phase for open-tubular CECELECTROPHORESIS, Issue 22 2009Jian-Lian Chen Abstract An open-tubular (OT) CEC column was designed to anchor ionizable succinate-functionalized ligands onto a silica hydride-based stationary phase through surface etching, silanization, and hydrosilation reactions beginning from a bare fused-silica tube. The modified columns that were produced in each step were monitored by analysis of the effect of performance of EOF on the changes of pH values, concentrations, and the amount of ACN added in the running buffers. By tracking the EOF patterns between columns, the author determined that the surface composition of the final product column was a combination of silanols, silica hydrides, and succinate ligands. Furthermore, lower loading volumes of the succinate ligands prepared for the hydrosilation reaction served to complete the mixed-mode OT-CEC columns, and subsequently to carry out the separation of six phenyl alcohols. Studies on the elution order of these alcohols identified the presence of chromatographic interactions in addition to electrophoresis. Based on the employment of a solvation parameter model, these interactions likely included dispersion interactions, dipole-type interactions, and interactions arising through the polarizable electrons in the solute. The optimum buffer conditions for CEC separations of phenyl alcohols, carbonyl-substituted phenols, and a mixture of nucleosides and thymine were a phosphate buffer (50,mM, pH 10.51), a borate buffer (50,mM, pH 8.62), and a borate buffer (50,mM, pH 9.50), respectively. Overall, the hydride-based stationary phases with ionizable ligands were successfully applied to the OT-CEC separations, and these results confidently propose an ideal route to the synthesis of novel OT-CEC columns. [source] A novel approach for analysis of oligonucleotide,cisplatin interactions by continuous elution gel electrophoresis coupled to isotope dilution inductively coupled plasma mass spectrometry and matrix-assisted laser desorption/ionization mass spectrometryELECTROPHORESIS, Issue 7 2008Wolfram Brüchert Abstract In this work we present a novel approach for in vitro studies of cisplatin interactions with 8-mer oligonucleotides. The approach is based on the recently developed coupling of continuous elution gel electrophoresis (GE) to an inductively coupled plasma-sector field mass spectrometer (ICP-SFMS) with the aim of monitoring the interaction process between this cytostatic drug and the nucleotides. In contrast to existing methods, the electrophoretic separation conditions used here allow both the determination of the reaction kinetics in more detail as well as the observation of dominant intermediates. Two different nucleotides sequences have been investigated for comparison purposes, one containing two adjacent guanines (5,-TCCGGTCC-3,) and one with a combination of thymine and guanine (5,-TCCTGTCC-3,), respectively. In order to gain further structural information, MALDI-TOF MS measurements have been performed after fraction collection. This allows for identification of the intermediates and the final products and confirms the stepwise coordination of cisplatin via monoadduct to bisadduct formation. Furthermore, the ICP-MS results were quantitatively evaluated in order to calculate the kinetics of the entire process. [source] Enhanced separation of purine and pyrimidine bases using carboxylic multiwalled carbon nanotubes as additive in capillary zone electrophoresisELECTROPHORESIS, Issue 16 2006Xin Xiong Abstract This paper describes the enhanced separation of adenine (A), hypoxanthine (HX), 8-azaadenine (8-AA), thymine (T), cytosine (C), uracil (U) and guanine (G) by CZE dispersing carboxylic multiwalled carbon nanotubes (c-MWNTs) into the running buffer. The effect of important factors such as c-MWNT nanoparticle concentration, the acidity and concentration of running buffer, and separation voltage were investigated to acquire the optimum conditions. The seven purine and pyrimidine bases could be well separated within 16,min in a 35,cm effective length fused-silica capillary at a separation voltage of +8.0,kV in a 23,mM tetraborate buffer (pH,9.2) containing 8.0×10,5,g/mL c-MWNTs. Under the optimal conditions, the linear ranges were of 2,250,,g/mL for A (R2,=,0.995), 3,200,,g/mL for U (R2,=,0.990) and G (R2,=,0.992), 3,250,,g/mL for T (R2,=,0.998), 2,200,,g/mL for C (R2,=,0.985) and 4,200,,g/mL for HX (R2,=,0.988) and 8-AA (R2,=,0.990). The detection limits were 0.9,,g/mL for A (S/N,=,3), 2.4,,g/mL for U, 2.0,,g/mL for T, 1.5,,g/mL for C, 2.5,,g/mL for G and 3.0,,g/mL for HX and 8-AA. The proposed method was successfully applied for determining five purine and pyrimidine bases in yeast RNA. [source] Synthesis of 3,-BODIPY-Labeled Active Esters of Nucleotides and a Chemical Primer Extension Assay on BeadsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 19 2010Kerstin Gießler Abstract A solution-phase synthesis of active esters of 3,-fluorophore-labeled deoxynucleoside 5,-monophosphates was developed for thymine and cytosine as nucleobases by using two different BODIPY dyes. Starting from the respective 2,-amino-2,,3,-dideoxynucleoside-5,-monophosphate, the fluorescent oxyazabenzotriazolides can be prepared in one-pot procedures involving labeling and activation. Screening of a range of supports led to a chemical primer extension assay on beads with in situ detection of nucleobases in target DNA through optical read-out. [source] XNA, (xylo Nucleic Acid): A Summary and New DerivativesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 11 2005B. Ravindra Babu Abstract Fully modified homopyrimidine 2'-deoxy- xylo nucleic acid (dXNA) form triple helixes with complementary DNA/RNA with thermal stabilities comparable to those of the corresponding DNA:DNA and DNA:RNA duplexes. However, a single or few insertions of dXNA monomers in a DNA strand significantly lower duplex stabilities. The dXNA monomers are known to adopt predominantly an N -type furanose conformation in solution. With a desire to increase the binding affinity, seven sugar-modified XNA monomers (H, F, N, M, K, P and Q) have been synthesised and their effect on hybridization towards DNA and RNA complements studied. The introduction of 2'-fluoro and 2'-hydroxy substituents was expected to induce conformational restriction towards C3'- endo -type furanose conformation of monomer F derived from 1-(2'-deoxy-2'-fluoro-,- D -xylofuranosyl)thymine and monomer H derived from 1-(,- D -xylofuranosyl)thymine. The presence of functionalites facing the minor groove as in 1-(2'-amino-2'-deoxy-2'- N,4'- C -methylene-,- D -xylofuranosyl)thymine (monomer N), 1-[4- C -(N -methylpiperazinyl)methyl-,- D -xylofuranosyl]thymine (monomer P), 1-(4- C -piperazinylmethyl-,- D -xylofuranosyl)thymine (monomer Q), 1-(4- C -hydroxymethyl-,- D -xylofuranosyl)thymine (monomer M) and 9-(4- C -hydroxymethyl-,- D -xylofuranosyl)adenine (monomer K) was studied, with monomer N being locked in an N -type furanose conformation. Besides, an efficient synthesis of known xylo -LNA phosphoramidite 19, required for the incorporation of 1-(2'- O,4'- C -methylene-,- D -xylofuranosyl)thymine (monomer L) is described. For comparison, hydridization data of various XNAs reported in the literature are included in the discussion section. The thermal denaturation studies show that XNAs containing conformationally locked monomers (N and L) display improved binding affinity, and that partially modified DNA/XNA chimera, or fully modified XNA display preferential hybridization towards RNA complements. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Synthesis of Novel Nucleo-,-Amino Acids and Nucleobase-Functionalized ,-PeptidesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 18 2003Arndt M. Brückner Abstract Four novel ,-amino acids bearing the canonical nucleobases guanine, cytosine, adenine, and thymine in the side chain, are synthesized starting from Boc- L -aspartic acid 4-benzyl ester. The syntheses are accomplished in six steps by the nucleophilic substitution of (S)-,-(tert -butoxycarbonylamino)-,-bromopentanoic acid benzyl ester with the corresponding nucleobase derivative as the key step. The guaninyl and cytosinyl ,-amino acids were built into ,-peptides that were studied by temperature-dependent CD and UV spectroscopy. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Effects of ,-aminoisobutyric acid on leptin production and lipid homeostasis: mechanisms and possible relevance for the prevention of obesityFUNDAMENTAL & CLINICAL PHARMACOLOGY, Issue 3 2010Karima Begriche Abstract ,-Aminoisobutyric acid (BAIBA) is a catabolite of thymine and antiretroviral thymine analogues AZT and d4T. We recently discovered that this ,-amino acid is able to enhance fatty acid oxidation and reduce body weight in mice through an increased production of leptin by the white adipose tissue (WAT). Furthermore, BAIBA could have favourable effects on nonalcoholic steatohepatitis in a leptin-independent manner. In the present review, we shall recall the circumstances that led us to discover the effects of BAIBA on body fat mass and lipid homeostasis. In addition, we put forward several hypothetical mechanisms whereby BAIBA could enhance leptin secretion by WAT and present some anti-inflammatory effects in the liver. We also discuss in this review (i) the deleterious impacts caused by the absence of, or low leptin expression on lipid homeostasis and body weight in humans and animals and (ii) recent data from other investigators suggesting that increasing leptin levels and/or responsiveness may be indeed an attractive pharmacological strategy in order to prevent (and/or treat) obesity, at least in some individuals. [source] The distribution of constitutional and somatic mutations in the neurofibromatosis 2 gene,HUMAN MUTATION, Issue 4 2006Michael E. Baser Abstract Constitutional heterozygous inactivating mutations in the neurofibromatosis 2 (NF2) tumor suppressor gene cause the autosomal dominant disease NF2, and biallelic inactivating somatic NF2 mutations are found in a high proportion of unilateral sporadic vestibular schwannoma (USVS) and sporadic meningioma. We surveyed the distributions of constitutional NF2 mutations in 823 NF2 families, 278 somatic NF2 mutations in USVS, and 208 somatic NF2 mutations in sporadic meningioma. Based on the available NF2 mutation data, the most dominant influence on the spectra of mutations in exons 1,15 are C>T transitions that change arginine codons (CGA) to stop codons (TGA) due to spontaneous deamination of methylcytosine to thymine in CpG dinucleotides. The paucity of reported mutations in exon 9 and the absence of reported mutations in exons 16 and 17 may be related to structure,function relationships in the NF2 protein. Hum Mutat 27(4), 297-306, 2006. © 2006 Wiley-Liss, Inc. [source] Sequence and organization of the mitochondrial genome of the Chagas disease vector, Triatoma dimidiataINSECT MOLECULAR BIOLOGY, Issue 3 2001E. M. Dotson Abstract The 17 019 bp mitochondrial genome of Triatoma dimidiata is composed of thirteen protein coding sequences, twenty-two tRNAs, small and large ribosomal units, and a control region. The gene order and orientation are identical to that of Drosophila yakuba. The nucleotide composition is biased toward adenine and thymine (69.5% A + T). The 2.1 kb putative control region, known as the A + T rich region in most insects, has an A + T bias of 66%, but contains a 400 bp sequence that is 77.5% A + T and two other distinct regions: (1) one with a lower A + T bias (60.1%) and (2) a region of eight tandem repeat units. The identified 1.4 kb nuclear copy of mitochondrial sequences encompasses the string of Gs and the beginning of the cytochrome c oxidase 1 gene but lacks the 1.8 kb region spanning the eight tandem repeats and the 5, end of the NADH dehydrogenase subunit II gene. [source] Coarse-grained model of nucleic acid basesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2010Maciej Maciejczyk Abstract Atomistic simulations of nucleic acids are prohibitively expensive and, consequently, reduced models of these compounds are of great interest in the field. In this work, we propose a physics-based coarse-grained model of nucleic-acid bases in which each base is represented by several (3,5) interaction centers. van der Waals interactions are modeled by Lennard-Jones spheres with a 12,6 potential energy function. The charge distribution is modeled by a set of electric dipole moments located at the centers of the Lennard-Jones spheres. The method for computing the Lennard-Jones parameters, electric dipole moments (their magnitude and orientation) and positions of the interaction centers is described. Several models with different numbers of interaction centers were tested. The model with three-center cytosine, four-center guanine, four-center thymine, and five-center adenine satisfactorily reproduces the canonical Watson,Crick hydrogen bonding and stacking interaction energies of the all-atom AMBER model. The computation time with the coarse-grained model is reduced seven times compared with that of the all-atom model. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Activation barriers for DNA alkylation by carcinogenic methane diazonium ionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2006Kaushalya S. Ekanayake Abstract Methylation reactions of the DNA bases with the methane diazonium ion, which is the reactive intermediate formed from several carcinogenic methylating agents, were examined. The SN2 transition states of the methylation reactions at N7, N3, and O6 of guanine; N7, N3, and N1 of adenine; N3 and O2 of cytosine; and O2 and O4 of thymine were calculated using the B3LYP density functional method. Solvation effects were examined using the conductor-like polarizable continuum method and the combined discrete/SCRF method. The transition states for reactions at guanine N3, adenine N7, and adenine N1 are influenced by steric interactions between the methane diazonium ion and exocyclic amino groups. Both in the gas phase and in aqueous solution, the methylation reactions at N atoms have transition states that are looser, and generally occur earlier along the reaction pathways than reactions at O atoms. The forming bonds in the transition states in water are 0.03 to 0.13 Å shorter than those observed in the gas phase, and the activation energies are 13 to 35 kcal/mol higher. The combined discrete/SCRF solvation energy calculations using base-water complexes with three water molecules yield base solvation energies that are larger than those obtained from the CPCM continuum method, especially for cytosine. Reactivities calculated using barriers obtained with the discrete/SCRF method are consistent with the experimentally observed high reactivity at N7 of guanine. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 277,286, 2006 [source] TDDFT investigation on nucleic acid bases: Comparison with experiments and standard approachJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2004M.K. Shukla Abstract A comprehensive theoretical study of electronic transitions of canonical nucleic acid bases, namely guanine, adenine, cytosine, uracil, and thymine, was performed. Ground state geometries were optimized at the MP2/6-311G(d,p) level. The nature of respective potential energy surfaces was determined using the harmonic vibrational frequency analysis. The MP2 optimized geometries were used to compute electronic vertical singlet transition energies at the time-dependent density functional theory (TDDFT) level using the B3LYP functional. The 6-311++G(d,p), 6-311(2+,2+)G(d,p), 6-311(3+,3+)G(df,pd), and 6-311(5+,5+)G(df,pd) basis sets were used for the transition energy calculations. Computed transition energies were found in good agreement with the corresponding experimental data. However, in higher transitions, the Rydberg contaminations were also obtained. The existence of ,,* type Rydberg transition was found near the lowest singlet ,,* state of all bases, which may be responsible for the ultrafast deactivation process in nucleic acid bases. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 768,778, 2004 [source] TGSA-Flex: Extending the capabilities of the Topo-Geometrical superposition algorithm to handle flexible moleculesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2004Xavier Gironés Abstract In this work, an extension of the already studied Topo-Geometrical Superposition Approach (TGSA) is presented. TGSA, a general-purpose, fast, automatic, and user-intuitive three-dimensional molecular alignment procedure, was originally designed to superpose rigid molecules simply based on atomic numbers, molecular coordinates, and connectivity. The algorithm is further developed to enable handling rotations around single bonds; in this way, common structural features, which were not properly aligned due to conformational causes, can be brought together, thus improving the molecular similarity picture of the final alignment. The present procedure, implemented in Fortran 90 and named TGSA-Flex, is deeply detailed and tested over four molecular sets: amino acids, nordihydroguaiaretic acid (NDGA) derivatives, HIV-1 protease inhibitors, and 1-[2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT) derivatives. TGSA-Flex performance is evaluated by means of computational time, number of superposed atoms (also comparing it with respect to the rigid approach), and index of fit between the compared structures. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 153,159, 2004 [source] Systematic quantum chemical study of DNA-base tautomersJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2004M. Piacenza Abstract The relative energies of the energetically low-lying tautomers of pyridone, cytosine, uracil, thymine, guanine, and iso-cytosine are studied by a variety of different quantum chemical methods. In particular, we employ density functional theory (DFT) using the six functionals HCTH407, PBE, BP86, B-LYP, B3-LYP, and BH-LYP, and the ab initio methods Hartree-Fock (HF), standard second-order Møller-Plesset perturbation theory (MP2), an improved version of it (SCS-MP2), and quadratic configuration interaction including single and double excitations (QCISD) and perturbative triple corrections [QCISD(T)]. A detailed basis set study is performed for the formamide/formamidic acid tautomeric pair. In general, large AO basis sets of at least valence triple-, quality including f-functions (TZV) are employed, which are found to be necessary for an accurate energetic description of the various structures. The performance of the more approximate methods is evaluated with QCISD(T)/TZV(2df,2dp) data taken as reference. In general it is found that DFT is not an appropriate method for the problem. For the tautomers of pyridone and cytosine, most density functionals, including the popular B3-LYP hybrid, predict a wrong energetic order, and only for guanine, the correct sequence of tautomers is obtained with all functionals. Out of the density functionals tested, BH-LYP, which includes a rather large fraction of HF exchange, performs best. A consistent description of the nonaromatic versus aromatic tautomers seems to be a general problem especially for pure, nonhybrid functionals. Tentatively, this could be assigned to the exchange potentials used while the functional itself, including the correlation part, seems to be appropriate. Out of the ab initio methods tested, the new SCS-MP2 approach seems to perform best because it effectively reduces some outliers obtained with standard MP2. It outperforms the much more costly QCISD method and seems to be a very good compromise between computational effort and accuracy. © 2003 Wiley Periodicals, Inc. J Comput Chem 1: 83,98, 2004 [source] Syntheses of 2H-labelled dihydropyrimidinediones and their metabolitesJOURNAL OF LABELLED COMPOUNDS AND RADIOPHARMACEUTICALS, Issue 1 2001Georg Heinkele Abstract Starting with uracil or thymine, [5,5,6,6- 2H4]-dihydrouracil and [5,6,6,,,,,,,- 2H6]-dihydrothymine were synthesised in high yields by catalytic deuteriation. Subsequent hydrolyses resulted in the corresponding ,-ureidoalkanoic acids and ,-aminoacids. Copyright © 2001 John Wiley & Sons, Ltd. [source] Gas-phase theoretical prediction of the metal affinity of copper(I) ion for DNA and RNA basesJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 3 2003Nino Russo Abstract The most stable tautomeric forms of free DNA and RNA bases were considered as substrates for the interaction of Cu+ ion. Several suitable attachment sites were selected that involved mono- and bi-coordination of the cation. B3LYP/6,311 + G(2df,2p) bond energies showed that copper ion has the major affinity for guanine and cytosine bases. The proposed values of Cu+ ion affinity are 59.9, 60.0, 80.2, 88.0 and 69.0 kcal mol,1 for uracil, thymine, cytosine, guanine and adenine, respectively. The preference for the mono- or bi-coordination depends on the particular tautomer for each base. Copyright © 2003 John Wiley & Sons, Ltd. [source] Clustering of nucleobases with alkali metals studied by electrospray ionization tandem mass spectrometry: implications for mechanisms of multistrand DNA stabilizationJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 7 2002Kim J. Koch Abstract 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 correlates with previously reported solution-phase data on sodium cation stabilized guanosine, thymine and uracil quartet structures believed to be responsible for telomere stabilization. In the presence