当前位置： SCI文献检索 > BIOCHEMISTRY期刊下所有文献 > Effects of the A.T/T.A degeneracy of pyrrole--imidazole polyamide recognition in the minor groove of DNA.

Effects of the A.T/T.A degeneracy of pyrrole--imidazole polyamide recognition in the minor groove of DNA.

Abstract：

:Pairing rules have been developed to predict the sequence specificity of minor groove binding polyamides containing pyrrole (Py) and imidazole (Im) amino acids. An Im/Py pair distinguishes G.C from C.G and both of these from A.T/T.A base pairs. A Py/Py pair appears not to distinguish A.T from T.A base pairs. To test the extent of this degeneracy, the affinity and binding orientation of the hairpin polyamide ImPyPy-gamma-PyPyPy-beta-Dp were measured for eight possible five base pair 5'-TG(A,T)(3)-3' match sites. Affinity cleavage experiments using a polyamide with an EDTA.Fe(II) moiety at the carboxy terminus, ImPyPy-gamma-PyPyPy-beta-Dp-EDTA.Fe(II), are consistent with formation of an oriented 1:1 hairpin polyamide complex at all eight 5'-TG(A,T)(3)-3' binding sites [20 mM HEPES, 200 mM NaCl, 50 mg/ml glycogen, pH 7.0, 22 degrees C, 5 mM DTT, 1 mM Fe(II)]. Quantitative DNase I footprint titration experiments reveal that ImPyPy-gamma-PyPyPy-beta-Dp binds all eight 5'-TG(A,T)(3)-3' target sites with only a 12-fold difference in the equilibrium association constants between the strongest site, 5'-TGTTT-3' (Ka = 2.1 x 10(8) M-1), and the weakest site, 5'-TGAAT-3' (Ka = 1.8 x 10(7) M-1) (10 mM Tris.HCl, 10 mM KCl, 10 mM MgCl2, 5 mM CaCl2, pH 7.0, 22 degrees C). This relatively small range indicates that the Py/Py pair is approximately degenerate for recognition of A,T base pairs, affording generality with regard to targeting sequences of mixed A.T/T.A composition.

journal_name

Biochemistry

journal_title

Biochemistry

authors

White S,Baird EE,Dervan PB

doi

10.1021/bi960744i

subject

Has Abstract

pub_date

1996-09-24 00:00:00

pages

12532-7

issue

38

eissn

0006-2960

issn

1520-4995

pii

bi960744i

journal_volume

35

pub_type

杂志文章

相关文献

BIOCHEMISTRY文献大全
  • Kinetic analysis of NodST sulfotransferase using an electrospray ionization mass spectrometry assay.

    abstract：:A novel and efficient enzyme kinetics assay using electrospray ionization mass spectrometry was developed and applied to the bacterial carbohydrate sulfotransferase (NodST). NodST catalyzes the sulfuryl group transfer from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to chitobiose, generating 3'-phosphoadenosine 5'-ph...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi020457g

    authors： Pi N,Armstrong JI,Bertozzi CR,Leary JA

    更新日期：2002-11-05 00:00:00

  • Membrane-binding amphipathic alpha-helical peptide derived from CTP:phosphocholine cytidylyltransferase.

    abstract：:A peptide corresponding to a portion of the amphipathic alpha-helical region of CTP:phosphocholine cytidylyltransferase was synthesized. This region of the enzyme was proposed to be the membrane-binding domain [Kalmar, G.B., Kay, R.J., Lachance, A., Aebersold, R., & Cornell, R.B. (1990) Proc. Natl. Acad. Sci. U.S.A. 8...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00180a029

    authors： Johnson JE,Cornell RB

    更新日期：1994-04-12 00:00:00

  • Probing inhibitor-induced conformational changes along the interface between tissue factor and factor VIIa.

