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Base Pairs (base + pair)
Kinds of Base Pairs Terms modified by Base Pairs Selected AbstractsSynthesis and Structural Properties of New Oligodeoxynucleotide Analogues Containing a 2,,5,-Internucleotidic Squaryldiamide Linkage Capable of Formation of a Watson,Crick Base Pair with Adenine and a Wobble Base Pair with Guanine at the 3,-Downstream Junction SiteEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 10 2004Kousuke Sato Abstract A TpT dimer analogue (U2,sq5,T), in which the 3,-5, phosphodiester linkage was replaced by a 2,-5, squaryldiamide linkage and the 5,-upstream T was replaced by a 3,-deoxyuridine, was synthesized in almost quantitative yield from diethyl squarate. This new dimer structural motif was designed to eliminate the squaryldiamide skeleton-induced overall strain in T3,sq5,T, previously incorporated into DNA fragments as a new TpT mimic, through the change in the connection mode from the 3,-5, linkage to a 2,-5, linkage. Spectral analyses of U2,sq5,T suggest that the overall structure of this dimer mimic is basically similar to that of TpT. A DNA 10mer 5,-d(CGCAU2,sq5,TAGCC)-3, incorporating this dimer was synthesized. From the CD analysis, it turned out that the overall structure of a DNA duplex of 5,-d(CGCAU2,sq5,TAGCC)-3,/3,-d(GCGTAATCGG)-5, is closer to that of the unmodified duplex than the DNA duplex of 5,-d(CGCAT3,sq5,TAGCC)-3,/3,-d(GCGTAATCGG)-5,. Interestingly, extensive Tm experiments suggest that d(CGCAU2,sq5,TAGCC)-3, exhibits intriguing inherent hybridization affinity not only for the completely complementary oligodeoxynucleotide 3,-d(GCGAATCGG)-5,, but also for 3,-d(GCGTAGTCGG)-5,, with a mismatched dG. The unique property of the 3,-downstream dT moiety of U2,sq5,T , the ability to recognize both dA and dG , was also supported by more detailed computational analysis of U2,sq5,T and TpT. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] pH-Independent Recognition of the dG,,,dC Base Pair in Triplex DNA: 9-Deazaguanine N7 -(2,-Deoxyribonucleoside) and Halogenated Derivatives Replacing Protonated dCHELVETICA CHIMICA ACTA, Issue 4 2006Frank Seela Abstract Triplex-forming oligonucleotides (TFOs) containing 9-deazaguanine N7 -(2,-deoxyribonucleoside) 1a and halogenated derivatives 1b,c were synthesized employing solid-phase oligonucleotide synthesis. For that purpose, the phosphoramidite building blocks 5a,c and 8a,c were synthesized. Multiple incorporations of 1a,c in place of dC were performed within TFOs, which involved the sequence of five consecutive 1a,c,,,dG,,,dC triplets as well as of three alternating 1a,c,,,dG,,,dC and dT,,,dA,,,dT triplets. These TFOs were designed to bind in a parallel orientation to the target duplex. Triplex forming properties of these oligonucleotides containing 1a,c in the presence of Na+ and Mg2+ were studied by UV/melting-curve analysis and confirmed by circular-dichroism (CD) spectroscopy. The oligonucleotides containing 1a in the place of dC formed stable triplexes at physiological pH in the case of sequence of five consecutive 1a,,,dG,,,dC triplets as well as three alternating 1a,c,,,dG,,,dC and dT,,,dA,,,dT triplets. The replacement of 1a by 9-halogenated derivatives 1b,c further enhanced the stability of DNA triplexes. Nucleosides 1a,c also stabilized duplex DNA. [source] In-Stem Molecular Beacon Containing a Pseudo Base Pair of Threoninol Nucleotides for the Removal of Background Emission,ANGEWANDTE CHEMIE, Issue 38 2009Hiromu Kashida Dr. Aus heißt auch aus: Ein neuartiger molekularer Beacon wurde entwickelt, der in der Stamm-Region Pseudobasenpaare aus dem Fluorophor (Perylen) und dem Fluoreszenzlöscher (Anthrachinon) enthält, wobei D -Threoninol-Einheiten als Verbindungsstück dienen (in-stem molecular beacon, ISMB). Der ISMB war in der Lage, eine Einzeldeletionsmutante von der Wildtypsequenz zu unterscheiden, ohne dass Hintergrundemission auftrat (siehe Bild). [source] Low-Energy-Barrier Proton Transfer Induced by Electron Attachment to the Guanine,,,Cytosine Base PairCHEMPHYSCHEM, Issue 4 2010Anna Szyperska Abstract The photoelectron spectrum of the anion of the guanine,,,cytosine base apair (GC)., is recorded for the first time. The observed variation in the spectral peak-height ratios with the source conditions suggests the presence of two or more anionic isomers. Two maxima of the broad bands in the photoelectron spectrum were measured at about 1.9 and about 2.6 eV. These values are very well reproduced by the vertical detachment energies of the B3LYP/6-31++G(d,p) calculated low-energy anionic structures, which are 1) the Watson,Crick base-pair anion with proton transferred from N1 of guanine to N3 of cytosine, 2) its analogue in which the proton is transferred from N9 of guanine to N7 of guanine, and 3) the global minimum geometry, which is formed from the latter anion by rotation of guanine about the axis approximately defined by C2 of guanine and C4 of cytosine. Furthermore, a minor difference in the stabilities of the two lowest energy anions explains the experimentally observed source (temperature) dependence of the PES spectrum. A rational procedure, based on the chemistry involved in the formation of anionic dimers, which enables the low-energy anions populated in the photoelectron spectrum to be identified is proposed. In contrast to the alternative combinatorial approach, which in the studied case would lead to carrying out quantum chemical calculations for 2000,2500 structures, the procedure