of potassium, cesium or ammonium cations, pentameric magic number clusters are formed from thymine and uracil, while in solution the nucleoside isoguanosine yields clusters of this favored size. The formation of magic number metaclusters occurs for thymine and uracil in the presence of ammonium cations. These doubly charged 10- and 15-mers are tentatively attributed to the formation of pentamer/ammonium cation/ pentamer sandwich structures. Copyright © 2002 John Wiley & Sons, Ltd. [source] Precision synthesis and characterization of thymine-functionalized polyisobutyleneJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 16 2010Mustafa Y. Sen Abstract A new two-step synthesis of polyisobutylene (PIB) with precisely one thymine functionality per chain (PIB-T) is reported. The primary hydroxyl-functionalized PIB (PIB-OH) precursor was prepared by direct functionalization via living carbocationic polymerization of isobutylene initiated by the ,-methylstyrene epoxide/TiCl4 system. Matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) of a low molecular weight PIB-OH precursor demonstrated the effectiveness of direct functionalization by this method. A PIB-acrylate precursor (PIB-Ac) was obtained from such a PIB-OH, and the PIB-T was subsequently prepared by Michael addition of thymine across the acrylate double bond. MALDI-ToF MS of the products verified that all polymer chains carried precisely one thymine group. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 3501,3506, 2010 [source] Nucleobases modified azo-polysiloxanes, materials with potential application in biomolecules nanomanipulationJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 18 2007Nicolae Hurduc Abstract Here we show the possibility to obtain azopolysiloxanes modified with nucleobases (adenine and thymine) with potential application in immobilization and nanomanipulation of biomolecules. We propose a photofluidization mechanism based on the concept of the conformational instability, which can explain the presence of the fluid state below the glass transition. The azopolymers were characterized by 1H NMR, GPC, DSC, DTG, UV spectroscopy, AFM analysis, and molecular simulations. Depending on the type of nucleobase used, the surface of the azopolysiloxane film can be structured in different ways under UV irradiation. Photoisomerization studies in solid state were carried out to demonstrate the influence of the operational conditions (presence or absence of natural visible light) on the polymeric film UV response. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4240,4248, 2007 [source] Raman microspectroscopic study on low-pH-induced DNA structural transitions in the presence of magnesium ionsJOURNAL OF RAMAN SPECTROSCOPY, Issue 10 2002C. M. Muntean Low-pH-induced DNA structural changes were investigated in the pH range 6.8,2.10 by Raman microspectroscopy. Measurements were carried out on calf thymus DNA in the presence of low concentrations of Mg2+ ions. Vibrational spectra are presented in the wavenumber region 500,1650 cm,1. Large changes in the Raman spectra of calf-thymus DNA were observed on lowering the pH value. These are due to protonation and unstacking of the DNA bases during DNA melting and also to changes in the DNA backbone conformation. The intensities of the Raman bands of guanine (681 cm,1), adenine (728 cm,1), thymine (752 cm,1) and cytosine (785 cm,1), typical of the C2,- endo - anti conformation of B-DNA, are discussed. The B-form marker near 835 cm,1 and the base vibrations in the higher wavenumber region (1200,1680 cm,1) are analysed. Effects of low pH value upon the protonation mechanism of opening AT and changing the protonation of GC base pairs in DNA are discussed. Copyright © 2002 John Wiley & Sons, Ltd. [source] Conformational study of AZT in aqueous solution and adsorbed on a silver surface by means of Raman spectroscopyJOURNAL OF RAMAN SPECTROSCOPY, Issue 1 2002Laura Rivas The adsorption and conformation of the anti-HIV drug AZT, and also thymine and 2,-deoxythymidine, were studied on Ag colloids by surface-enhanced Raman spectroscopy, showing that the conformational change induced by the adsorption on an Ag surface is similar to that induced by an alkaline pH, both related to deprotonation of the N-3 atom leading to the C-3,- endo conformer. Copyright © 2002 John Wiley & Sons, Ltd. [source] A SERS probe of adenyl residues available for intermolecular interactions.JOURNAL OF RAMAN SPECTROSCOPY, Issue 11 2001Part I, adenyl, fingerprint' This work validated a SERS probe able to compare adenyl reactivity in DNA and RNA. A Creighton silver colloid including adenine (A) [or 2, -deoxyadenosine 5, -phosphate (pdA)] from 2 × 10,3 to 2 × 10,8M is stabilized in the absence or presence of chloride. Concentration-dependent SER spectral profiles reveal how A may interact with (Ag)n+ sites. At concentration ,2 × 10,5M adsorption of (A)n clusters prevents the colloid from undergoing salt effects. Adsorption via N1/N3 is allowed whereas C6NH2 is involved in self-association. At [A] <2 × 10,5M with chloride, hydrogen bonding between chloride and the C6NH2 group enhances C6N electronegativity, which assists C6N/N7 cooperative adsorption. Complex A(Cl,) entities compete with individual chloride ions for adsorption on silver. Very similar C6N/N7 adenyl adsorption occurs for pdA but only above 2 × 10,5M. Chloride,adenyl bonding is reduced and pdA self-association is weaker than adenine self-association. Steric factors, repulsive electrostatic forces and phosphate competitive reactivity with respect to chloride may explain the much higher pdA concentration needed to saturate the silver surface compared with A. Mg2+,phosphate complexation entails concentration-dependent opposite effects on adenyl reactivity with (Ag)n+ sites. Cytosine, thymine and guanine base or corresponding nucleotides deliver weaker SER spectra and much higher SERS responses for chloride adsorption compared with A or pdA. This reveals a weaker adsorption of the oxo bases, assumed to result from alternative oxo and nitrogen interactions with the (Ag)n+ sites. Copyright © 2001 John Wiley & Sons, Ltd. [source] Predicting Anti-HIV-1 Activities of HEPT-analog Compounds by Using Support Vector ClassificationMOLECULAR INFORMATICS, Issue 9 2005Wencong Lu Abstract The support vector classification (SVC), as a novel approach, was employed to make a distinction within a class of non-nucleoside reverse transcriptase inhibitors. 1-[(2-hydroxyethoxy) methyl]-6-(phenyl thio)-thymine (HEPT) derivatives with high anti-HIV-1 activities and those with low anti-HIV-1 activities were compared on the basis of the following molecular descriptors: net atomic charge on atom 4, molecular volume, partition coefficient, molecular refractivity, molecular polarisability and molecular weight. By using the SVC, a mathematical model was constructed, which can predict the anti-HIV-1 activities of the HEPT-analogue compounds, with an accuracy of 100% as calculated on the basis of the leave-one-out cross-validation (LOOCV) test. The results indicate that the performance of the SVC model exceeds that of the stepwise discriminant analysis (SDA) model, for which a prediction accuracy of 94% was reported. [source] Mid-cell Z ring assembly in the absence of entry into the elongation phase of the round of replication in bacteria: co-ordinating chromosome replication with cell divisionMOLECULAR MICROBIOLOGY, Issue 3 2000A. Regamey We have shown previously that, when spores of a thymine-requiring strain of Bacillus subtilis were grown out in the absence of thymine, mid-cell Z rings formed over the nucleoid and much earlier than might be expected with respect to progression into the round of replication. It is now shown that such conditions allow no replication of oriC. Rather than replication, partial degradation of the oriC region occurs, suggesting that the status of this region is connected with the ,premature' mid-cell Z ring assembly. A correlation was observed between entry into the replication elongation phase and a block to mid-cell Z rings. The conformation of the nucleoid under various conditions of DNA replication inhibition or limitation suggests that relief of nucleoid occlusion is not primarily responsible for mid-cell Z ring formation in the absence of thymine. We propose the existence of a specific structure at mid-cell that defines the Z ring nucleation site (NS). It is suggested that this NS is normally masked by the replisome upon initiation of replication or soon after entry into the elongation phase, and subsequently unmasked relatively late in the round. During spore outgrowth