    abstract：:Upon injury of a blood vessel, activated factor VII (FVIIa) forms a high-affinity complex with its allosteric regulator, tissue factor (TF), and initiates blood clotting. Active site-inhibited factor VIIa (FVIIai) binds to TF with even higher affinity. We compared the interactions of FVIIai and FVIIa with soluble TF (...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi010283n

    authors： Osterlund M,Owenius R,Carlsson K,Carlsson U,Persson E,Lindgren M,Freskgård PO,Svensson M

    更新日期：2001-08-07 00:00:00

  • Interactions between phospholipids and NADH:ubiquinone oxidoreductase (complex I) from bovine mitochondria.

    abstract：:NADH:ubiquinone oxidoreductase (complex I) from bovine heart mitochondria is a highly complicated, energy transducing, membrane-bound enzyme. It contains 46 different subunits and nine redox cofactors: a noncovalently bound flavin mononucleotide and eight iron-sulfur clusters. The mechanism of complex I is not known. ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi051809x

    authors： Sharpley MS,Shannon RJ,Draghi F,Hirst J

    更新日期：2006-01-10 00:00:00

  • The observed inhibitory potency of 3'-azido-3'-deoxythymidine 5'-triphosphate for HIV-1 reverse transcriptase depends on the length of the poly(rA) region of the template.

    abstract：:The inhibitory potency of 3'-azido-3'-deoxythymidine 5'-triphosphate (AZTTP) against HIV-1 reverse transcriptase (HIV-1 RT) has been further evaluated. The results indicate that the previously reported low Ki values for AZTTP against HIV-1 RT (2.35 nM) are due neither to the to the direct tight binding of AZTTP to HIV...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00120a013

    authors： Ma QF,Bathurst IC,Barr PJ,Kenyon GL

    更新日期：1992-02-11 00:00:00

  • Identification of a cis-acting negative DNA element which modulates human hepatic triglyceride lipase gene expression.

    abstract：:The promoter fragment -1550/+129 of the human hepatic triglyceride lipase (HTGL) gene drives the expression of the CAT gene in HepG2 cells, albeit at very low levels. Transient transfections in HepG2 and HeLa cells of 5' deletion constructs indicated that the regulatory elements that control this expression are locate...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00088a018

    authors： Hadzopoulou-Cladaras M,Cardot P

    更新日期：1993-09-21 00:00:00

  • Energy-transfer dynamics in three light-harvesting mutants of Rhodobacter sphaeroides: a picosecond spectroscopy study.

    abstract：:Picosecond absorption spectroscopy has been used to investigate energy-transfer dynamics within the LH1 and LH2 light-harvesting complexes of three mutants of Rhodobacter sphaeroides. We demonstrate that both complexes are inhomogeneous; each contains a specialized pigment pool which absorbs maximally at a longer wave...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00465a008

    authors： Hunter CN,Bergström H,van Grondelle R,Sundström V

    更新日期：1990-04-03 00:00:00

  • Regulation of biological functions by an insulin receptor monoclonal antibody in insulin receptor beta-subunit mutants.

    abstract：:We investigated the effects of MA-5, a human-specific monoclonal antibody to the insulin receptor alpha-subunit, on transmembrane signaling in cell lines transfected with and expressing both normal human insulin receptors and receptors mutated in their beta-subunit tyrosine kinase domains. In cell lines expressing nor...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00116a025

    authors： Sung CK,Han XL,Brunetti A,Maddux B,Yamamoto-Honda R,Goldfine ID

    更新日期：1992-01-14 00:00:00

  • Reactions of benzylamines with methylamine dehydrogenase. Evidence for a carbanionic reaction intermediate and reaction mechanism similar to eukaryotic quinoproteins.

    abstract：:It had been previously reported that aromatic amines were not substrates for the bacterial quinoprotein methylamine dehydrogenase. In this study, benzylamine-dependent activity was also not observed in the steady-state assay of this enzyme with the artificial electron acceptor phenazine ethosulfate (PES). Benzylamines...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00128a012

    authors： Davidson VL,Jones LH,Graichen ME

    更新日期：1992-04-07 00:00:00

  • Conformational drift and cryoinactivation of lactate dehydrogenase.