described here reduces the computational problem to only 15 geometries. [source] Synthesis and Characterization of Oligodeoxynucleotides Containing Naphthyridine:Imidazopyridopyrimidine Base Pairs at their Sticky Ends.CHEMBIOCHEM, Issue 12 2006Application as Thermally Stabilized Decoy Molecules Abstract We describe the synthesis and properties of oligodeoxynucleotides (ODNs) containing 1,8-naphthyridine C-nucleoside (Na-NO) and imidazo[5,,4,:4,5]pyrido[2,3- d]pyrimidine nucleoside (Im-ON) at the termini. The modified ODNs were more resistant (6 to 40 times) than natural DNA to snake venom phosphodiesterase (SVPD). Although incorporation of one pair each of Na-NO:Im-ON on the sticky ends of the duplex was insufficient for thermal stabilization (+2.5,°C per pair relative to the G:C pair), the duplex containing two consecutive Na-NO:Im-ON pairs at its sticky ends was markedly stabilized thermally. The stabilizing effect of the incorporation of additional Na-NO:Im-ON pairs is estimated to be +7.8,°C per pair. Application as thermally stabilized decoy molecules to NF-,B (p50) was also demonstrated. The DNA duplexes containing the Na-NO:Im-ON pairs (ODN,I:ODN,II and ODN,III:ODN,IV) acted as competitors to the natural NF-,B-binding duplex (ODN,V: ODN,VI), and the calculated IC50 values of ODN,I:ODN,II and ODN,III:ODN,IV were 20.1±13.3 and 10.9±4.8 nM, respectively, greater than that of ODN,V:ODN,VI. [source] Structures and Stabilities of Small DNA Dumbbells with Watson,Crick and Hoogsteen Base PairsCHEMBIOCHEM, Issue 7 2003Nuria Escaja Dr. Abstract The structures and stabilities of cyclic DNA octamers of different sequences have been studied by NMR and CD spectroscopy and by restrained molecular dynamics. At low oligonucleotide concentrations, some of these molecules form stable monomeric structures consisting of a short stem of two base pairs connected by two mini-loops of two residues. To our knowledge, these dumbbell-like structures are the smallest observed to date. The relative stabilities of these cyclic dumbbells have been established by studying their melting transitions. Dumbbells made up purely of GC stems are more stable than those consisting purely of AT base pairs. The order of the base pairs closing the loops also has an important effect on the stabilities of these structures. The NMR data indicate that there are significant differences between the solution structures of dumbbells with G,C base pairs in the stem compared to those with A,T base pairs. In the case of dumbbells with G,C base pairs, the residues in the stem form a short segment of a BDNA helix stabilized by two Watson,Crick base pairs. In contrast, in the case of d,pCATTCATT,, the stem is formed by two A,T base pairs with the glycosidic angles of the adenine bases in a syn conformation, most probably forming Hoogsteen base pairs. Although the conformations of the loop residues are not very well defined, the thymine residues at the first position of the loop are observed to fold back into the minor groove of the stem. [source] Excited-State Double Proton Transfer in Model Base Pairs: The Stepwise Reaction on the Heterodimer of 7-Azaindole AnaloguesCHEMPHYSCHEM, Issue 2 2008Wan-Ting Hsieh Abstract A four fused-ring system 11-propyl-6H-indolo[2,3-b]quinoline (6,HIQ) is strategically designed and synthesized; it possesses a central moiety of 7-azaindole (7AI) and undergoes excited-state double proton transfer (ESDPT). Despite a barrierless type of ESDPT in the 6,HIQ dimer, femtosecond dynamics and a kinetic isotope effect provide indications for a stepwise ESDPT process in the 6,HIQ/7AI heterodimer, in which 6,HIQ (deuterated 6,HIQ) delivers the pyrrolyl proton (deuteron) to 7AI (deuterated 7AI) in less than 150 fs, forming an intermediate with a charge-transfer-like ion pair, followed by the transfer of a pyrrolyl proton (deuteron) from cation-like 7AI (deuterated 7AI) to the pyridinyl nitrogen of the anion-like 6,HIQ (deuterated 6,HIQ) in ,1.5±0.3 ps (3.5±0.3 ps). The barrier of second proton transfer is estimated to be 2.86 kcal,mol,1 for the 6,HIQ/7AI heterodimer. [source] Ionization-Induced Proton Transfer in Model DNA Base Pairs: A Theoretical Study of the Radical Ions of the 7-Azaindole DimerCHEMPHYSCHEM, Issue 12 2004Hsing-Yin Chen Dr. Abstract Proton-transfer reactions of the radical anion and cation of the 7-Azaindole (7AI) dimer were investigated by means of density functional theory (DFT). The calculated results for the dimer anion and cation were very similar. Three equilibrium structures, which correspond to the non-proton-transferred (normal), the single-proton-transferred (SPT) and the double-proton-transferred (tautomeric) forms, were found. The transition states for proton-transfer reactions were also located. The calculations showed that the first proton-transfer reaction (normal,SPT) is exothermic and almost barrier-free; therefore, it should occur spontaneously in the period of a vibration. In contrast, the second proton-transfer reaction (SPT,tautomer) was found to be far less-probable in terms of reaction energy and barrier. Hence, it was concluded that both (7AI)2and (7AI)2exist in the SPT form. The conclusion was further confirmed by the calculated electron vertical detachment energy (VDE) of the SPT form of (7AI)2, 1.33 eV, which is very close to the experimental measurement of 1.35 eV. The calculated VDEs of the normal and tautomeric (7AI)2forms were too small compared to the experimental value. The proton transfer process was found to be multidimensional