Duplex

Distribution by Scientific Domains
Distribution within Chemistry

Kinds of Duplex

  • base-intercalated duplex
  • dna duplex
  • linear duplex
  • oligonucleotide duplex
  • rna duplex
  • sirna duplex

  • Terms modified by Duplex

  • duplex d
  • duplex dna
  • duplex formation
  • duplex imaging
  • duplex scanning
  • duplex sonography
  • duplex stability
  • duplex stainless steel
  • duplex structure
  • duplex ultrasonography
  • duplex ultrasound

  • Selected Abstracts


    DNA and RNA in Anhydrous Media: Duplex, Triplex, and G-Quadruplex Secondary Structures in a Deep Eutectic Solvent,

    ANGEWANDTE CHEMIE, Issue 36 2010
    Irena Mamajanov
    Verlockende Aussichten! Tiefeutektische Solventien (DESs) sind nichtflüchtige Medien, die sich für viele chemische Reaktionen eignen. In einem wasserfreien DES bilden Nucleinsäuren Duplex-, Triplex- und G-Quadruplex-Strukturen (die sich teilweise von denen in wässrigen Medien unterscheiden), sodass katalytische Nucleinsäuren und Enzym-Nucleinsäure-Komplexe vielleicht auch in diesen Solventien genutzt werden können. [source]


    Probing the Molecular Recognition of a DNA,RNA Hybrid Duplex,

    ANGEWANDTE CHEMIE, Issue 18 2010
    Richard
    Verquerer und verquerer! Ein Biarylpyrimidin-Ligand (siehe Bild: N,blau, H,cyan, S,gelb) zeigt eine ausgeprägte Struktur- und Sequenzselektivität für den Poly(dA),Poly(rU)-Hybriddoppelstrang. Bei einer unerwarteten Bindungsform kann dieser Ligand durch Interkalation mit zehn Basenpaaren wechselwirken. Eine starke Korrelation zwischen Hybriddoppelstrang- und DNA-Tripelstrang-Bindung zeigt neue Wege des Ligandendesigns auf. [source]


    Duplex ultrasonography and varicose veins

    BRITISH JOURNAL OF SURGERY (NOW INCLUDES EUROPEAN JOURNAL OF SURGERY), Issue 5 2007
    N. J. M. London
    Duplex scans for all [source]


    Lower limb ulceration: a detailed study of aetiology in 555 patients

    BRITISH JOURNAL OF SURGERY (NOW INCLUDES EUROPEAN JOURNAL OF SURGERY), Issue 4 2000
    J. Naik
    Background: The purpose of the study was to investigate the aetiology of lower limb ulceration. Methods: The aetiology of lower limb ulceration was reviewed in 555 patients with 689 ulcerated limbs referred to a single-visit leg ulcer clinic. Results: The mean age of the patients was 70 (range 27,95) years and 335 (60 per cent) were women. The aetiology of the ulceration in 689 limbs was venous in 496 (72 per cent), arterial in 14 (2 per cent), mixed venous and arterial in 101 (15 per cent), with other causes in 78 (11 per cent). Of the 496 venous ulcers, 261 (53 per cent) had isolated superficial reflux, 233 (47 per cent) had deep venous reflux, of which 165 (71 per cent) had full-length and 68 (29 per cent) segmental reflux, and two patients had isolated perforator reflux. Deep venous obstruction was present in 16 limbs (3 per cent) with venous ulcers and 14 of these demonstrated continuous flow in the long saphenous vein (LSV). Of the 261 ulcerated legs with isolated superficial reflux, 197 (75 per cent) had LSV reflux only, 22 (8 per cent) had short saphenous vein (SSV) reflux only and 41 (16 per cent) had combined LSV and SSV reflux. Of those with LSV reflux, 65 per cent had a medial malleolar ulcer and 20 per cent had a lateral malleolar lesion. Of those with SSV reflux, 62 per cent had a lateral malleolar ulcer and 38 per cent had a medial malleolar ulcer. Conclusion: Half of the ulcerated legs have superficial venous reflux; these combined with the superficial and segmental deep venous reflux group comprise the 65 per cent of patients who may benefit from superficial venous surgery. Continuous flow in the LSV should alert the clinician to deep venous obstruction, in which circumstance compression therapy should be used with extreme caution. Duplex is central to the investigation of the ulcerated leg. © 2000 British Journal of Surgery Society Ltd [source]


