Chemical synthesis of LNA-2-thiouridine and its influence on stability and selectivity of oligonucleotide binding to RNA.

Abstract:

:Hybridization to RNA is important for many applications, including antisense therapeutics, RNA interference, and microarray screening. Similar thermodynamic stabilities of A-U and G-U base pairs result in difficulties in selective binding to RNA. Moreover, A-U pairs are weaker than G-C pairs so that binding is sometimes weak when many A-U pairs are present. It is known, however, that replacement of uridine with 2-thiouridine significantly improves binding and selectivity. To test for additional improvement of binding and of the specificity for binding A over G, LNA-2-thiouridine was synthesized for the first time and incorporated into many LNA-2'-O-methyl-RNA/RNA duplexes. UV melting was used to measure the thermodynamic effect of replacing 2'-O-methyluridine with 2'-O-methyl-2-thiouridine or LNA-2-thiouridine. The 2-thiouridine usually enhances binding and selectivity. Selectivity is optimized when a single 2-thiouridine is placed at an internal position in a duplex.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Carlucci M,Kierzek E,Olejnik A,Turner DH,Kierzek R

doi

10.1021/bi901506f

subject

Has Abstract

pub_date

2009-11-24 00:00:00

pages

10882-93

issue

46

eissn

0006-2960

issn

1520-4995

journal_volume

48

pub_type

杂志文章
  • Protein arginine deiminase 4: evidence for a reverse protonation mechanism.

    abstract::The presumed role of an overactive protein arginine deiminase 4 (PAD4) in the pathophysiology of rheumatoid arthritis (RA) suggests that PAD4 inhibitors could be used to treat an underlying cause of RA, potentially offering a mechanism to stop further disease progression. Thus, the development of such inhibitors is of...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi700095s

    authors: Knuckley B,Bhatia M,Thompson PR

    更新日期:2007-06-05 00:00:00

  • The metastasis-associated extracellular matrix protein osteopontin forms transient structure in ligand interaction sites.

    abstract::Osteopontin (OPN) is an acidic hydrophilic glycophosphoprotein that was first identified as a major sialoprotein in bones. It functions as a cell attachment protein displaying a RGD cell adhesion sequence and as a cytokine that signals through integrin and CD44 cell adhesion molecules. OPN is also implicated in human ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi200291e

    authors: Platzer G,Schedlbauer A,Chemelli A,Ozdowy P,Coudevylle N,Auer R,Kontaxis G,Hartl M,Miles AJ,Wallace BA,Glatter O,Bister K,Konrat R

    更新日期:2011-07-12 00:00:00

  • Formation of radiation-induced cross-links between thymine and tyrosine: possible model for cross-linking of DNA and proteins by ionizing radiation.

    abstract::A model for radiation-induced cross-linking of DNA and proteins has been developed. It is based on initial formation of free radicals on a DNA base, i.e., thymine, and on an amino acid, i.e., tyrosine. It was demonstrated that interaction of these radicals is highly favored as measured by their kinetics and the cross-...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00322a034

    authors: Simic MG,Dizdaroglu M

    更新日期:1985-01-01 00:00:00

  • Synthesis and characterization of a new fluorogenic active-site titrant of serine proteases.

    abstract::The molecule 3',6'-bis(4-guanidinobenzoyloxy)-5-[N'-(4-carboxyphenyl)thioureido[spirop]isobenzofuran-1-(3H),9'-[9H]xanthen]-3-one, abbreviated FDE, was designed and synthesized as a fluorogenic active-site titrant for serine proteases. It is an analogue of p-nitrophenyl p-guanidino-benzoate (NPGB) in which a fluoresce...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00518a010

    authors: Livingston DC,Brocklehurst JR,Cannon JF,Leytus SP,Wehrly JA,Peltz SW,Peltz GA,Mangel WF

    更新日期:1981-07-21 00:00:00

  • Crystallographic study of Glu58Ala RNase T1 x 2'-guanosine monophosphate at 1.9-A resolution.

    abstract::Glu58 is known to participate in phosphodiester transesterification catalyzed by the enzyme RNase T1. For Glu58 RNase T1, an altered mechanism has been proposed in which His40 replaces Glu58 as the base catalyst [Steyaert, J., Hallenga, K., Wyns, L., & Stanssens, P. (1990) Biochemistry 29, 9064-9072]. Glu58Ala Rnase T...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00173a006

    authors: Pletinckx J,Steyaert J,Zegers I,Choe HW,Heinemann U,Wyns L

    更新日期:1994-02-22 00:00:00

  • Significance of hydrophobic S4-P4 interactions in subtilisin 309 from Bacillus lentus.