in nature involving not only proton motion but also intermolecular rocking motion. In addition, IR spectra were calculated and reported. The spectra of the three structures showed very different features and, therefore, can be considered as fingerprints for future experimental identifications. The implications of these results to biology and spectroscopy are also briefly discussed. [source] Impedance Spectroscopy: A Powerful Tool for Rapid Biomolecular Screening and Cell Culture MonitoringELECTROANALYSIS, Issue 23 2005Isaac Abstract Dielectric spectroscopy or Electrochemical impedance spectroscopy (EIS) is traditionally used in corrosion monitoring, coatings evaluation, batteries, and electrodeposition and semiconductor characterization. However, in recent years, it is gaining widespread application in biotechnology, tissue engineering, and characterization of biological cells, disease diagnosis and cell culture monitoring. This article discusses the principles and implementation of dielectric spectroscopy in these bioanalytical applications. It provides examples of EIS as label-free, mediator-free strategies for rapid screening of biocompatible surfaces, monitoring pathogenic bacteria, as well as the analysis of heterogeneous systems, especially biological cells and tissues. Descriptions are given of the application of nanoparticles to improve the analytical sensitivities in EIS. Specific examples are given of the detection of base pair mismatches in the DNA sequence of Hepatitis B disease, TaySach's disease and Microcystis spp. Others include the EIS detection of viable pathogenic bacteria and the influence of nanomaterials in enhancing biosensor performance. Expanding applications in tissue engineering such as adsorption of proteins onto thiolated hexa(ethylene glycol)-terminated (EG6) self-assembled monolayer (SAM) are discussed. [source] Impact of Human Genome Project on treatment of frail and edentulous patients,GERODONTOLOGY, Issue 1 2004Ichiro Nishimura Objective:, Because of ongoing increases in life expectancy and deferment of edentulousness to older age, dentists are facing a different challenge to satisfy elderly denture wearers with a higher prevalence of chronic diseases. This discussion introduces the Human Genome databases as novel and powerful resources to re-examine the core problems experienced by frail and edentulous patients. Background:, Recent studies demonstrated that mandibular implant overdentures do not necessarily increase masticatory function, perception and satisfaction in denture wearers with adequate edentulous residual ridges. It has been demonstrated that the rate of edentulous residual ridge resorption significantly varies among individuals. The prognosis and cost-effectiveness of denture treatment, with or without implants, may largely depend on how the edentulous ridge is maintained. However, reliable clinical methods permitting dentists to predict the long-term health of the edentulous residual ridge are lacking. Materials and methods:, With the completion of the Human Genome Project, the genomic sequence database from this multinational consortium will provide a unique resource to determine the genetic basis of similarity and diversity of humans. Results:, One base pair in every 100 to 300 base pairs of the genome sequence varies among humans, suggesting that genetic diagnosis using the single nucleotide polymorphisms (SNPs) may provide a novel opportunity to differentiate our edentulous patients. Conclusions:, Future dental service for the elderly will require a personalized care paradigm, using highly sensitive diagnostic technology such as SNP genomic analysis, for recommending the treatment with greatest potential benefit. [source] Masking selected sequence variation by incorporating mismatches into melting analysis probes,HUMAN MUTATION, Issue 3 2006Rebecca L. Margraf Abstract Hybridization probe melting analysis can be complicated by the presence of sequence variation (benign polymorphisms or other mutations) near the targeted mutation. We investigated the use of "masking" probes to differentiate alleles with similar probe melting temperatures. Selected sequence variation was masked by incorporating mismatches (deletion, unmatched nucleotide, or universal base) into hybridization probes at the polymorphic location. Such masking probes create a probe/target mismatch with all possible alleles at the selected polymorphic location. Any allele with additional variation at another site is identified by a lower probe melting temperature than alleles that vary only at the masked position. This "masking technique" was applied to RET protooncogene and HPA6 mutation detection using unlabeled hybridization probes, a saturating dsDNA dye, and high-resolution melting analysis. Masking probes clearly distinguished all targeted mutations from polymorphisms when at least 1 base pair (bp) separated the mutation from the masked variation. We were able to mask polymorphisms immediately adjacent to mutations, except in certain cases, such as those involving single-base deletion probes when both adjacent positions had the same polymorphic nucleotides. The masking probes can also localize mutations to specific codons or nucleotide positions. Masking probes can simplify melting analysis of complex regions and eliminate the need for sequencing. Hum Mutat 27(3), 269,278, 2006. © 2006 Wiley-Liss, Inc. [source] A genetic polymorphism in the coding region of the gastric intrinsic factor gene (GIF) is associated with