    Fluorescent 5-Alkynyl-2,-Deoxyuridines: High Emission Efficiency of a Conjugated Perylene Nucleoside in a DNA Duplex

    CHEMBIOCHEM, Issue 5 2006
    Mikhail V. Skorobogatyi
    Abstract Four fluorescent 5-alkynyl-2,-deoxyuridines were studied in DNA oligonucleotides and their duplexes. The fluorescence response to hybridization differs dramatically for nucleosides containing a perylene fluorochrome either conjugated or not conjugated to the nucleobase. The conjugated nucleoside, 5-(perylen-3-ylethynyl)-2,-deoxyuridine, shows enhanced long-wavelength emission in the DNA duplex, in contrast to the blue fluorescence of perylene on a flexible linker (in 5-[(perylen-3-yl)methoxyprop-1-ynyl]-2,-deoxyuridine), which is quenched upon duplex formation. [source]


    Oligonucleotide , Minor Groove Binder 1:2 Conjugates: Side by Side Parallel Minor Groove Binder Motif in Stabilization of DNA Duplex

    CHEMINFORM, Issue 6 2005
    Vladimir A. Ryabinin
    Abstract For Abstract see ChemInform Abstract in Full Text. [source]


    An Efficient Fluorescence Resonance Energy Transfer (FRET) between Pyrene and Perylene Assembled in a DNA Duplex and Its Potential for Discriminating Single-Base Changes

    CHEMISTRY - A EUROPEAN JOURNAL, Issue 8 2010
    Hiromu 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]


    Polymerase-Catalysed Incorporation of Glucose Nucleotides into a DNA Duplex

    CHEMISTRY - A EUROPEAN JOURNAL, Issue 22 2009
    Marleen Renders
    Abstract Active but unselective: Nucleoside triphosphates possessing glucose moieties (such as those depicted) instead of the natural furanose rings are recognised by the active sites of polymerases. Polymerases therefore seem to be very unspecific in their recognition patterns. The enzymatic recognition of six-membered ring nucleoside triphosphates,in particular the 6,-triphosphates of (,- D -glucopyranosyl)thymine, (2,,3,-dideoxy-,- D -glucopyranosyl)thymine, (3,,4,-dideoxy-,- D -glucopyranosyl)thymine and (2,,3,-dideoxy-,- D -glucopyranosyl)adenine,was investigated. Despite the facts that the pyranose nucleic acids obtained by polymerisation of these monomers do not hybridise in solution with DNA and that the geometry of a DNA strand in a natural duplex differs from that of a pyranose nucleic acid, elongation of the DNA duplex with all four nucleotide analogues by Vent,(exo,) polymerase was observed. Modelling experiments showed that hydrogen bonds are formed when 2,,3,-dideoxy-,-homo-T building blocks or ,- D - gluco -T building blocks are incorporated opposite adenosine residues in the template but not when they are incorporated opposite thymine residues in the template. The model shows a near perfect alignment of a secondary hydroxy group at the end of the primer and the ,-phosphate group of the incoming triphosphate. The results of these experiments provide new information on the role of the active site of the enzyme in the polymerisation reaction. [source]


    Discrimination of G-Quadruplexes from Duplex and Single-Stranded DNAs with Fluorescence and Energy-Transfer Fluorescence Spectra of Crystal Violet