    abstract：:Solutions of porcine lactate dehydrogenase of micromolar concentration kept at 4 degrees C for several days lose the greater part of their enzymic activity but recover it when returned to room temperature. The rate of spoiling decreases and the rate of recovery increases with the concentration of the solutions. The de...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00360a024

    authors： King L,Weber G

    更新日期：1986-06-17 00:00:00

  • A kinetic study of interactions of (Rp)- and (Sp)-adenosine cyclic 3',5'-phosphorothioates with type II bovine cardiac muscle adenosine cyclic 3',5'-phosphate dependent protein kinase.

    abstract：:The stereoselectivity of the adenosine cyclic 3',5'-phosphate (cAMP) binding sites on the regulatory subunit of the type II bovine cardiac muscle cAMP-dependent protein kinase was investigated by examining the interactions of (Rp)- and (Sp)-adenosine cyclic 3',5'-phosphorothioates (cAMPS) with these sites. While activ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00261a028

    authors： O'Brian CA,Roczniak SO,Bramson HN,Baraniak J,Stec WJ,Kaiser ET

    更新日期：1982-08-31 00:00:00

  • Signal transduction mechanism of a peptide mimetic of interferon-gamma.

    abstract：:The C-terminus of interferon-gamma (IFNgamma) contains a nuclear localization sequence (NLS) required for the activation and nuclear translocation of the transcription factor STAT1alpha and induction of IFNgamma-activated genes. On the basis of this and other studies, we developed a peptide mimetic of IFNgamma that po...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi036213t

    authors： Subramaniam PS,Flowers LO,Haider SM,Johnson HM

    更新日期：2004-05-11 00:00:00

  • Solution conformation of the type I collagen alpha-1 chain N-telopeptide studied by 1H NMR spectroscopy.

    abstract：:The solution conformation of the type I collagen alpha-1 chain N-telopeptide has been studied by CD and 1H NMR spectroscopy at 600 MHz in CD3OH/H2O (60/40 v/v) and H2O solutions. The 19 amino acids form the N-terminal end of the alpha-1 polypeptide chain. By the combined application of several two-dimensional, phase-s...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00446a006

    authors： Otter A,Kotovych G,Scott PG

    更新日期：1989-10-03 00:00:00

  • Structure of Alcaligenes faecalis nitrite reductase and a copper site mutant, M150E, that contains zinc.

    abstract：:The structures at 2.0 and 2.25 A resolution of native and recombinant nitrite reductase from Alcaligenes faecalis show that they are identical to each other and very similar to nitrite reductase from Achromobacter cycloclastes. The crystallographic structure of a mutant, M150E, which unlike the wild-type protein canno...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00038a003

    authors： Murphy ME,Turley S,Kukimoto M,Nishiyama M,Horinouchi S,Sasaki H,Tanokura M,Adman ET

    更新日期：1995-09-26 00:00:00

  • Assignment and analysis of fluorine nuclear magnetic resonance spectra of 4-fluorotryptophan myoglobins and hemoglobins.

    abstract：:We have obtained the 470 MHz 19F NMR spectra of wild type [4-F]Trp-labeled myoglobins (MbCO, MbO2, deoxyMb, metMb, and MbCN) and hemoglobins (HbCO, HbO2, and deoxyHb), as well as those of several mutants (W7F Mb, betaW15F Hb, betaW37S Hb, and betaY130F Hb, all as the carbonmonoxy adducts), prepared via site-directed m...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi961664h

    authors： Pearson JG,Montez B,Le H,Oldfield E,Chien EY,Sligar SG

    更新日期：1997-03-25 00:00:00

  • Evidence for targeted gene delivery to Hep G2 hepatoma cells in vitro.