congenital intrinsic factor deficiency,HUMAN MUTATION, Issue 1 2004Marilyn M. Gordon Abstract Congenital intrinsic factor (IF) deficiency is a disorder characterized by megaloblastic anemia due to the absence of gastric IF (GIF, GenBank NM_005142) and GIF antibodies, with probable autosomal recessive inheritance. Most of the reported patients are isolated cases without genetic studies of the parents or siblings. Complete exonic sequences were determined from the PCR products generated from genomic DNA of five affected individuals. All probands had the identical variant (g.68A>G) in the second position of the fifth codon in the coding sequence of the gene that introduces a restriction enzyme site for Msp I and predicts a change in the mature protein from glutamine5 (CAG) to arginine5 (CGG). Three subjects were homozygous for this base exchange and two subjects were heterozygous, one of which was apparently a compound heterozygote at positions 1 and 2 of the fifth codon ([g.67C>G] + [g.68A>G]). The other patient, heterozygous for position 2, had one heterozygous unaffected parent. Most parents were heterozygous for this base exchange, confirming the pattern of autosomal recessive inheritance for congenital IF deficiency. cDNA encoding GIF was mutated at base pair g.68 (A>G) and expressed in COS-7 cells. The apparent size, secretion rate, and sensitivity to pepsin hydrolysis of the expressed IF were similar to native IF. The allelic frequency of g.68A>G was 0.067 and 0.038 in two control populations. This sequence aberration is not the cause of the phenotype, but is associated with the genotype of congenital IF deficiency and could serve as a marker for inheritance of this disorder. Hum Mutat 23:85,91, 2004. © 2003 Wiley-Liss, Inc. [source] Sequence-dependent proton-transfer reaction in stacked GC pair III: The influence of proton transfer to conductivityINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 12 2010Yasuyuki Nakanishi Abstract We have computed current,voltage character of natural DNA and its proton-transferred structure by scattering theory based on density functional theory. The current is not observed if the electron path contains only hydrogen bonding such as one base pair. The current becomes larger if the electron path contains ,,, stacking molecule such as two base pairs. We also found that the conductivity of pseudo-ion pair (C+G,/G,C+), which is derived from proton-transfer reaction in CG/GC, differs from that of the original structure. On the other hand, the current changes dramatically if the electrode connects to guanine or cytosine, which can be explained by the difference of electron affinities. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Interaction between the fluorinated amphiphilic copolymer poly(2,2,3,4,4,4-hexafluorobutyl methacrylate)- graft -poly(SPEG) and DNAJOURNAL OF APPLIED POLYMER SCIENCE, Issue 1 2010Ling Li Abstract A synthesized copolymer, synthesized from HFMA (hexaflurobutyl methacrylate) and SPEG (PHFMA- g -PSPEG), was synthesized. PHFMA- g -PSPEG intercalated to the DNA base pair via a strong hydrophobic force, and this was conformed by ultraviolet spectroscopy, transmittance measurements, micropolarity measurements, resonance light scattering (RLS) spectroscopy, and particle size measurements. The copolymer was used as a new probe to detect DNA according to the RLS technique. The hydrophobic interaction between PHFMA- g -PSPEG and DNA significantly enhanced the RLS signal, and the enhanced RLS intensity at 422 nm was proportional to the nucleic acid concentration within the range of 0.09,0.90 mg/L with a detection limit (3,) of 4.0 ,g/L. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010 [source] Remarkably low mtDNA control-region diversity and shallow population structure in Pacific cod Gadus macrocephalusJOURNAL OF FISH BIOLOGY, Issue 5 2010M. Liu To investigate the genetic diversity and describe the population structure in Gadus macrocephalus, a 452 base pair (bp) fragment of the mitochondrial DNA control region was analysed in 259 individuals. The results showed remarkably low nucleotide diversity and a lack of genealogical structure. Small but significant genetic differentiations, however, were detected among north-western Pacific populations, but no large-scale regional differences were detected. These results indicate that populations of G. macrocephalus in the north-western Pacific are genetically subdivided and represent evolutionary lineages that should be managed individually. [source] The Caenorhabditis elegans lev-8 gene encodes a novel type of nicotinic acetylcholine receptor , subunitJOURNAL OF NEUROCHEMISTRY, Issue 1 2005Paula R. Towers Abstract We have cloned Caenorhabditis elegans lev-8 and demonstrated that it encodes a novel nicotinic acetylcholine receptor (nAChR) subunit (previously designated ACR-13), which has functional roles in body wall and uterine muscles as part of a levamisole-sensitive receptor. LEV-8 is an ,,subunit and is the first to be described from the ACR-8-like group, a new class of nAChR with atypical acetylcholine-binding site (loop C) and channel-lining motifs. A single base pair change in the first intron of lev-8 in lev-8(x15) mutants leads to alternative splicing and the introduction of a premature stop codon. lev-8(x15) worms are partially resistant to levamisole-induced egg laying and paralysis, phenotypes rescued by expression of the wild-type gene. lev-8(x15) worms also show reduced rates of pharyngeal pumping. Electrophysiological