    CHEMISTRY - A EUROPEAN JOURNAL, Issue 4 2009
    De-Ming Kong Dr.
    Abstract G-rich nucleic acid sequences with the potential to form G-quadruplex structures are common in biologically important regions. Most of these sequences are present with their complementary strands, so the development of a sensitive biosensor to distinguish G-quadruplex and duplex structures and to determine the competitive ability of quadruplex to duplex structures has received a great deal of attention. In this work, the interactions between two triphenylmethane dyes (malachite green (MG) and crystal violet (CV)) and G-quadruplex, duplex, or single-stranded DNAs were studied by fluorescence spectroscopy and energy-transfer fluorescence spectroscopy. Good discrimination between quadruplexes and duplex or single-stranded DNAs can be achieved by using the fluorescence spectrum of CV or the energy-transfer fluorescence spectra of CV and MG. In addition, by using energy-transfer fluorescence titrations of CV with G-quadruplexes, the binding-stoichiometry ratios of CV to G-quadruplexes can be determined. By using the fluorescence titrations of G-quadruplex,CV complexes with C-rich complementary strands, the fraction of G-rich oligonucleotide that engages in G-quadruplex structures in the presence of the complementary sequence can be measured. This study may provide a simple method for discrimination between quadruplexes and duplex or single-stranded DNAs and for measuring G-quadruplex percentages in the presence of the complementary C-rich sequences. [source]


    Structure of the ,-Homo-DNA:RNA Duplex and the Function of Twist and Slide To Catalogue Nucleic Acid Duplexes

    CHEMISTRY - A EUROPEAN JOURNAL, Issue 1 2007
    Koen Nauwelaerts Dr.
    Abstract High-resolution NMR studies of an ,-homo-DNA:RNA duplex reveal the formation of a right-handed parallel-oriented helix. It differs significantly from a standard A- or B-type helix by a small twist value (26.2°), which leads to a helical pitch of 13.7 base pairs per helical turn, a negative inclination (,1.78 Å) and a large x displacement (5.90 Å). The rise (3.4 Å) is similar to that found in B-DNA. The solution of this new helix structure has stimulated us to develop a mathematical and geometrical model based on slide and twist parameters to describe nucleic acid duplexes. All existing duplexes can be positioned within this landscape, which can be used to understand the helicalization process. [source]


    Can Copper(II) Mediate Hoogsteen Base-Pairing in a Left-Handed DNA Duplex?

    CHEMPHYSCHEM, Issue 3 2010
    A Pulse EPR Study
    Abstract Pulse EPR spectroscopy is used to investigate possible structural features of the copper(II) ion coordinated to poly(dG-dC),poly(dG-dC) in a frozen aqueous solution, and the structural changes of the polynucleotide induced by the presence of the metal ion. Two different copper species were identified and their geometry explained by a molecular model. According to this model, one species is exclusively coordinated to a single guanine with the N7 nitrogen atom forming a coordinative bond with the copper. In the other species, a guanine and a cytosine form a ternary complex together with the copper ion. A copper crosslink between the N7 of guanine and N3 of cytosine is proposed as the most probable coordination site. Moreover, no evidence was found for an interaction of either copper species with a phosphate group or equatorial water molecules. In addition, circular dichroism (CD) spectroscopy showed that the DNA of the CuII -poly(dG-dC),poly(dG-dC) adducts resembles the left-handed Z-form. These results suggest that metal-mediated Hoogsteen base pairing, as previously proposed for a right-handed DNA duplex, can also occur in a double-stranded left-handed DNA. [source]


    Oligonucleotide Duplexes with Tethered Photoreactive Ruthenium(II) Complexes: Influence of the Ligands and Their Linker on the Photoinduced Electron Transfer and Crosslinking Processes of the Two Strands

    EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 4 2009
    Stéphanie Deroo
    Abstract The photoreactivity of new RuII -oligonucleotide conjugates is investigated in the presence of their complementary strands. The goal is to determine the origins of different effects of parameters that control the photocrosslinking process of the two strands. Therefore, two RuII compounds, either [Ru(tap)3]2+or [Ru(tap)2phen]2+ (tap = 1,4,5,8-tetraazaphenanthrene, phen = 1,10-phenanthroline) with different oxidation powers, were tethered with different linkers to either the 5,- or 3,-phosphate end of the probe strand before hybridization with the complementary strand. These systems were studied by time-resolved emission spectroscopy, UV/Vis absorption experiments, PAGE and MS (ESI) analyses. The best yields of photocrosslinking (45,%) obtained with [Ru(tap)3]2+ tethered to the 3,-position are due to (i) a higher oxidation power of the complex and (ii) its attachment at the 3,-position. Indeed, this tethering favours the interaction of the Ru compound with the duplex and, therefore, inhibits its photodechelation. This work allows better design of sequence-specific DNA photodamaging agents prior to biological applications.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source]