in the absence of thymine, this checkpoint control over mid-cell Z ring assembly breaks down prematurely. [source] Photosensitizing Properties of Triplet ,-Lapachones in Acetonitrile SolutionPHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 1 2009José Carlos Netto-Ferreira The photochemical reactivity of ,-lapachone (1), nor -,-lapachone (2) and 1,2-naphthoquinone (3) towards amino acids and nucleobases or nucleosides has been examined employing the nanosecond laser flash photolysis technique. Excitation (, = 355 nm) of degassed solutions of 1,3, in acetonitrile, resulted in the formation of their corresponding triplet excited states. These transients were efficiently quenched by l -tryptophan, l -tryptophan methyl ester, l -tyrosine, l -tyrosine methyl ester and l -cysteine (kq , 109 L mol,1 s,1). For l -tryptophan, l -tyrosine and their methyl esters new transients were formed in the quenching process, which were assigned to the corresponding radical pair resulting from an initial electron transfer from the amino acids or their esters to the excited quinone, followed by a fast proton transfer. No measurable quenching rate constants could be observed in the presence of thymine and thymidine. On the other hand, efficient rate constants were obtained when 1,3 were quenched by 2,-deoxyguanosine (kq , 109 L mol,1 s,1). The quantum efficiency of singlet oxygen (1O2) formation from 1 to 3 was determined employing time-resolved near-IR emission studies upon laser excitation and showed considerably high values in all cases (,, = 0.6), which are fully in accord with the ,,* character of these triplets in acetonitrile. [source] Sequence, Structure and Energy Transfer in DNA,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 3 2007Thomas M. Nordlund Excitation energy transfer in DNA has similarities to charge transfer, but the transport is of an excited state, not of mass or charge. Use of the fluorescent, modified adenine base 2-aminopurine (2AP) as an energy trap in short (3- to 20-base) single- and double-stranded DNA oligomers is reviewed. Variation of 2AP's neighboring sequence shows (1) relatively efficient transfer from adenine compared to that from cytosine and thymine, (2) efficient transfer from guanine, but only when 2AP is at the 3, end, (3) approximate equality of efficiencies for 3, to 5, and 5, to 3, directional transfer in adenine tracks. The overall, average transfer distance at room temperature is about four adenine bases or less before de-excitation. The transfer fluorescence excitation spectral shape is similar to that of the absorption spectrum of the neighboring normal bases, confirming that initial excitation of the normal bases, followed by emission from 2AP (i.e. energy transfer), is occurring. Transfer apparently may take place both along one strand and cross-strand, depending on the oligomer sequence. Efficiency increases when the temperature is decreased, rising above 50% (overall efficiency) in decamers of adenine below ,60°C (frozen media). Modeling of the efficiencies of transfer from the nearest several adenine neighbors of 2AP in these oligomers suggests that the nearest two neighbors transfer with near 100% efficiency. As bases in B DNA, as well as in single-stranded DNA, are separated by less than 5 Å (less than the size of a base), standard Förster transfer theory should not apply. Indeed, while both theory and experiment show efficiency decreasing with donor,acceptor distance, the experimental dependence clearly disagrees with Förster 1/r6 dependence. It is not yet clear what the best theoretical approach is, but any calculation must deal accurately with the excited states of bases, including strong base,base interactions and structural fluctuations, and should reflect the increase of efficiency with temperature decrease and the relative insensitivity to strandedness (single, double). Attempts to use DNA as a molecular "fiber optic" face three primary challenges. First, reasonable efficiency over more than a base or two occurs only in adenine stretches at temperatures well below freezing. Second, transfer in these adenine tracks is efficient in both directions. Third, absorption of UV light occurs randomly, making excitation at a specific site on this "fiber optic" a challenge. [source] | ||||||||||||||||||||||||||||||||||