    abstract::The subtilisins have an extended substrate binding cleft comprising at least 8 subsites. Two pockets at the S1 and S4 sites are particularly conspicuous, and the interactions between substrate and these two pockets are very important for the substrate specificity. Phe residues have mutationally been introduced at one ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00062a016

    authors: Bech LM,Sørensen SB,Breddam K

    更新日期:1993-03-23 00:00:00

  • Molecular design of new inhibitors of peroxidase activity of cytochrome c/cardiolipin complexes: fluorescent oxadiazole-derivatized cardiolipin.

    abstract::Interaction of a mitochondria-specific anionic phospholipid, cardiolipin (CL), with an intermembrane protein, cytochrome c (cyt c), yields a peroxidase complex. During apoptosis, the complex induces accumulation of CL oxidation products that are essential for detachment of cyt c from the mitochondrial membrane, induct...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi801507s

    authors: Borisenko GG,Kapralov AA,Tyurin VA,Maeda A,Stoyanovsky DA,Kagan VE

    更新日期:2008-12-23 00:00:00

  • Distinct phosphate backbone contacts revealed by some mutant peptides of zinc finger protein Spl: effect of protein-induced bending on DNA recognition.

    abstract::By using some mutant peptides of transcription factor Spl, phosphate backbone contacts with the DNA binding protein containing three zinc fingers have been investigated by alkylation interference, circular permutation, DNase I footprinting, and methylation protection methods. The ethylation interference analyses of Sp...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi952530r

    authors: Nagaoka M,Sugiura Y

    更新日期:1996-07-02 00:00:00

  • Beta-tubulin isotypes purified from bovine brain have different relative stabilities.

    abstract::The highly conserved nature and tissue specificity of the seven vertebrate beta-tubulin isotypes provide circumstantial evidence that functional differences among isotypes may exist in vivo. Compelling evidence from studies of bovine brain beta-isotypes indicated significant conformational and functional differences i...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi972763d

    authors: Schwarz PM,Liggins JR,Ludueña RF

    更新日期:1998-03-31 00:00:00

  • Redundancy of mammalian proteasome beta subunit function during endoplasmic reticulum associated degradation.

    abstract::Misfolded proteins in the endoplasmic reticulum (ER) are degraded by N-terminal threonine proteases within the 26S proteasome. Each protease is formed by an activated beta subunit, beta5/X, beta1/Y, or beta2/Z, that exhibits chymotrypsin-like, peptidylglutamyl-peptide hydrolyzing, or trypsin-like activity, respectivel...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi011322y

    authors: Oberdorf J,Carlson EJ,Skach WR

    更新日期:2001-11-06 00:00:00

  • Beta-elimination of indole from L-tryptophan catalyzed by bacterial tryptophan synthase: a comparison between reactions catalyzed by tryptophanase and tryptophan synthase.

    abstract::Although tryptophan synthase catalyzes a number of pyridoxal phosphate dependent beta-elimination and beta-replacement reactions that are also catalyzed by tryptophanase, a principal and puzzling difference between the two enzymes lies in the apparent inability of tryptophan synthase to catalyze beta-elimination of in...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00363a010

    authors: Ahmed SA,Martin B,Miles EW

    更新日期:1986-07-29 00:00:00

  • Interaction of cytochrome c with flavocytochrome b2.

    abstract::Flavocytochrome b2 from Saccharomyces cerevisiae couples L-lactate dehydrogenation to cytochrome c reduction. At 25 degrees C, 0.10 M ionic strength, and saturating L-lactate concentration, the turnover rate is 207 s-1 [per cytochrome c reduced; Miles, C. S., Rouviere, N., Lederer, F., Mathews, F. S., Reid, G. A., Bla...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9522561

    authors: Daff S,Sharp RE,Short DM,Bell C,White P,Manson FD,Reid GA,Chapman SK

    更新日期:1996-05-21 00:00:00

  • Control of the redox potential of cytochrome c and microscopic dielectric effects in proteins.

    abstract::X-ray structural information provides the opportunity to explore quantitatively the relation between the microenvironments of heme proteins and their redox potentials. This can be done by considering the protein as a "solvent" for its redox center and calculating the difference between the electrostatic energy of the ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00355a035

    authors: Churg AK,Warshel A

    更新日期:1986-04-08 00:00:00

  • Crystal structure of homoserine transacetylase from Haemophilus influenzae reveals a new family of alpha/beta-hydrolases.

    abstract::Homoserine transacetylase catalyzes one of the required steps in the biosynthesis of methionine in fungi and several bacteria. We have determined the crystal structure of homoserine transacetylase from Haemophilus influenzae to a resolution of 1.65 A. The structure identifies this enzyme to be a member of the alpha/be...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi051951y

    authors: Mirza IA,Nazi I,Korczynska M,Wright GD,Berghuis AM

    更新日期:2005-12-06 00:00:00

  • Protochlorophyllide oxidoreductase: "dark" reactions of a light-driven enzyme.

