Abstract：
:We have used DNase I footprinting to examine the formation of antiparallel DNA triple helices on DNA fragments containing the homopurine target sites (GGA)2GGX(GGA)2GG.(CCT)2CCZ(CCT)2CC (where X.Z is each base pair in turn), with the GA- and GT-rich oligonucleotides, (GGA)2GGN(GGA)2GG and (GGT)2GGN(GGT)2GG (N = each base in turn). These were designed to form G.GC and A.AT or T.AT triplets with a central N.XZ mismatch, which should bind in an antiparallel orientation. We find that almost all combinations generate DNase I footprints at low micromolar concentrations. At each target site, the relative binding of the GA- and GT-containing oligonucleotides was not the same, suggesting that these two triplexes adopt different conformations. For a central GC base pair, the most stable complex is observed with a third strand generating a G.GC triplet as expected. A.GC is also stable, especially in the GT oligonucleotides. For a central AT base pair, all four bases form stable complexes though T.AT is favored for the GA-rich thirds strands and A.AT for the GT-rich strands. For a central CG base pair, the stable complexes are seen with third strands generating T.CG triplets, though A.CG and C.CG are stable with GT- and GA-containing oligonucleotides, respectively. C.TA is the best triplet at a central TA base pair. The third strands with central guanines avoided the formation of G.YR triplets on the fragments containing central pyrimidines, producing DNase I footprints which had slipped relative to the target site. These oligonucleotides bound at a different location, generating complexes containing 11 contiguous stable triplets at the 3'-end of the third strand. The results suggest rules for designing the best third strand oligonucleotides for targeting sequences in which homopurine tracts are interrupted by pyrimidines.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Chandler SP,Fox KRdoi
10.1021/bi9609679subject
Has Abstractpub_date
1996-11-26 00:00:00pages
15038-48issue
47eissn
0006-2960issn
1520-4995pii
bi9609679journal_volume
35pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract：:The enzyme hydrogenase, from the photosynthetic bacterium Chromatium, was purified to homogeneity after solubilization of the particulate enzyme with deoxycholate. The purification procedure included ammonium sulfate fractionation, treatment with manganous phosphate gel, heating at 63 degrees, DEAE-cellulose chromatog...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00683a001
更新日期：1975-06-17 00:00:00
abstract：:The first committed step of fatty acid and polyketides biosynthesis, the biotin-dependent carboxylation of an acyl-CoA, is catalyzed by acyl-CoA carboxylases (ACCases) such as acetyl-CoA carboxylase (ACC) and propionyl-CoA carboxylase (PCC). ACC and PCC in Streptomyces coelicolor are homologue multisubunit complexes t...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi1005305
更新日期：2010-08-31 00:00:00
abstract：:If cytochrome c oxidase is subjected to pressure during the aerobic steady state, large spectral changes are apparent. These seem to be associated with the inhibition of electron transport within the oxidase. The volume change for the transition is about 80 mL/mol. When the oxidase in the aerobic steady state, with po...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00414a026
更新日期：1988-07-12 00:00:00
abstract：:Antifreeze proteins (AFPs) inhibit the growth of ice by binding to the surface of ice crystals, preventing the addition of water molecules to cause a local depression of the freezing point. AFPs from insects are much more effective at depressing the freezing point than fish AFPs. Here, we have investigated the possibi...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi035605x
更新日期：2004-01-13 00:00:00
abstract：:Cytochrome bo from Escherichia coli is a ubiquinol oxidase which is a member of the superfamily of heme-copper respiratory oxidases. This superfamily, which includes the eukaryotic cytochrome c oxidases, has in common a bimetallic center consisting of a high-spin heme component and a copper atom (CuB) which is the sit...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00092a029
更新日期：1993-10-19 00:00:00
abstract：:Human transferrin (Tf) is responsible for the binding and transport of iron in the bloodstream of vertebrates. Delivery of this bound iron to cells occurs by a process of receptor-mediated endocytosis during which Tf releases its iron at the reduced endosomal pH of approximately 5.6. Iron release from Tf involves a la...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi002050m
更新日期：2001-02-13 00:00:00
abstract：:Alditol oxidase (AldO) from Streptomyces coelicolor A3(2) is a soluble monomeric flavin-dependent oxidase that performs selective oxidation of the terminal primary hydroxyl group of several alditols. Here, we report the crystal structure of the recombinant enzyme in its native state and in complex with both six-carbon...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi701886t
