T4 RNA Ligase joins 2'-deoxyribonucleoside 3',5'-bisphosphates to oligodeoxyribonucleotides.

Abstract:

:T4 RNA ligase catalyzes the ATP-dependent addition of a single 2'-deoxyribonucleoside 3',5'-bisphosphate to the 3'-hydroxyl of an oligodeoxyribonucleotide. The bisphosphate is joined to the deoxyoligomer by a 3' leads to 5' phosphodiester bond and the product, which is terminated by a 3'-phosphate, is one nucleotide longer than the substrate. Bisphosphates of dAdo, dCyd, dGuo, dThd, and dUrd are donors and oligodeoxyribonucleotides with dA, dC, dG, dT, or dU 3' termini act as acceptors. The preferred residue for both donor and acceptor is dCyd. Deoxyoligomers from 3 to 12 residues in length are active as acceptors. To obtain good yields, high concentration of enzyme, long incubation time at low temperature, and manganous rather than Mg(II) ion are required. Under optimal conditions, yields calculated with respect to deoxyoligomer converted to product vary from 40 to greater than 95%. The turnover number of the enzyme for DNA joining is extremely low but, because the preparation is nearly free of DNases, there is less than 3% degradation of substrate or product after 6 days of reaction. We anticipate that this reaction will serve as the basis for a method for the stepwise enzymatic synthesis of DNA of defined sequence.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Hinton DM,Baez JA,Gumport RI

doi

10.1021/bi00617a004

subject

Has Abstract

pub_date

1978-11-28 00:00:00

pages

5091-7

issue

24

eissn

0006-2960

issn

1520-4995

journal_volume

17

pub_type

杂志文章
  • A Novel Soluble Peptide with pH-Responsive Membrane Insertion.

    abstract::Several diseases, such as cancer, are characterized by acidification of the extracellular environment. Acidosis can be employed as a target to specifically direct therapies to the diseased tissue. We have used first principles to design an acidity-triggered rational membrane (ATRAM) peptide with high solubility in sol...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.5b00856

    authors: Nguyen VP,Alves DS,Scott HL,Davis FL,Barrera FN

    更新日期:2015-11-03 00:00:00

  • Studies on the hydrolytic properties of (serine) carboxypeptidase Y.

    abstract::The activity of serine carboxypeptidases is dependent on a catalytic triad, an oxyanion hole, and a binding site equivalent to those found in the serine endopeptidases. The action of carboxypeptidase Y on substrates containing amino acids, alcohols, and amines as leaving groups is described. It is demonstrated that th...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi952758e

    authors: Stennicke HR,Mortensen UH,Breddam K

    更新日期:1996-06-04 00:00:00

  • Chemical modification of mitochondrial transhydrogenase: evidence for two classes of sulfhydryl groups.

    abstract::Chemical-modification studies on submitochondrial particle pyridine dinucleotide transhydrogenase (EC 1.6.1.1) demonstrate the presence of one class of sulfhydryl group in the nicotinamide adenine dinucleotide phosphate (NADP) site and another peripheral to the active site. Reaction of the peripheral sulfhydryl group ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00615a015

    authors: Earle SR,O'Neal SG,Fisher RR

    更新日期:1978-10-31 00:00:00

  • SH2 domain proteins as high-affinity receptor tyrosine kinase substrates.

    abstract::Activation of a growth factor receptor tyrosine kinase (RTK) is accompanied by a rapid autophosphorylation of the receptor on tyrosine residues. Receptor activation has been shown to promote the association of signal-transducing proteins containing SH2 domains (second domain of src homology). These receptor-associated...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00089a028

    authors: Sierke SL,Koland JG

    更新日期:1993-09-28 00:00:00

  • Cholesterol dynamics in membranes of raft composition: a molecular point of view from 2H and 31P solid-state NMR.

    abstract::Lipidic membrane systems that have been reported to be composed of sphingomyelin (SM)-cholesterol (Chol) microdomains or "rafts" by Dietrich et al. [palmitoyloleoyl-phosphatidylcholine(POPC)/SM/Chol, 1/1/1; Dietrich, C., Bagatolli, L. A., Volovyk, Z. N., Thompson, N. L., Levi, M., Jacobson, K., and Gratton, E. (2001) ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi026717b

    authors: Aussenac F,Tavares M,Dufourc EJ

    更新日期:2003-02-18 00:00:00

  • Selective binding to polynucleotides of the hybrid intercalating groove binder bis(pyrrolecarboxamide)-oxazolopyridocarbazole: a molecular modeling study.