    Use of Short Duplexes for the Analysis of the Sequence-Dependent Cleavage of DNA by a Chemical Nuclease, a Manganese Porphyrin

    CHEMBIOCHEM, Issue 12 2005
    Sophie Mourgues
    Abstract A manganese porphyrin, manganese(III)-bis(aqua)- meso -tetrakis(4- N -methylpyridiniumyl)porphyrin, in the presence of KHSO5 is able to perform deoxyribose or guanine oxidation depending on its mode of interaction with DNA. These two reactions involve an oxygen-atom transfer or an electron transfer, respectively. The oxidative reactivity of the manganese-oxo porphyrin was compared on short oligonucleotide duplexes of different sequences. The major mechanism of DNA damage is due to deoxyribose hydroxylation at a site of strong interaction, an (A,T)3 sequence. Guanine oxidation by electron transfer was found not to be competitive with this major mechanism. It was found that a single intrastrand guanine was three orders of magnitude less reactive than an (A,T)3 sequence. The reactivity of a 5,-GG sequence was found to be intermediate and was estimated to be two orders of magnitude less than that of an (A,T)3 site. Short oligonucleotide duplexes, as double-stranded-DNA models, proved to be convenient tools for the study of the comparative reactivity of this reagent toward different sequences of DNA. However, they showed a particular reactivity at their terminal base pairs (the "end effect") that biased their modeling capacity for double-helix-DNA models. [source]


    Solution Structure and Stability of Tryptophan-Containing Nucleopeptide Duplexes

    CHEMBIOCHEM, Issue 1 2003
    Irene Gómez-Pinto
    Abstract Covalently linked peptide,oligonucleotide hybrids were used as models for studying tryptophan,DNA interactions. The structure and stability of several hybrids in which peptides and oligonucleotides are linked through a phosphodiester bond between the hydroxy group of a homoserine (Hse) side chain and the 3,-end of the oligonucleotide, have been studied by both NMR and CD spectroscopy and by restrained molecular dynamics methods. The three-dimensional solution structure of the complex between Ac-Lys-Trp-Lys-Hse(p3,dGCATCG)-Ala-OH (p=phosphate, Ac=acetyl) and its complementary strand 5,dCGTAGC has been determined from a set of 276 experimental NOE distances and 33 dihedral angle constraints. The oligonucleotide structure is a well-defined duplex that belongs to the B-form family of DNA structures. The covalently linked peptide adopts a folded structure in which the tryptophan side chain stacks against the 3,-terminal guanine moiety, which forms a cap at the end of the duplex. This stacking interaction, which resembles other tryptophan,nucleobase interactions observed in some protein,DNA complexes, is not observed in the single-stranded form of Ac-Lys-Trp-Lys-Hse(p3,dGCATCG)-Ala-OH, where the peptide chain is completely disordered. A comparison with the pure DNA duplex, d(5,GCTACG3,),(5,CGTAGC3,), indicates that the interaction between the peptide and the DNA contributes to the stability of the nucleopeptide duplex. The different contributions that stabilize this complex have been evaluated by studying other nucleopeptide compounds with related sequences. [source]


    Dynamics of the Delocalized Charges of a Radical Anion in A,T DNA Duplexes

    CHEMISTRY - A EUROPEAN JOURNAL, Issue 45 2009
    Ryuhei Yamagami Dr.
    Gone in the blink of any eye: The transient spectrum of the electron adducts of A,T pairs initially obtained shows that the unpaired electron is localized to the A site (see picture). Subsequently charge transfer from transients (A,T)., to T., occurs over the time range of microseconds. [source]