recordings from body wall muscle show that currents recorded in response to levamisole have reduced amplitude in lev-8(x15) compared with wild-type animals. Consistent with these phenotypic observations, green fluorescent protein fused to LEV-8 is expressed in body wall and uterine muscle, motor neurons and epithelial-derived socket cells. Thus, LEV-8 is a levamisole receptor subunit and exhibits the most diverse expression pattern of any invertebrate nAChR subunit studied to date. [source] GENETIC DIVERGENCE CORRELATES WITH MORPHOLOGICAL AND ECOLOGICAL SUBDIVISION IN THE DEEP-WATER ELK KELP, PELAGOPHYCUS PORRA (PHAEOPHYCEAE)JOURNAL OF PHYCOLOGY, Issue 5 2000Kathy Ann Miller Pelagophycus porra (Leman) Setchell has a narrow distribution confined to deep water from the Channel Islands off the southern California coast to central Baja California, Mexico. Distinct morphotypes are consistently correlated with distinctive habitats, that is, windward exposures characterized by strong water motion and rocky substrates, and sheltered areas with soft substrates found on the lee sides of the islands. We tested the hypothesis that morphologically and ecologically distinct forms reflect genetically distinct stands. Individuals representing populations from three islands and the mainland were compared using RFLP analyses of the nuclear rDNA internal transcribed spacers (ITS1 and ITS2), chloroplast trnL (UAA) intron sequences, and random amplified polymorphic DNA (RAPDs). No variation was found in a survey of 20 restriction sites of ITS1 (ca. 320 base pair [bp]) and ITS2 (ca. 360 bp) among individuals from six populations. Likewise, comparisons of trnL intron (241 bp) sequences among nine individuals from seven populations were identical with the exception of a CATAGT insert in two adjacent stands. A RAPD analysis of 24 individuals from nine populations (4 windward and 5 leeward) using 16 primers generated 166 bands. Thirty-eight percent of the bands did not vary, 16% were unique to a given individual, and 46% were variable. Neighbor joining analysis produced a well-resolved tree with moderately high bootstrap support in which windward and leeward populations were easily distinguished. The lack of divergence in both the fast evolving nuclear rDNA-ITS and the chloroplast trnL intron does not support the morphotypes as different species. However, the compartmentalized differentiation shown in the RAPD data clearly points to isolation. This, and previous ecological studies that demonstrate habitat specificity suggest that leeward stands probably comprise a species in statu nascendi. [source] Substituent effects of phthalimide-based nucleoside analogs on binding a CG Watson,Crick base pairJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 10 2007Z. Xiao Abstract Five differently substituted phthalimide nucleosides were studied by NMR spectroscopic techniques for their ability to recognize and bind a cytosine,guanosine (CG) Watson,Crick base pair in CD2Cl2. Whereas only rather weak binding was observed for analogs with an amino, acetamido, or benzamido substituent, strong binding was observed with the analogs carrying an ureido and n -butyl ureido residue. 2D NOE measurements at low temperatures confirm the proposed binding mode for the high-affinity ligands but indicate binding interactions for the weakly bound analogs different from the expected geometry. Copyright © 2007 John Wiley & Sons, Ltd. [source] The influence of polymer concentration, applied voltage, modulation depth and pulse frequency on DNA separation by pulsed field CEJOURNAL OF SEPARATION SCIENCE, JSS, Issue 17-18 2010Zhenqing Li Abstract DNA fragments (0.1,10,kbp (kbp, kilo base pair)) separation by square-wave pulsed field CE in hydroxyethylcellulose (HEC, 1300,K) polymer was performed in this work. The effects of polymer concentration, pulse field strength, pulse frequency and modulation depth were investigated. We found that low HEC (about 0.1%) concentration is suitable for the separation of small DNA fragments (<1,kbp), whereas higher HEC concentration (>0.5%) is appropriated for high-mass DNA molecular (>1,kbp) separation. The mobility of DNA fragments is nearly linearly related to average separation voltage under pulsed field conditions. Higher modulation depth is suited to separate the longer DNA fragments and lower modulation depth favors the resolution of short DNA fragments. Thus, the intermediate modulation depth (100%) and pulse frequency (about 31.3,Hz) are prerequisite for high-resolution DNA separation. [source] Genetic variation in the bovine myostatin gene in UK beef cattle: Allele frequencies and haplotype analysis in the South DevonANIMAL GENETICS, Issue 5 2000J A Smith Work on Belgian Blue cattle revealed that an 11 base pair (bp) deletion within the bovine myostatin gene (GDF8) is associated with the double-muscled phenotype seen in this breed. Investigations focusing on other European breeds known to show double-muscling identified several mutations within the coding region of the gene associated with the double-muscled phenotype in different breeds. The number of mutations found suggest that myostatin is highly variable within beef cattle. Variations that alter the structure of the gene product such that the protein is inactivated are associated with the most pronounced form of double-muscling as seen in the Belgian Blue. However, other mutations may have a less extreme affect on muscle development. While overt double-muscling gives rise to a high incidence of