更新日期：2008-01-22 00:00:00
abstract：:Recycling of yeast fumarase to permit repetition of its reaction chemistry requires two proton transfers and two conformational changes, in pathways that are different in detail but thematically similar in the two directions. In the malate --> fumarate direction, simple anions such as acetate accelerate the fumarate-o...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi9821521
更新日期：1998-12-22 00:00:00
abstract：:Inducible dimers are powerful tools for controlling biological processes through colocalizing signaling molecules. To be effective, an inducible system should have a dissociation constant in the "off" state that is greater (i.e., weaker affinity) than the concentrations of the molecules that are being controlled, and ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.6b00529
更新日期：2016-09-20 00:00:00
abstract：:The three-dimensional conformation of a 24-nucleotide variant of the RNA binding sequence for the coat protein of bacteriophage R17 has been analyzed using NMR, molecular dynamics, and energy minimization. The imino proton spectrum is consistent with base pairing requirements for coat protein binding known from bioche...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00019a030
更新日期：1995-05-16 00:00:00
abstract：:The human transferrin receptor (TfR) has three N-linked oligosaccharides. A combination of site-directed mutagenesis and carbohydrate and protein chemistry was used to characterize the structures of the N-linked oligosaccharides and to map their locations. We find that the type of oligosaccharide at each position was ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi962884y
更新日期：1997-04-29 00:00:00
abstract：:We report on the determination of the solution structure of two sequence-related oligonucleotides, d(GTACGTAC)2 and d(CATCGATG)2. Results have been obtained by using a combined approach of (a) two-dimensional NMR, including proton and phosphorus experiments, (b) restrained molecular mechanics performed with sugar phas...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00037a045
更新日期：1995-09-19 00:00:00
abstract：:Electron donation from the soluble cytochrome (cyt) c2 to the photooxidized primary donor, P+, of reaction centers isolated from Rhodobacter sphaeroides was studied by using chemical zero-length cross-linking. This cross-linking stabilizes a 1:1 covalent complex between subunit M of the reaction center and cyt c2. In ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi961350u
更新日期：1997-02-11 00:00:00
abstract：:The fusion of different protein domains via peptide linkers is a powerful, modular approach to obtain proteins with new functions. A detailed understanding of the conformational behavior of peptide linkers is important for applications such as fluorescence resonance energy transfer (FRET)-based sensor proteins and mul...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi061288t
更新日期：2006-11-07 00:00:00
abstract：:In many crustaceans, changing concentrations of several low molecular weight compounds modulates hemocyanin oxygen binding, resulting in lower or higher oxygen affinities of the pigment. The nonphysiological effector caffeine and the physiological modulator urate, the latter accumulating in the hemolymph of the lobste...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi050507s
更新日期：2005-08-02 00:00:00
abstract：:As discovered by Grazi & Trombetta [Grazi, E., & Trombetta, G. (1978) Biochem. J. 175, 361], fructose-1,6-bisphosphate aldolase of rabbit muscle causes the slow formation of inorganic phosphate (Pi) and methylglyoxal when incubated with dihydroxyacetone phosphate (DHAP). In addition, these authors found an acid-labile...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00508a026
更新日期：1981-03-03 00:00:00
abstract：:The time-resolved fluorescence decay of plant PSI-LHCI has been analyzed and compared with its component parts, the PSI core and the peripheral antenna LHCI, in an attempt to (i) define the physical domains associated with the multicomponent decay-associated spectra (DAS) and determine the origin of the kinetically sl...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi060243p
更新日期：2006-06-06 00:00:00
abstract：:The Sir2 enzyme family is responsible for a newly classified chemical reaction, NAD(+)-dependent protein deacetylation. New peptide substrates, the reaction mechanism, and the products of the acetyl transfer to NAD(+) are described for SIR2. The final products of SIR2 reactions are the deacetylated peptide and the 2' ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi011858j
更新日期：2001-12-25 00:00:00