    2-Phenanthrenyl,DNA: Synthesis, Pairing, and Fluorescence Properties

    CHEMISTRY - A EUROPEAN JOURNAL, Issue 3 2009
    Nikolay
    Abstract Three 2,-phenanthrenyl- C -deoxyribonucleosides with donor (phenNH2), acceptor (phenNO2), or no (phenH) substitution on the phenanthrenyl core were synthesized and incorporated into oligodeoxyribonucleotides. Duplexes containing either one or three consecutive phenR residues, which were located opposite each other, were formed. Within these residues, the phenR residues are expected to recognize each other through interstrand stacking interactions, in much the same way as described previously for biphenyl DNA. The thermal, thermodynamic, and fluorescence properties of such duplexes were determined by UV melting analysis and fluorescence spectroscopy. Depending on the nature of the substituent, the thermal stability of single-modified duplexes can vary between ,2.7 to +11.3,°C in Tm and that of triple-modified duplexes from +7.8 to +11.1,°C. Van,t Hoff analysis suggested that the observed higher thermodynamic stability in phenH- and phenNO2 -containing duplexes is of enthalpic origin. A single phenH or phenNO2 residue in a bulge position also stabilizes a corresponding duplex. If a phenNO2 residue is placed in a bulge position next to a base mismatch this can lead, in a sequence-dependent manner, to duplex destabilization. The phenNO2 residue was found to be a highly efficient (10,100-fold) quencher of phenH and phenNH2 fluorescence if placed in the opposite position to the fluorophores. When phenH and phenNH2 residues were placed opposite each other, efficient quenching of phenH and enhancement of phenNH2 fluorescence was found, which is an indicator for electron- or energy-transfer processes between the aromatic units. [source]


    Structure of the ,-Homo-DNA:RNA Duplex and the Function of Twist and Slide To Catalogue Nucleic Acid Duplexes

    CHEMISTRY - A EUROPEAN JOURNAL, Issue 1 2007
    Koen Nauwelaerts Dr.
    Abstract High-resolution NMR studies of an ,-homo-DNA:RNA duplex reveal the formation of a right-handed parallel-oriented helix. It differs significantly from a standard A- or B-type helix by a small twist value (26.2°), which leads to a helical pitch of 13.7 base pairs per helical turn, a negative inclination (,1.78 Å) and a large x displacement (5.90 Å). The rise (3.4 Å) is similar to that found in B-DNA. The solution of this new helix structure has stimulated us to develop a mathematical and geometrical model based on slide and twist parameters to describe nucleic acid duplexes. All existing duplexes can be positioned within this landscape, which can be used to understand the helicalization process. [source]


    Oligonucleotide N3,,P5, Phosphoramidates and Thio -Phoshoramidates as Potential Therapeutic Agents

    CHEMISTRY & BIODIVERSITY, Issue 3 2010
    Sergei
    Abstract Nucleic acids analogues, i.e., oligonucleotide N3,,P5, phosphoramidates and N3,,P5, thio -phosphoramidates, containing 3,-amino-3,-deoxy nucleosides with various 2,-substituents were synthesized and extensively studied. These compounds resist nuclease hydrolysis and form stable duplexes with complementary native phosphodiester DNA and, particularly, RNA strands. An increase in duplexes' melting temperature, ,Tm, relative to their phosphodiester counterparts, reaches 2.2,4.0° per modified nucleoside. 2,-OH- (RNA-like), 2,- O -Me-, and 2,- ribo -F-nucleoside substitutions result in the highest degree of duplex stabilization. Moreover, under close to physiological salt and pH conditions, the 2,-deoxy- and 2,-fluoro-phosphoramidate compounds form extremely stable triple-stranded complexes with either single- or double-stranded phosphodiester DNA oligonucleotides. Melting temperature, Tm, of these triplexes exceeds Tm values for the isosequential phosphodiester counterparts by up to 35°. 2,-Deoxy-N3,,P5, phosphoramidates adopt RNA-like C3,- endo or N -type nucleoside sugar-ring conformations and hence can be used as stable RNA mimetics. Duplexes formed by 2,-deoxy phosphoramidates with complementary RNA strands are not substrates for RNase H-mediated cleavage in vitro. Oligonucleotide phosphoramidates and especially thio -phosphoramidates conjugated with lipid groups are cell-permeable and demonstrate high biological target specific activity in vitro. In vivo, these compounds show good bioavailability and efficient biodistribution to all major organs, while exerting acceptable toxicity at therapeutically relevant doses. Short oligonucleotide N3,,P5, thio -phosphoramidate conjugated to 5,-palmitoyl group, designated as GRN163L (Imetelstat), was recently introduced as a potent human telomerase inhibitor. GRN163L is not an antisense agent; it is a direct competitive inhibitor of human telomerase, which directly binds to the active site of the enzyme and thus inhibits its activity. This compound is currently in multiple Phase-I and Phase-I/II clinical trials as potential broad-spectrum anticancer agent. [source]