dystocia (calving difficulty), it is possible that some variants may give enhanced muscling, but with limited calving problems. We describe sequence analysis of the myostatin gene in ten beef breeds commonly used in the UK and show that the 11-bp deletion responsible for double-muscling in the Belgian Blue is also present in the South Devon cattle population. Allele frequencies and haplotypes in the South Devon and a polymerase chain reaction (PCR) based test for the deletion are described. PCR amplification across the deleted region provides a quick and effective test with clear identification of heterozygous individuals. We discuss our results with regard to the effect of genotype on phenotype and differences observed between the Belgian Blue and the South Devon. [source] First look at RNA in l -configurationACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2004RNA in l -configuration Nucleic acid molecules in the mirror image or l -configuration are unknown in nature and are extraordinarily resistant to biological degradation. The identification of functional l -oligonucleotides called Spiegelmers offers a novel approach for drug discovery based on RNA. The sequence r(CUGGGCGG)·r(CCGCCUGG) was chosen as a model system for structural analysis of helices in the l -configuration as the structure of the d -form of this sequence has previously been determined in structural studies of 5S RNA domains, in particular domain E of the Thermus flavus 5S rRNA [Perbandt et al. (2001), Acta Cryst. D57, 219,224]. Unexpectedly, the results of crystallization trials showed little similarity between the d - and the l -forms of the duplex in either the crystallization hits or the diffraction performance. The crystal structure of this l -RNA duplex has been determined at 1.9,Å resolution with Rwork and Rfree of 23.8 and 28.6%, respectively. The crystals belong to space group R32, with unit-cell parameters a = 45.7, c = 264.6,Å. Although there are two molecules in the asymmetric unit rather than one, the structure of the l -form arranges helical pairs in a head-to-tail fashion to form pseudo-continuous infinite helices in the crystal as in the d -form. On the other hand, the wobble-like G·C+ base pair seen in the D-RNA analogue does not appear in the l -RNA duplex, which forms a regular double-helical structure with typical Watson,Crick base pairing. [source] Crystallization and preliminary X-ray analysis of human endonuclease 1 (APE1) in complex with an oligonucleotide containing a 5,6-dihydrouracil (DHU) or an ,-anomeric 2,-deoxyadenosine (,dA) modified baseACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2010Pascal Retailleau The multifunctional human apurinic/apyrimidinic (AP) endonuclease 1 (APE1) is a key enzyme involved in both the base-excision repair (BER) and nucleotide-incision repair (NIR) pathways. In the NIR pathway, APE1 incises DNA 5, to a number of oxidatively damaged bases. APE1 was crystallized in the presence of a 15-mer DNA containing an oxidatively damaged base in a single central 5,6-dihydrouracil (DHU)·T or ,-anomeric 2,-deoxyadenosine (,dA)·T base pair. Diffraction data sets were collected to 2.2 and 2.7,Å resolution from DNA-DHU,APE1 and DNA-,dA,APE1 crystals, respectively. The crystals were isomorphous and contained one enzyme molecule in the asymmetric unit. Molecular replacement was performed and the initial electron-density maps revealed that in both complexes APE1 had crystallized with a degradation DNA product reduced to a 6-mer, suggesting that NIR and exonuclease reactions occurred prior to crystallization. [source] Novel sequence insertion in a Mâori patient with transfusion-dependent , -thalassaemiaBRITISH JOURNAL OF HAEMATOLOGY, Issue 3 2005Hilary A. Blacklock Summary Although , -thalassaemia is common throughout the world, it has not been previously described in Polynesia. We report a novel sequence insertion where homozygosity for the defect results in transfusion-dependent anaemia. The repeated 45 base pair (bp) insertion causes duplication of the start codon and consequent transcription from the original initiation code would be predicted to lead to the production of an irrelevant seven-residue peptide, while residual translation from the novel initiation site would result in diminished yields of , -globin and consequent clinical ,+ -thalassaemia. [source] p53 intronic point mutation, aberrant splicing and telomeric associations in a case of B-chronic lymphocytic leukaemiaBRITISH JOURNAL OF HAEMATOLOGY, Issue 1 2000Teresa Bromidge We report a case of chronic lymphocytic leukaemia (CLL) with telomeric associations and a p53 intronic point mutation. Karyotypic analysis revealed clonal and non-clonal telomeric associations, accompanied by clonal cytogenetic abnormalities and also in isolation. The p53 mutation, which occurred at the invariant base pair ,2 of the splice acceptor site in intron 7 resulted in the abolition of correct splicing of exon 7 to exon 8. Multiple aberrant splice products were characterized, all of which differed from wildtype in the DNA binding domain. Fluorescence in situ hybridization demonstrated that the clone retained two copies of the p53 gene and wild-type p53 transcript was detected on cloning of reverse transcriptase polymerase chain reaction (RT-PCR) product, indicating that one wild-type allele remained. However, a plasmid clone with correct splicing at the exon 7/8 boundary, but with a 21 bp deletion in exon 8, was also found at low frequency. This finding indicates clonal