    abstract::The light-driven enzyme NADPH:protochlorophyllide oxidoreductase (POR) catalyzes the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide), a key regulatory step in the chlorophyll biosynthesis pathway. As POR is light activated, it allows intermediates in the reaction pathway to be observed by initiat...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0268448

    authors: Heyes DJ,Ruban AV,Hunter CN

    更新日期:2003-01-21 00:00:00

  • Examination of sodium/glucose cotransport by using a visible glucose analogue.

    abstract::The glucose derivative, 2,2,6,6-tetramethylpiperidine-1-oxylglucose (TEMPO-glucose) was synthesized and examined for its ability to substitute for glucose as a substrate for the intestinal brush border membrane Na+/glucose cotransporter. TEMPO-glucose inhibited Na(+)-dependent phlorizin binding with an apparent KI of ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00231a012

    authors: Peerce BE

    更新日期:1991-04-30 00:00:00

  • PsbU provides a stable architecture for the oxygen-evolving system in cyanobacterial photosystem II.

    abstract::PsbU is a lumenal peripheral protein in the photosystem II (PS II) complex of cyanobacteria and red algae. It is thought that PsbU is replaced functionally by PsbP or PsbQ in plant chloroplasts. After the discovery of PsbP and PsbQ homologues in cyanobacterial PS II [Thornton et al. (2004) Plant Cell 16, 2164-2175], w...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi047539k

    authors: Inoue-Kashino N,Kashino Y,Satoh K,Terashima I,Pakrasi HB

    更新日期:2005-09-13 00:00:00

  • Modified-peptide inhibitors of amyloid beta-peptide polymerization.

    abstract::Cellular toxicity resulting from nucleation-dependent polymerization of amyloid beta-peptide (Abeta) is considered to be a major and possibly the primary component of Alzheimer's disease (AD). Inhibition of Abeta polymerization has thus been identified as a target for the development of therapeutic agents for the trea...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi982824n

    authors: Findeis MA,Musso GM,Arico-Muendel CC,Benjamin HW,Hundal AM,Lee JJ,Chin J,Kelley M,Wakefield J,Hayward NJ,Molineaux SM

    更新日期:1999-05-25 00:00:00

  • Cysteine-rich secretory protein 3 is a ligand of alpha1B-glycoprotein in human plasma.

    abstract::Human cysteine-rich secretory protein 3 (CRISP-3; also known as SGP28) belongs to a family of closely related proteins found in mammals and reptiles. Some mammalian CRISPs are known to be involved in the process of reproduction, whereas some of the CRISPs from reptiles are neurotoxin-like substances found in lizard sa...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi048823e

    authors: Udby L,Sørensen OE,Pass J,Johnsen AH,Behrendt N,Borregaard N,Kjeldsen L

    更新日期:2004-10-12 00:00:00

  • Helix variants of troponin C with tailored calcium affinities.

    abstract::Muscle fiber contraction is regulated through calcium-induced changes in the conformation of troponin C. In this study, we explored the relationship between the stability of a specific helix in the protein and the metal ion affinity of associated binding sites. Serial replacement of the amino acid at position 130 caus...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00088a038

    authors: Trigo-Gonzalez G,Awang G,Racher K,Neden K,Borgford T

    更新日期:1993-09-21 00:00:00

  • Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics.

    abstract::The solution conformation of potato carboxypeptidase inhibitor (CPI) has been investigated by 1H NMR spectroscopy. The spectrum is assigned in a sequential manner by using two-dimensional NMR techniques to identify through-bond and through-space (less than 5 A) connectivities. A set of 309 approximate interproton dist...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00398a069

    authors: Clore GM,Gronenborn AM,Nilges M,Ryan CA

    更新日期:1987-12-01 00:00:00

  • Tetrahydrobiopterin-free neuronal nitric oxide synthase: evidence for two identical highly anticooperative pteridine binding sites.

    abstract::The properties of neuronal nitric oxide synthase containing one tetrahydrobiopterin (BH4) per dimer [nNOS(BH4+)] were compared to those of the BH4-free enzyme [nNOS(BH4-)]. The stimulation by BH4 of the formation of L-citrulline at the expense of H2O2 production unambiguously demonstrated that BH4 is essential in coup...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi961931j

    authors: Gorren AC,List BM,Schrammel A,Pitters E,Hemmens B,Werner ER,Schmidt K,Mayer B

    更新日期:1996-12-24 00:00:00

  • Proteolysis of the cytochrome d complex with trypsin and chymotrypsin localizes a quinol oxidase domain.