    Post-karyokinesis centrosome movement leaves a trail of unanswered questions

    CYTOSKELETON, Issue 3 2002
    Young Y. Ou
    Abstract The centrosome is a complex structure composed of a large number of proteins (pericentriolar material, PCM) usually organized around a pair of centrioles (or a centriole duplex). This structure is capable of nucleating and organizing microtubules, duplication, and motility. In general, episodes of dramatic centrosome movement correlate with periods of cellular reorganization and nowhere is cellular reorganization more apparent, or more important, than in the periods before and after cell division. It is now clear that centrosome movement occurs not only prior to cell division but also at its completion, in concert with cytokinesis. The focus of this review is the newly emerging picture of centrosome activity during the post-karyokinesis period and the role that this activity might play in the transition of cells from mitosis to interphase. Cell Motil. Cytoskeleton 51:123,132, 2002. © 2002 Wiley-Liss, Inc. [source]


    Identification of CpG methylation of the SNRPN gene by methylation-specific multiplex PCR

    ELECTROPHORESIS, Issue 2 2009
    Chia-Cheng Hung
    Abstract In this article, we show that methylation-specific multiplex PCR (MS-multiplex PCR) is a sensitive and specific single assay for detecting CpG methylation status as well as copy number aberrations. We used MS-multiplex PCR to simultaneously amplify three sequences: the 3, ends of the SNRPN gene (for unmethylated sequences), the KRITI gene (as internal control), and the promoter of the SNRPN gene containing CpG islands (for methylated sequences) after digestion with a methylation-sensitive restriction enzyme (HhaI). We established this duplex assay for the analysis of 38 individuals with Prader,Willi syndrome, 2 individuals with Angelman syndrome, and 28 unaffected individuals. By comparing the copy number of the three regions, the methylation status and the copy number changes can be easily distinguished by MS-multiplex PCR without the need of bisulfite treatment of the DNA. The data showed that MS-multiplex PCR allows for the estimation of the methylation level by comparing the copy number aberrations of unknown samples to the standards with a known methylated status. The in-house-designed MS-multiplex PCR protocol is a relatively simple, cost-effective, and highly reproducible approach as a significant strategy in clinical applications for epigenetics in a routine laboratory. [source]


    Oligonucleotide Duplexes with Tethered Photoreactive Ruthenium(II) Complexes: Influence of the Ligands and Their Linker on the Photoinduced Electron Transfer and Crosslinking Processes of the Two Strands

    EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 4 2009
    Stéphanie Deroo
    Abstract The photoreactivity of new RuII -oligonucleotide conjugates is investigated in the presence of their complementary strands. The goal is to determine the origins of different effects of parameters that control the photocrosslinking process of the two strands. Therefore, two RuII compounds, either [Ru(tap)3]2+or [Ru(tap)2phen]2+ (tap = 1,4,5,8-tetraazaphenanthrene, phen = 1,10-phenanthroline) with different oxidation powers, were tethered with different linkers to either the 5,- or 3,-phosphate end of the probe strand before hybridization with the complementary strand. These systems were studied by time-resolved emission spectroscopy, UV/Vis absorption experiments, PAGE and MS (ESI) analyses. The best yields of photocrosslinking (45,%) obtained with [Ru(tap)3]2+ tethered to the 3,-position are due to (i) a higher oxidation power of the complex and (ii) its attachment at the 3,-position. Indeed, this tethering favours the interaction of the Ru compound with the duplex and, therefore, inhibits its photodechelation. This work allows better design of sequence-specific DNA photodamaging agents prior to biological applications.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source]