evolution, resulting in complete loss of wild-type p53. The intronic point mutation was not present in DNA extracted from cervical tissue indicating that it was a leukaemic phenomenon. This is the first case of an intronic point mutation to be reported in CLL. This mutation led to chaotic p53 expression and, interestingly, occurred in a case showing telomeric associations, a rare phenomenon in B-CLL. [source] Damage Detection and Base Flipping in Direct DNA Alkylation RepairCHEMBIOCHEM, Issue 3 2009Cai-Guang Yang Prof. Abstract The foreign lesion: The mechanistic questions for DNA base damage detection by repair proteins are discussed in this Minireview. Repair proteins could either probe and locate a weakened base pair that results from base damage, or passively capture an extrahelical base lesion in the first step of damage searching on double-stranded DNA. How some repair proteins, such as AGT (see figure), locate base lesions in DNA is still not fully understood. To remove a few damaged bases efficiently from the context of the entire genome, the DNA base repair proteins rely on remarkably specific detection mechanisms to locate base lesions. This efficient molecular recognition event inside cells has been extensively studied with various structural and biochemical tools. These studies suggest that DNA base damage can be located by repair proteins by using two mechanisms: a repair protein can probe and detect a weakened base pair that results from mutagenic or cytotoxic base damage; alternatively, a protein can passively capture and stabilize an extrahelical base lesion. Our chemical and structural studies on the direct DNA repair proteins hAGT, C-Ada and ABH2 suggest that these proteins search for weakened base pairs in their first step of damage searching. We have also discovered a very unique base-flipping mechanism used by the DNA repair protein AlkB. This protein distorts DNA and favors single stranded DNA (ssDNA) substrates over double-stranded (dsDNA) ones. Potentially, it locates base lesions in dsDNA by imposing a constraint that targets less rigid regions of the duplex DNA. The exact mechanism of how AlkB and related proteins search for damage in ssDNA and dsDNA still awaits further studies. [source] An Efficient Fluorescence Resonance Energy Transfer (FRET) between Pyrene and Perylene Assembled in a DNA Duplex and Its Potential for Discriminating Single-Base ChangesCHEMISTRY - A EUROPEAN JOURNAL, Issue 8 2010Hiromu Kashida Dr. Abstract To increase the apparent Stokes' shift of perylene, pyrene (donor) and perylene (acceptor) were assembled in a DNA duplex to achieve the efficient fluorescence resonance energy transfer (FRET) from pyrene to perylene. Multiple donors were introduced in the vicinity of acceptors through D -threoninol and natural base pairs were inserted between the dyes. Accordingly, donors and acceptors could be accumulated inside the DNA without forming an undesired excimer/exciplex. When two pyrene moieties were located in proximity to one perylene with one base pair inserted between them, efficient FRET occurred within the duplex. Thus, strong emission at 460,nm was observed from perylene when excited at 345,nm at which pyrene has its absorption. The apparent Stokes' shift became as large as 115,nm with a high apparent FRET efficiency (,>1). However, the introduction of more than two pyrenes did not enhance the fluorescence intensity of perylene, due to the short Förster radius (R0) of the donor pyrene. Next, this FRET system was used to enlarge the Stokes' shift of the DNA probe, which can discriminate a one-base deletion mutant from wild type with a model system by incorporation of multiple donors into DNA. Two perylene moieties were tethered to the DNA on both sides of the intervening base, and two pyrenes were further inserted in the vicinity of the perylenes as an antenna. Hybridization of this FRET probe with a fully matched DNA allowed monomer emission of perylene when the pyrenes were excited. In contrast, excimer emission was generated by hybridization with a one-base deletion mutant. Thus, the apparent Stokes' shift was enhanced without loss of efficiency in the detection of the deletion mutant. [source] Mechanism of Charge Separation in DNA by Hole Transfer through Consecutive AdeninesCHEMISTRY - A EUROPEAN JOURNAL, Issue 12 2008Kiyohiko Kawai Prof. Abstract To investigate the mechanism of charge separation in DNA with consecutive adenines adjacent to a photosensitizer (Sens), a series of naphthalimide (NI) and 5-bromouracil (brU)-modified DNAs were prepared, and the quantum yields of formation of the charge-separated states (,) upon photo-excitation of the Sens NI in DNA were measured. The , was modulated by the incorporation site of brU, which changes the oxidation potential of its complementary A through hydrogen bonding and the hole-transfer rates between adenines. The results were interpreted as charge separation by means of the initial charge transfer between NI in the singlet excited state and the second- and third-nearest adenine to the NI. In addition, the oxidation of the A nearest to NI leads to the rapid charge recombination within a contact ion pair. This suggests that the charge-separation process can be refined to maximize the , by putting a redox-inactive spacer base pair between a photosensitizer and an A,T stretch. [source] Synthesis and Hybridization Properties of Modified Oligodeoxynucleotides Carrying Non-Natural BasesCHEMISTRY & BIODIVERSITY, Issue 2 2009Anna Aviñó Abstract The