    abstract::In order to further characterize the binding of the hybrid molecule NetOPC [bis(pyrrolecarboxamide)-oxazolopyridocarbazole conjugate] to double-stranded DNA, we have performed a molecular modeling study to investigate the binding modes of the complexes possibly formed between NetOPC and synthetic polynucleotides poly ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00172a018

    authors: Goulaouic H,Carteau S,Subra F,Mouscadet JF,Auclair C,Sun JS

    更新日期:1994-02-15 00:00:00

  • Photooxidation of cytochrome b559 in oxygen-evolving photosystem II.

    abstract::Cytochrome b559 (cyt b559) is an intrinsic and essential component of the photosystem II (PSII) protein complex, but its function, stoichiometry, and electron-transfer kinetics in the physiological system are not well-defined. In this study, we have used flash-detection optical spectroscopy to measure the kinetics and...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00161a025

    authors: Buser CA,Diner BA,Brudvig GW

    更新日期:1992-11-24 00:00:00

  • pH dependence of the inhibition of chymotrypsin by a peptidyl trifluoromethyl ketone.

    abstract::The effects of pH on the kinetics of association and dissociation of chymotrypsin and the dipeptidyl trifluoromethyl ketone (TFK) N-acetyl-L-leucyl-L-phenylalanyltrifluoromethane (1) were examined through the pH range 4-9.5. The pH dependence of the association rate (kon) is similar to that of kcat/Km for ester and pe...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00449a017

    authors: Brady K,Liang TC,Abeles RH

    更新日期:1989-11-14 00:00:00

  • Fate of the (2Fe-2S)(2+) cluster of Escherichia coli biotin synthase during reaction: a Mössbauer characterization.

    abstract::Biotin synthase, the enzyme which catalyzes the last step of the biosynthesis of biotin, contains only (2Fe-2S)(2+) clusters when isolated under aerobic conditions. Previous results showed that reduction by dithionite or photoreduced deazaflavin converts the (2Fe-2S)(2+) to (4Fe-4S)(2+,+). However, until now, no detai...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi034426c

    authors: Tse Sum Bui B,Benda R,Schünemann V,Florentin D,Trautwein AX,Marquet A

    更新日期:2003-07-29 00:00:00

  • Structure and mechanism of an ADP-glucose phosphorylase from Arabidopsis thaliana.

    abstract::The X-ray crystal structure of the At5g18200.1 protein has been determined to a nominal resolution of 2.30 A. The structure has a histidine triad (HIT)-like fold containing two distinct HIT-like motifs. The sequence of At5g18200.1 indicates a distant family relationship to the Escherichia coli galactose-1-P uridylyltr...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi052232m

    authors: McCoy JG,Arabshahi A,Bitto E,Bingman CA,Ruzicka FJ,Frey PA,Phillips GN Jr

    更新日期:2006-03-14 00:00:00

  • A novel delta(3),delta(2)-enoyl-CoA isomerase involved in the biosynthesis of the cyclohexanecarboxylic acid-derived moiety of the polyketide ansatrienin A.

    abstract::The side chain of the antifungal polyketide ansatrienin A produced by Streptomyces collinus contains a cyclohexanecarboxylic acid (CHC) derived moiety. This CHC in the coenzyme A activated form (CHC-CoA) is derived from shikimic acid via a pathway in which the penultimate step is the isomerization of 2-cyclohexenylcar...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0005714

    authors: Patton SM,Cropp TA,Reynolds KA

    更新日期:2000-06-27 00:00:00

  • Electrostatic effects in myoglobin. Application of the modified Tanford-Kirkwood theory to myoglobins from horse, California grey whale, harbor seal, and California sea lion.

    abstract::The modified Tanford-Kirkwood electrostatic theory (Shire et al., 1974a) was applied to ferrimyoglobins from the following animal species: sperm whale (Physeter catodon), horse, California grey whale (Eschrichtius gibbosus), harbor seal (Phoca vitulina), and California sea lion (Zalophus californianus). Computations w...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00678a002

    authors: Shire SJ,Hanania GI,Gurd FR

    更新日期:1975-04-08 00:00:00

  • Electrophoretic mobilities and diffusion coefficients of hemoglobin at high pH.

    abstract::Diffusion studies by photon correlation of scattered laser light confirm the dissociation of the tetrameric form of human carboxyhemoglobin to dimers above pH 10 and provide new estimates of the subunit dissociation equilibrium constants in this pH range. Electrophoretic light-scattering experiments under the same con...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00616a014

    authors: Haas DD,Ware BR

    更新日期:1978-11-14 00:00:00

  • Hydration of dA.dT polymers: role of water in the thermodynamics of ethidium and propidium intercalation.