    Prevalence and outcome of asymptomatic carotid stenosis: a population-based ultrasonographic study

    EUROPEAN JOURNAL OF NEUROLOGY, Issue 4 2002
    P. P. Mineva
    The aims of this epidemiological population-based cohort study were to examine the prevalence and outcomes of asymptomatic carotid stenosis (ACS) detected by duplex scanning and its relations to other vascular risk factors. A total of 500 volunteers, 200 men and 300 women, without signs and symptoms of cerebrovascular disease, aged 50,79 years, were enrolled in the study. The prevalence of ACS of 50% or greater was 6.4%. Only severe carotid stenosis was detected in 0.4% of the subjects examined. Significant relationships between ACS and coronary heart disease (CHD) [odds ratio (OR)=8.00], peripheral arterial disease (PAD) (OR=3.66), cigarette smoking in men (OR=4.39) and obesity in women (OR=0.31) were found. The biennial incidence rate of cerebral ischaemic events was 9.4%. A progression of ACS was revealed in 14% and a regression in 6.25% of the subjects. The patients with progressing ACS to more than 70% diameter reduction reached the end-points. Follow-up with repeated duplex scans in patients with advancing ACS of 50% or greater, especially smokers with CHD and PAD, is recommended. [source]


    Microstructural Characterization of Lamellar Features in TiAl by FIB Imaging,

    ADVANCED ENGINEERING MATERIALS, Issue 6 2010
    Dennis Peter
    A novel experimental procedure is introduced to determine phase fractions and the distribution of individual phases of TiAl-based two-phase alloys using the focused ion beam (FIB) technique. Two , -titanium aluminide alloys with a fine-grained duplex and a nearly lamellar microstructure are examined. The special FIB-based preparation procedure results in high contrast ion beam-induced images for all investigated alloys and allows to quantify the phase contents easily by automated microstructural analysis. Fine two-phase structures, e.g. lamellar colonies in , -TiAl, can be imaged in high resolution with respect to different phases. To validate the FIB-derived data, we compare them to results obtained with another method to determine phase fractions, electron back-scatter diffraction (EBSD). This direct comparison shows that the FIB-based technique generally provides slightly higher ,2 -fractions, and thus helps to overcome the limited lateral resolution near grain boundaries and interfaces associated with the conventional EBSD approach. Our study demonstrates that the FIB-based technique is a simple, fast, and more exact way to determine high resolution microstructural characteristics with respect to different phase constitutions in two-phase TiAl alloys and other such materials with fine, lamellar microstructures. [source]


    Indole in DNA: Comparison of a Nucleosidic with a Non-Nucleosidic DNA Base Substitution

    EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 3 2009
    Janez Barbaric
    Abstract The synthetic incorporation of indole as an artificial DNA base into oligonucleotides by two different structural approaches is described. For both types of modification, the indole moiety is attached through the C-3 position to the oligonucleotides. As a mimic of natural nucleosides, the indole nucleoside of ,-2,-deoxyribofuranoside (In) was synthesized. The corresponding In-modified duplexes were compared with duplexes that contained the indole group connected through (S)-3-amino-1,2-propanediol as an acyclic linker between the phosphodiester bridges of the oligonucleotides. This linker was tethered to the C-3 position of the indole heterocycle either directly (In,) or by a carbamate function (In,). The melting temperatures of the corresponding indole-modified DNA duplexes were measured and compared. Interestingly, not only the In, and In, modifications but also the natural-like In base surrogate destabilize the DNA duplex strongly. This result supports our approach to apply the acyclic glycol linker to incorporate aromatic molecules as artificial DNA base substitutions. The major advantage of acyclic glycol linkers [such as the applied (S)-3-amino-1,2-propanediol] is that the corresponding modifications are synthetically more easily and readily accessible, as it avoids the preparation of the nucleosidic bond and the separation and purification of the ,- and ,-anomers. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source]