abstract：:The interaction of the 2'-phosphate-containing nucleotides (NADP+, NADPH, 2'-phosphoadenosine 5'-diphosphoribose, and adenosine 2',5'-bisphosphate) with NADP+ -specific isocitrate dehydrogenase was studied by using 31P NMR spectroscopy. The separate resonances corresponding to free and bound nucleotides, characteristi...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00303a015
更新日期：1984-04-10 00:00:00
abstract：:The experiments described here explore the role of local sequence in the folding of cellular retinoic acid binding protein I (CRABP I). This is a 136-residue, 10-stranded, antiparallel beta-barrel protein with seven beta-hairpins and is a member of the intracellular lipid binding protein (iLBP) family. The relative ro...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi034304k
更新日期：2003-07-08 00:00:00
abstract：:Amphotericin B (AmB) is a polyene macrolide antibiotic isolated from Streptomyces nodosus. The antifungal activity of AmB can be attributed to the formation of an ion-channel assembly in the presence of ergosterol (Erg), in which there are two different AmB-Erg orientations, parallel and antiparallel, as reported prev...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.6b00193
更新日期：2016-06-21 00:00:00
abstract：:The ATP hydrolysis and protein-binding and release cycle of the molecular chaperone DnaK is regulated by the accessory proteins GrpE and DnaJ. Here we describe a study of the formation of complexes between the molecular chaperone DnaK, its nucleotide exchange factor GrpE, and the fluorescent ADP analog N8-[4-[(N'-meth...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi962835l
更新日期：1997-03-25 00:00:00
abstract：:Flavo-diiron proteins (FDPs) function as anaerobic nitric oxide scavengers in some microorganisms, catalyzing reduction of nitric to nitrous oxide. The FDP from Thermotoga maritima can be prepared in a deflavinated form with an intact diferric site (deflavo-FDP). Hayashi et al. [(2010) Biochemistry 49, 7040-7049] repo...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi500836z
更新日期：2014-09-09 00:00:00
abstract：:Studies were undertaken to assess the postulated involvement of subunit III in the proton-linked functions of cytochrome c oxidase. The effect of pH on the steady-state kinetic [corrected] parameters of subunit III containing and subunit III depleted cytochrome oxidase was determined by using beef heart and rat liver ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00417a016
更新日期：1988-08-23 00:00:00
abstract：:Escherichia coli cAMP receptor protein (CRP) controls more than 20 genes. There are significant differences in the promoter regions in these genes. Thus, an elucidation of the mechanism of CRP action requires knowledge about the mode of selectivity in these promoters. An earlier study [Heyduk, T., & Lee, J. C. (1990) ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi952187q
更新日期：1996-01-30 00:00:00
abstract：:Although enzymes of thermophilic organisms are often very resistant to thermal denaturation, they are usually less active than their mesophilic or psychrophilic homologues at moderate or low temperatures. To explore the structural features that would improve the activity of a thermophilic enzyme at less than optimal t...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi200925f
更新日期：2011-10-11 00:00:00
abstract：:The mechanism of bovine intestinal 5'-nucleotide phosphodiesterase was investigated by determining kinetic constants of systematically varied substrates, with emphasis on esters of phosphonic acids (which have much higer Vmax values than conventional phosphodiester substrates), and by pre-steady-state kinetics using b...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00625a011
更新日期：1977-03-22 00:00:00
abstract：:By use of six highly purified exoglycosidases with well-defined specificity, the oligosaccharide units of human plasma beta 2-glycoprotein I (beta 2I) were modified by sequential enzymatic degradation. The released monosaccharides (NeuAc, Gal, GlcNAc, and Man) were quantified, and the carbohydrate compositions of the ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00478a020
更新日期：1990-07-03 00:00:00
abstract：:The linkage between substrate and regulatory effector binding to separate sites on allosteric enzymes results in shifts in their sigmoidal kinetics to regulate metabolism. Control of branched chain amino acid biosynthesis in Escherichia coli occurs in part through shifts in the sigmoidal dependence of alpha-ketobutyra...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00029a016
更新日期：1995-07-25 00:00:00
abstract：:We have reexamined the binding properties of the antitumor drug daunomycin using double-helical oligonucleotides 16 base pairs long that were designed to contain preferred binding sites for the drug. The preferred sites are contained in a six base pair core which is flanked on the 5' and 3' ends by tracts of adenines....
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00170a011
更新日期：1994-02-01 00:00:00