impact of the presence of nonnatural bases on the properties of oligodeoxynucleotides has been studied. First, oligodeoxynucleotides carrying 2,-deoxyzebularine were prepared, and the stability of duplexes carrying this analogue was determined by DNA melting experiments. Melting temperatures and thermodynamic data indicated the preference of 2,-deoxyzebularine for 2,-deoxyguanosine, which behaves as a 2,-deoxycytidine analogue, forming a less stable base pair due to the absence of the amino group at position 4. Moreover, the duplex,hairpin equilibrium of a self-complementary oligodeoxynucleotide carrying several natural and nonnatural bases including 2,-deoxyzebularine as a central mispair, was studied. Depending on the base present in the middle of the sequence, it is possible to affect the stability of the bimolecular duplex modulating the duplex,hairpin equilibrium. Magnesium ions were shown to stabilize preferentially the bimolecular duplex form. The results indicate the importance of the modifications and the role of cations in shifting the structural equilibrium. [source] Gas-Phase Watson,Crick and Hoogsteen Isomers of the Nucleobase Mimic 9-Methyladenine,2-PyridoneCHEMPHYSCHEM, Issue 7 2006Jann A. Frey Abstract 2-Pyridone (pyridin-2-one) is a mimic of the uracil and thymine nucleobases, with only one NH and CO group. It provides a single H-bonding site, compared to three for the canonical pyrimidine nucleobases. Employing the supersonically cooled 9-methyladenine,2-pyridone (9MAd,2PY) complex, which is the simplest base pair to mimic adenine-uracil or adenine-thymine, we show that its gas-phase UV spectrum consists of contributions from two isomers. Based on the H-bonding sites of 9-methyladenine, these are the Watson,Crick and Hoogsteen forms. Combining two-color two-photon ionisation (2C-R2PI), UV-UV depletion and laser-induced fluorescence spectroscopies allows separation of the two band systems, revealing characteristic intermolecular in-plane vibrations of the two isomers. The calculated S0 and S1 intermolecular frequencies are in good agreement with the experimental ones. Ab initio calculations predict the Watson,Crick isomer to be slightly more stable (D0=,16.0 kcal,mol,1) than the Hoogsteen isomer (D0=,15.0 kcal,mol,1). The calculated free energies ,fG0 of the Watson,Crick and Hoogsteen isomers agree qualitatively with the experimental isomer concentration ratio of 3:1. [source] Phylogenetic Reanalysis of the Saudi Gazelle and Its Implications for ConservationCONSERVATION BIOLOGY, Issue 4 2001Robert L. Hammond The Saudi gazelle ( Gazella saudiya) was endemic to the Arabian peninsula but is now considered extinct in the wild and is potentially a candidate for captive breeding and reintroduction. Using 375 base pairs of mitochondrial DNA (mtDNA) cytochrome b gene derived from museum samples collected from the wild prior to the presumed extinction of this species, we show that G. saudiya is the sister taxon of the African dorcas gazelle ( G. dorcas). Reciprocal monophyly of G. saudiya mtDNA haplotypes with G. dorcas, coupled with morphological distinctiveness, suggests that it is an evolutionarily significant unit. These data indicate that captive populations identified previously as potential sources of G. saudiya for captive breeding appear incorrectly designated and are irrelevant to the conservation of G. saudiya. The polymerase chain reaction,restriction fragment length polymorphism ( PCR-RFLP) analysis of several private collections of living gazelles in Saudi Arabia provides no evidence for the survival of G. saudiya. We recommend that field surveys be undertaken to establish whether G. saudiya is indeed extinct in the wild and that other private collections within the Arabian peninsula be screened genetically. We urge caution when captive animals of unknown provenance are used to investigate the phylogenetics of cryptic species groups. Resumen: La identificación de poblaciones taxonómicamente apropiadas de especies en peligro para programas de reproducción en cautiverio y de reintroducción es fundamental para su éxito. La Gacela Saudi (Gazella saudiya) fue endémica a la península de Arabia pero ahora está considerada como extinta en su medio y es un candidato potencial para reproducción en cautiverio y reintroducción. Utilizando 375 pares de bases de ADN mitocondrial (ADNmt) del gene citocromo b derivados de muestras de museos colectadas en el medio silvestre antes de la extinción de la especie, mostramos que G. saudiya es el taxón hermano de la gacela dorcas africana (G. dorcas). La monofilia recíproca de haplotipos de ADNmt de G. saudiya con G. dorcas, aunado a diferencias morfológicas, sugiere que es una unidad evolutiva significativa. Estos datos indican que las poblaciones cautivas identificadas previamente como fuente potencial de G. saudiya para reproducción en cautiverio están incorrectamente identificadas y son irrelevantes para la conservación de G. saudiya. El análisis PCR-RFLP de varias colecciones privadas de gacelas vivas en Arabia Saudita no proporcionan evidencia para la supervivencia de G. saudiya. Recomendamos que se realicen muestreos en el campo para establecer si en efecto G. saudiya está extinta en su hábitat y que se examinen genéticamente las otras colecciones privadas en la península Arábiga. Recomendamos precaución cuando animales cautivos de origen desconocido son utilizados para investigar la filogenia de grupos de especies crípticas. [source] | ||||||||||||||||||||||||||||||||||||||||||||||