    Anthraquinones as Artificial DNA Building Blocks

    EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 13 2008
    Nicolas Bouquin
    Abstract Synthesis and properties of oligodeoxynucleotides containing anthraquinone-derived building blocks with flexible linkers are described. Starting from the 1,4-, 1,5-, 1,8- and 2,6-dihydroxyanthraquinone isomers, the corresponding phosphoramidites were prepared and incorporated into oligonucleotides. The site of linker attachment was found to be of critical importance for hybrid stability. Whereas the 2,6-isomer led to a significant stabilization, all other isomers had a negative effect on the stability of the duplex. Spectroscopic studies showed that the anthraquinones behave as fluorescence quenchers. Models of anthraquinone-modified double-stranded hybrids are proposed. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source]


    Pyrrolidino DNA with Bases Corresponding to the 2-Oxo Deletion Mutants of Thymine and Cytosine: Synthesis and Triplex-Forming Properties

    EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 24 2007
    Alain 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]


    Synthesis 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 Site

    EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 10 2004
    Kousuke 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]


    Metal-Assisted Hybridization of Oligonucleotides, Evaluation of Circular 2,- O -Me RNA as Ligands for the TAR RNA Target

    EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 6 2003
    Laurence Zapata
    Abstract Two complementary oligonucleotides were conjugated with terpyridine ligands at their nearby 5,- and 3,-ends. Addition of a stoichiometric amount of a transition metal (Zn2+, Fe2+) resulted in a large increase in the melting temperature of the duplex. The conjugation of TPY to stem-loop oligomers provided an efficient procedure for the cyclisation of the oligomer after the addition of metal ions. Such a short stem-loop oligomer was designed to target the HIV-1 TAR RNA through loop,loop interactions. The addition of Zn2+ ions yielded a good ligand (Kd = 30 nM) for this RNA structural element. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source]


    DNA base repair , recognition and initiation of catalysis

    FEMS MICROBIOLOGY REVIEWS, Issue 6 2009
    Bjørn Dalhus
    Abstract Endogenous DNA damage induced by hydrolysis, reactive oxygen species and alkylation modifies DNA bases and the structure of the DNA duplex. Numerous mechanisms have evolved to protect cells from these deleterious effects. Base excision repair is the major pathway for removing base lesions. However, several mechanisms of direct base damage reversal, involving enzymes such as transferases, photolyases and oxidative demethylases, are specialized to remove certain types of photoproducts and alkylated bases. Mismatch excision repair corrects for misincorporation of bases by replicative DNA polymerases. The determination of the 3D structure and visualization of DNA repair proteins and their interactions with damaged DNA have considerably aided our understanding of the molecular basis for DNA base lesion repair and genome stability. Here, we review the structural biochemistry of base lesion recognition and initiation of one-step direct reversal (DR) of damage as well as the multistep pathways of base excision repair (BER), nucleotide incision repair (NIR) and mismatch repair (MMR). [source]


    Sequence-specific termination by T7 RNA polymerase requires formation of paused conformation prior to the point of RNA release

    GENES TO CELLS, Issue 4 2001
    Hoseok Song
    Background The sequence-specific, hairpin-independent termination signal for the bacteriophage RNA polymerases in Escherichia coli rrnB t1 terminator consists of two modules. The upstream module includes the conserved sequence and the downstream one is U-rich. Results Elongation complexes of T7 RNA polymerase paused 2 bp before reaching the termination site at a 500 µm concentration of NTP. At 5,50 µm NTP, however, they paused and terminated there or resumed elongation beyond the termination site. Only at higher concentrations of NTP (500 µm), the pause complex proceeded slowly to and became incompetent at the termination site. At 4 bp or more before the termination site, the unprotected single-stranded region of transcription bubble shrank at the trailing edge to 4,5 bp from ,10 bp, resulting from duplex formation of the conserved sequence. The pause and bubble collapse were not observed with an inactive mutant of the termination signal. Conclusion Sequence-specific termination requires the slow elongation mode of paused conformation, working only at high concentrations of NTP for a few bp prior to the RNA release site. The collapse of bubble that was observed several base pairs before the termination site and/or the resulting duplex might subsequently lead to the paused conformation of T7 elongation complexes. [source]