    abstract::The cytochrome d complex is a two-subunit, membrane-bound terminal oxidase in the aerobic respiratory chain of Escherichia coli. The enzyme catalyzes the two-electron oxidation of ubiquinol and the four-electron reduction of oxygen to water. Previous work demonstrated that the site for ubiquinol oxidation was selectiv...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00228a007

    authors: Dueweke TJ,Gennis RB

    更新日期:1991-04-09 00:00:00

  • Effect of erythrocyte transbilayer phospholipid distribution on fusion with vesicular stomatitis virus.

    abstract::To identify the specific component(s) in the target membrane involved in fusion of vesicular stomatitis virus (VSV), we examined the interaction of the virus with human erythrocyte membranes with asymmetric and symmetric bilayer distributions of phospholipids. Fusion was monitored spectrofluorometrically by the octade...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00469a005

    authors: Herrmann A,Clague MJ,Puri A,Morris SJ,Blumenthal R,Grimaldi S

    更新日期:1990-05-01 00:00:00

  • Fluorescence energy transfer between Ca2+ transport ATPase molecules in artificial membranes.

    abstract::The purified ATPase of sarcoplasmic reticulum was covalently labeled with N-iodoacetyl-N'-(5-sulfo-1-naphthyl)ethylenediamine (1,5-IAEDANS) or with iodoacetamidofluorescein (IAF). In reconstituted vesicles containing both types of ATPase molecules fluorescence energy transfer was observed from the IAEDANS (donor) to t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00626a003

    authors: Vanderkooi JM,Ierokomas A,Nakamura H,Martonosi A

    更新日期:1977-04-05 00:00:00

  • Optimization of alternate-strand triple helix formation at the 5'CpG3' and 5'GpC3' junction steps.

    abstract::Oligonucleotide-directed triple helix formation normally requires a long tract of oligopyrimidine.oligopurine sequence. This limitation can be partially overcome by alternate-strand triple helix (or switch triple helix) formation which enables recognition of alternating oligopurine/oligopyrimidine sequences. The prese...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi980618+

    authors: Marchand C,Sun JS,Bailly C,Waring MJ,Garestier T,Hélène C

    更新日期:1998-09-22 00:00:00

  • Characterization of a transient intermediate formed in the liver alcohol dehydrogenase catalyzed reduction of 3-hydroxy-4-nitrobenzaldehyde.

    abstract::The compounds 3-hydroxy-4-nitrobenzaldehyde and 3-hydroxy-4-nitrobenzyl alcohol are introduced as new chromophoric substrates for probing the catalytic mechanism of horse liver alcohol dehydrogenase (LADH). Ionization of the phenolic hydroxyl group shifts the spectrum of the aldehyde from 360 to 433 nm (pKa = 6.0), wh...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00385a017

    authors: MacGibbon AK,Koerber SC,Pease K,Dunn MF

    更新日期:1987-06-02 00:00:00

  • Biosynthesis of lipid A in Escherichia coli: identification of UDP-3-O-[(R)-3-hydroxymyristoyl]-alpha-D-glucosamine as a precursor of UDP-N2,O3-bis[(R)-3-hydroxymyristoyl]-alpha-D-glucosamine.

    abstract::The lipid A disaccharide of the Escherichia coli envelope is synthesized from the two fatty acylated glucosamine derivatives UDP-N2,O3-bis[(R)-3-hydroxytetradecanoyl]-alpha-D- glucosamine (UDP-2,3-diacyl-GlcN) and N2,O3-bis[(R)-3-hydroxytetradecanoyl]-alpha-D-glucosamine 1-phosphate (2,3-diacyl-GlcN-1-P) [Ray, B. L., ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00406a017

    authors: Anderson MS,Robertson AD,Macher I,Raetz CR

    更新日期:1988-03-22 00:00:00

  • Solution structure of the lipophosphoglycan of Leishmania donovani.

    abstract::The three-dimensional solution structure of the repeating -PO4-6Gal beta 1-4Man alpha 1- disaccharide fragment of the lipophosphoglycan (LPG) derived from Leishmania donovani has been determined by use of a combination of homo- and heteronuclear NMR spin coupling constant measurements together with restrained molecula...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00118a004

    authors: Homans SW,Mehlert A,Turco SJ

    更新日期:1992-01-28 00:00:00

  • Proton transfer in benzyl alcohol dehydrogenase during catalysis: alternate proton-relay routes.

    abstract::His51 in horse liver alcohol dehydrogenase (ADHE) has been proposed to act as a proton donor/acceptor in the NAD+/NADH-dependent oxidation/reduction of alcohol/aldehyde. The residue corresponding to His51 of ADHE is Val51 (Val45 in the protein sequence) in benzyl alcohol dehydrogenase (BADH) encoded by TOL plasmid pWW...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi970726g

    authors: Inoue J,Tomioka N,Itai A,Harayama S

    更新日期:1998-03-10 00:00:00