    abstract::We report differences in the interaction of two structurally similar phenanthroline intercalators, ethidium and propidium, with poly(dA).poly(dT) and poly[d(A-T)] as a function of ionic strength based on titration microcalorimetry, fluorescence titration, and hydrostatic pressure measurements. Both ethidium and propid...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00472a009

    authors: Marky LA,Macgregor RB Jr

    更新日期:1990-05-22 00:00:00

  • Carboxymethylproline synthase from Pectobacterium carotorova: a multifaceted member of the crotonase superfamily.

    abstract::The simplest carbapenem antibiotic, (5R)-carbapen-2-em-3-carboxylic acid, is biosynthesized from primary metabolites in Pectobacterium carotorova by the action of three enzymes, carboxymethylproline synthase (hereafter named CarB), carbapenam synthetase, and carbapenem synthase. CarB, a member of the crotonase superfa...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0483662

    authors: Gerratana B,Arnett SO,Stapon A,Townsend CA

    更新日期:2004-12-21 00:00:00

  • Site-specific epitope tagging of G protein-coupled receptors by bioorthogonal modification of a genetically encoded unnatural amino acid.

    abstract::We developed a general strategy for labeling expressed membrane proteins with a peptide epitope tag and detecting the tagged proteins in native cellular membranes. First, we genetically encoded the unnatural amino acid p-azido-L-phenylalanine (azF) at various specific sites in a G protein-coupled receptor (GPCR), C-C ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi301292h

    authors: Naganathan S,Ye S,Sakmar TP,Huber T

    更新日期:2013-02-12 00:00:00

  • CofE catalyzes the addition of two glutamates to F420-0 in F420 coenzyme biosynthesis in Methanococcus jannaschii.

    abstract::The protein product of the Methanococcus jannaschii MJ0768 gene has been expressed in Escherichia coli, purified to homogeneity, and shown to catalyze the GTP-dependent addition of two l-glutamates to the l-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F(420)-0) to form F(420)-0-glutamyl-glutama...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi034779b

    authors: Li H,Graupner M,Xu H,White RH

    更新日期:2003-08-19 00:00:00

  • Structural and functional effects of tryptophans inserted into the membrane-binding and substrate-binding sites of human group IIA phospholipase A2.

    abstract::Phospholipase A(2) (PLA(2)) enzymes become activated by binding to biological membranes and hydrolyze phospholipids to free fatty acids and lyso-phospholipids, the precursors of inflammatory mediators. To understand the functional significance of amino acid residues at key positions, we have studied the effects of the...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi061440r

    authors: Nemec KN,Pande AH,Qin S,Bieber Urbauer RJ,Tan S,Moe D,Tatulian SA

    更新日期:2006-10-17 00:00:00

  • Isolation of peptides from the carboxyl carrier subunit of transcarboxylase. Role of the non-biotinyl peptide in assembly.

    abstract::Transcarboxylase is made up of a central hexameric subunit (S20,W similar 12 S), three peripheral dimeric metallo subunits (S20,W similar to 5 S), and six biotinyl carboxyl carrier subunits (S20,W similar to 1.3 S). The results presented here show that the carboxyl carrier subunit is required for assembly of the 12S a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00679a010

    authors: Ahmad F,Jacobson B,Chuang M,Brattin W,Wood HG

    更新日期:1975-04-22 00:00:00

  • The conserved seven-transmembrane sequence NP(X)2,3Y of the G-protein-coupled receptor superfamily regulates multiple properties of the beta 2-adrenergic receptor.

    abstract::The beta 2-adrenergic receptor (beta 2AR) is a member of a large superfamily of seven transmembrane domain, G-protein-coupled receptors. Within the putative seventh transmembrane domain of the beta 2AR is a sequence of amino acids, NPLIY, which is conserved with minor variations in all members of the superfamily. Prev...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00047a003

    authors: Barak LS,Ménard L,Ferguson SS,Colapietro AM,Caron MG

    更新日期:1995-11-28 00:00:00

  • Phosphorylation-dependent sumoylation of estrogen-related receptor alpha1.

    abstract::We previously showed that estrogen-related receptor alpha1 (ERRalpha1) can compete with estrogen receptor alpha (ERalpha) for binding to estrogen response elements (EREs), repressing transcription in the mammary carcinoma cell line MCF-7. Given that ERRalpha1 can function in the absence of ligands and exists as a phos...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi700316g

    authors: Vu EH,Kraus RJ,Mertz JE

    更新日期:2007-08-28 00:00:00

  • Oligomerization and ring closure of immunoglobulin E class antibodies by divalent haptens.