    abstract：:We have developed a system for targeting foreign DNA to hepatocytes in vitro using a soluble DNA carrier that takes advantage of receptor-mediated endocytosis to achieve internalization. The idea is based on the fact that hepatocytes possess a unique receptor that binds and internalizes galactose-terminal (asialo)glyc...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00403a008

    authors： Wu GY,Wu CH

    更新日期：1988-02-09 00:00:00

  • Thermal difference circular dichroism of Pf1 filamentous virus and effects of mercury(II), silver(I), and copper(II).

    abstract：:The circular dichroism (CD) of Pfl filamentous virus has been examined over the temperature range 0-40 degrees C, in the absence and presence of Hg(II), Ag(I), and Cu(II). Thermal difference CD spectra were obtained by subtraction of spectra recorded above and below a thermally induced structure transition near 12 deg...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00410a010

    authors： Casadevall A,Day LA

    更新日期：1988-05-17 00:00:00

  • Covalent structure of collagen: amino acid sequence of alpha 1(III)-CB9 from type III collagen of human liver.

    abstract：:The peptide alpha 1(III)-CB9 was prepared and purified from human liver, and its amino acid sequence was determined. Automated Edman degradation of the intact peptide and peptides derived from selective cleavage with hydroxylamine and digestions with trypsin, thermolysin, and Staph V8 protease enabled determination of...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00512a040

    authors： Seyer JM,Kang AH

    更新日期：1981-04-28 00:00:00

  • Isolation, physicochemical properties, and macromolecular composition of zona pellucida from porcine oocytes.

    abstract：:Oocytes released en masse from pig ovaries were isolated in large quantities by using sieving techniques. The isolated oocytes were gently homogenized, and the largely intact zona pellucida "ghosts" were purified by using sieving techniques. Sufficient amounts of zonae were recovered to permit, for the first time, ade...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00543a017

    authors： Dunbar BS,Wardrip NJ,Hedrick JL

    更新日期：1980-01-22 00:00:00

  • Perturbation of microtubule polymerization by quercetin through tubulin binding: a novel mechanism of its antiproliferative activity.

    abstract：:The dietary flavonoid quercetin has a broad range of biological activities, including potent antitumor activity against several types of tumors. Recently, it has been shown that quercetin inhibits cancer cells proliferation by depleting cellular microtubules and perturbing cellular microtubule functions. However, the ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi025952r

    authors： Gupta K,Panda D

    更新日期：2002-10-29 00:00:00

  • Induction of Translational Readthrough across the Thalassemia-Causing Premature Stop Codon in β-Globin-Encoding mRNA.

    abstract：:Nonsense mutations that result in premature stop codons in the HBB gene cause β-thalassemia. This disease is characterized by a reduced hemoglobin level due to the lack of β-globin. Compounds that induce translational readthrough across the thalassemia-causing premature stop codon will have therapeutic benefits. Curre...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.9b00761

    authors： Kar D,Sellamuthu K,Kumar SD,Eswarappa SM

    更新日期：2020-01-14 00:00:00

  • Using ethidium to probe nonequilibrium states of DNA condensed for gene delivery.

    abstract：:Here we explore the use of ethidium to determine relative affinities of different gene delivery vectors for DNA and describe an improved method for studying the interaction. Specifically, we investigate the binding of poly(amidoamine) dendrimers and show that the DNA-dendrimer-ethidium system is far from thermodynamic...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi1015887

    authors： Fant K,Nordén B,Lincoln P

    更新日期：2011-02-22 00:00:00

  • Quantification of quaternary structure stability in aggregation-prone proteins under physiological conditions: the transthyretin case.

    abstract：:The quaternary structure stability of proteins is typically studied under conditions that accelerate their aggregation/unfolding processes on convenient laboratory time scales. Such conditions include high temperature or pressure, chaotrope-mediated unfolding, or low or high pH. These approaches have the limitation of...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi500739q

    authors： Robinson LZ,Reixach N

    更新日期：2014-10-21 00:00:00

  • Conformationally restricted thrombin inhibitors resistant to proteolytic digestion.