    abstract::Cross-linking of antibodies constitutes a widespread initiation signal for their respective effector functions. Cross-linking IgE-class antibodies provide the triggering signal to mast cells for their degranulation process. To obtain a quantitative insight into these cross-linking processes, the interactions between a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00386a053

    authors: Schweitzer-Stenner R,Licht A,Lüscher I,Pecht I

    更新日期:1987-06-16 00:00:00

  • Characterization of the DNA binding activity of the ZFY zinc finger domain.

    abstract::The ZFY protein is a member of one of the most interesting classes of polydactyl zinc finger proteins. It has a domain of 13 tandem zinc fingers that is organized with an internal repeat of odd-even finger pairs. It has been proposed that each finger pair interacts with six base pairs within a turn of the double helix...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9018626

    authors: Grants J,Flanagan E,Yee A,Romaniuk PJ

    更新日期:2010-02-02 00:00:00

  • Effect of pH on the active site of an Arg121Cys mutant of the metallo-beta-lactamase from Bacillus cereus: implications for the enzyme mechanism.

    abstract::The zinc-dependent metallo-beta-lactamases are a group of bacterial enzymes that pose a threat to the future efficacy of present-day antibiotics. Their mechanism is poorly understood, and there are no clinically useful inhibitors. While most members of the group contain two tightly bound zinc ions in their active site...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi047709t

    authors: Davies AM,Rasia RM,Vila AJ,Sutton BJ,Fabiane SM

    更新日期:2005-03-29 00:00:00

  • Structural basis of the anionic interface preference and kcat* activation of pancreatic phospholipase A2.

    abstract::Pancreatic phospholipase A(2) (PLA2) shows a strong preference for the binding to the anionic interface and a consequent allosteric activation. In this paper, we show that virtually all the preference is mediated through 3 (Lys-53, -56, and -120) of the 12 cationic residues of bovine pancreatic PLA2. The lysine-to-met...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi000740k

    authors: Yu BZ,Poi MJ,Ramagopal UA,Jain R,Ramakumar S,Berg OG,Tsai MD,Sekar K,Jain MK

    更新日期:2000-10-10 00:00:00

  • pH-dependent charge equilibria between tyrosine-D and the S states in photosystem II. Estimation of relative midpoint redox potentials.

    abstract::The effect of protonation events on the charge equilibrium between tyrosine-D and the water-oxidizing complex in photosystem II has been studied by time-resolved measurements of the EPR signal IIslow at room temperature. The flash-induced oxidation of YD by the water-oxidizing complex in the S2 state is a monophasic p...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00217a037

    authors: Vass I,Styring S

    更新日期:1991-01-22 00:00:00

  • DNA-stimulated assembly of oligomeric bacteriophage 434 repressor: evidence for cooperative binding by recruitment.

    abstract::Typical of many transcriptional regulatory proteins, the lambdoid bacteriophage repressors bind cooperatively to multiple sites on DNA. This cooperative binding is essential for establishment and maintenance of phage lysogeny. In the phage, two repressor homodimers, one bound at each of the adjacent operator sites, in...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi027318j

    authors: Ciubotaru M,Koudelka GB

    更新日期:2003-04-15 00:00:00

  • Thermodynamics of reversible and irreversible unfolding and domain interactions of glucoamylase from Aspergillus niger studied by differential scanning and isothermal titration calorimetry.

    abstract::The stability of three forms of glucoamylase from Aspergillus niger has been investigated by differential scanning and isothermal titration calorimetry: Glucoamylase 1 (GA1), which consists of a catalytic domain and a starch-binding domain (SBD) connected by a heavily O-glycosylated linker region; glucoamylase 2 (GA2)...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi990185q

    authors: Christensen T,Svensson B,Sigurskjold BW

    更新日期:1999-05-11 00:00:00

  • Kinetic mechanism of active site assembly and chemical catalysis of DNA polymerase β.

    abstract::It has been inferred from structural and computational studies that the mechanism of DNA polymerases involves subtle but important discrete steps that occur between binding and recognition of the correct dNTP and chemical catalysis. These steps potentially include local conformational changes involving active site res...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi200954r

    authors: Balbo PB,Wang EC,Tsai MD

    更新日期:2011-11-15 00:00:00

  • Hydrogen-1 nuclear magnetic resonance study of the complexes of two diastereoisomers of folinic acid with dihydrofolate reductase.

    abstract::The 1H chemical shifts for the formyl and benzoyl protons of the individual diastereoisomeres of folinic acid bound to dihydrofolate reductase have been measured. For the tightly bound biologically active 6S, alpha S isomer, the "bound" signals were assigned by using transfer of saturation methods. In this case, only ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00510a019

    authors: Feeney J,Birdsall B,Albrand JP,Roberts GC,Burgen AS,Charlton PA,Young DW

    更新日期:1981-03-31 00:00:00