    abstract：:A new type of thrombin exo-site inhibitor has been designed with enhanced inhibitory potency and increased metabolic stability. With the aid of the model of the structure of the thrombin-hirudin fragment complex [Yue, S.-Y., DiMaio, J., Szewczuk, Z., Purisima, E. O., Ni, F., & Konishi, Y. (1992) Protein Eng. 5, 77-85]...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00153a004

    authors： Szewczuk Z,Gibbs BF,Yue SY,Purisima EO,Konishi Y

    更新日期：1992-09-29 00:00:00

  • Hypertrophic cardiomyopathy-linked mutation D145E drastically alters calcium binding by the C-domain of cardiac troponin C.

    abstract：:The role of the C-domain sites of cardiac troponin C in the modulation of the calcium signal remains unclear. In this study, we investigated the effects of hypertrophic cardiomyopathy-linked mutations A8V, E134D, and D145E in cardiac troponin C on the properties of the C-domain sites. The A8V mutation had essentially ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi100400h

    authors： Swindle N,Tikunova SB

    更新日期：2010-06-15 00:00:00

  • Novel Cl(-)-dependent intracellular pH regulation in murine MDR 1 transfectants and potential implications.

    abstract：:Previously [Luz et al. (1994) Biochemistry 33, 7239-7249], we determined that Cl(-)- and -HCO3-dependent pHi homeostasis was perturbed in multidrug resistant (MDR) cells created by transfecting LR73 Chinese hamster ovary fibroblasts with wild-type mu (murine) MDR 1 (Gros et al., 1991). Via single-cell photometry exper...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00202a021

    authors： Roepe PD,Weisburg JH,Luz JG,Hoffman MM,Wei LY

    更新日期：1994-09-13 00:00:00

  • Amino acid sequence of the nucleotide binding region of chloroplast coupling factor 1.

    abstract：:The labeling of chloroplast coupling factor 1 by 3'-O-(4-benzoyl)benzoyl-ATP (BzATP) was studied. When the enzyme was incubated with approximately 10 microM BzATP and 6 mM MgCl2 at pH 7.9 for approximately 20 min and passed through two Sephadex G-50 centrifuge columns, three BzATP molecules were bound per coupling fac...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00385a038

    authors： Admon A,Hammes GG

    更新日期：1987-06-02 00:00:00

  • Ligand stabilization of the beta 2 adrenergic receptor: effect of DTT on receptor conformation monitored by circular dichroism and fluorescence spectroscopy.

    abstract：:Treatment of the beta 2 adrenergic receptor with the reducing agent dithiothreitol (DTT) is known to abolish ligand binding to the receptor. Interestingly, the loss of binding can be prevented by preoccupation of the receptor with ligand. It is unclear, however, whether the ligand blocks access of DTT to the receptor,...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi961619+

    authors： Lin S,Gether U,Kobilka BK

    更新日期：1996-11-19 00:00:00

  • Active Site Metal Identity Alters Histone Deacetylase 8 Substrate Selectivity: A Potential Novel Regulatory Mechanism.

    abstract：:Histone deacetylase 8 (HDAC8) is a well-characterized member of the class I acetyl-lysine deacetylase (HDAC) family. Previous work has shown that the efficiency of HDAC8-catalyzed deacetylation of a methylcoumarin peptide varies depending on the identity of the divalent metal ion in the HDAC8 active site. Here we demo...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.7b00851

    authors： Castaneda CA,Lopez JE,Joseph CG,Scholle MD,Mrksich M,Fierke CA

    更新日期：2017-10-24 00:00:00

  • Mechanistic studies with deuterated dihydroorotates on the dihydroorotate oxidase from Crithidia fasciculata.

    abstract：:Deuterium-labeled dihydroorotates bearing one, two, or three deuteriums at the pair of C4 and C5 positions have been synthesized in high isotopic and chiral purity and characterized by NMR and mass spectroscopy. These substrates have been used with the FMN-containing biosynthetic dihydroorotate oxidase from Crithidia ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00307a033

    authors： Pascal RA Jr,Walsh CT

    更新日期：1984-06-05 00:00:00