Theoretical study on binding of Hoechst 33258 with oligonucleotides.

Abstract:

:Computer modelling with an energy minimization procedure is used here to obtain stereochemical and energetic details for complexes of the dye Hoechst 33258 with different oligonucleotide sequences. An optimised model of the dye with d(A)5 X d(T)5 is in conformity with previous proposed models. It has bifurcated hydrogen bonds between N2H and N4H of benzimidazole rings with N3 of adenine and O2 of thymine. Relative binding energies with different oligonucleotides show preference for AT containing sequences, with an intermediate affinity between that for netropsin and distamycin-2. Reduced binding is observed at high ionic concentration. The benzimidazole rings are twisted with respect to the phenol ring in the optimal model. This gives desired curvature to the molecule which is stabilised by intermolecular forces.

journal_name

FEBS Lett

journal_title

FEBS letters

authors

Gopalakrishna K,Kalia A,Royyuru AK,Mrigank,Atreyi M,Rao MV,Kothekar V

doi

10.1016/0014-5793(87)80120-5

subject

Has Abstract

pub_date

1987-05-04 00:00:00

pages

95-9

issue

1

eissn

0014-5793

issn

1873-3468

journal_volume

215

pub_type

杂志文章
  • Structural domains in RNAi.

    abstract::Structural and biochemical studies have begun to elucidate the pathway of RNA silencing that leads to the formation of the RISC complex. The outstanding feature of this pathway is the precise recognition and processing of double-stranded RNA. We present a review of recent structures that illustrate the molecular mecha...

    journal_title:FEBS letters

    pub_type: 杂志文章,评审

    doi:10.1016/j.febslet.2005.07.072

    authors: Collins RE,Cheng X

    更新日期:2005-10-31 00:00:00

  • Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain.

    abstract::Tom1 (Target of Myb1) is suggested to be involved in the transport of ubiquitinated proteins, through the interaction of its GAT (GGA and Tom1) domain with ubiquitin. Here, we demonstrate that the three-helix bundle of Tom1-GAT has two ubiquitin-binding sites recognizing the hydrophobic Ile44 surface of ubiquitin. The...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2005.08.076

    authors: Akutsu M,Kawasaki M,Katoh Y,Shiba T,Yamaguchi Y,Kato R,Kato K,Nakayama K,Wakatsuki S

    更新日期:2005-10-10 00:00:00

  • A critical appraisal of the mitochondrial coenzyme Q pool.

    abstract::The function of the coenzyme Q (CoQ) pool in the inner mitochondrial membrane is reviewed in view of recent findings suggesting a supramolecular organization of the mitochondrial respiratory complexes. In spite of the structural evidence for preferential aggregations of the inner membrane components, most kinetic evid...

    journal_title:FEBS letters

    pub_type: 杂志文章,评审

    doi:10.1016/s0014-5793(01)03172-6

    authors: Lenaz G

    更新日期:2001-12-07 00:00:00

  • Complex formation between calsequestrin and the ryanodine receptor in fast- and slow-twitch rabbit skeletal muscle.

    abstract::Linkage between the high-capacity Ca2+-binding protein calsequestrin and the ryanodine receptor is proposed to be essential for proper Ca2+-release during skeletal muscle excitation-contraction coupling. However, no direct biochemical evidence exists showing a connection between these high-molecular-mass complexes in ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(98)00621-8

    authors: Murray BE,Ohlendieck K

    更新日期:1998-06-16 00:00:00

  • Association of high molecular weight DNA fragmentation with apoptotic or non-apoptotic cell death induced by calcium ionophore.

    abstract::Calcium ionophore (A23187)-induced high molecular weight (HMW) and internucleosomal DNA fragmentation were investigated in human leukemia cell lines. An apoptosis-sensitive cell line, HL-60, showed HMW, internucleosomal DNA fragmentation and morphological changes of apoptosis by A23187. MOLT-4, which is resistant to a...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(95)00405-x

    authors: Kataoka A,Kubota M,Wakazono Y,Okuda A,Bessho R,Lin YW,Usami I,Akiyama Y,Furusho K

    更新日期:1995-05-15 00:00:00

  • Penicillin-binding proteins of beta-lactam-resistant strains of Staphylococcus aureus. Effect of growth conditions.

    abstract::Methicillin-resistant clinical isolates of Staphylococcus aureus are intrinsically resistant to beta-lactam antibiotics in that the resistance mechanism is unrelated to the possession of beta-lactamases. We have demonstrated that a new, high-molecular-mass penicillin-binding protein (PBP) is present in these strains w...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(85)80036-3

    authors: Reynolds PE,Brown DF

    更新日期:1985-11-11 00:00:00

  • The N intermediate of bacteriorhodopsin at low temperatures: stabilization and photoconversion.

    abstract::In aqueous suspensions of purple membranes (pH 10.2, 0.4 M KCl) an intermediate having an absorption maximum at 570-575 nm (at -196 degrees C) was produced by first heating the M intermediate up to -30 degrees C and then stabilizing it by subsequent cooling to -60 degrees C. We suggest that this species is the interme...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(90)80380-2

    authors: Balashov SP,Imasheva ES,Litvin FF,Lozier RH

    更新日期:1990-10-01 00:00:00

  • The intrachain disulfide bridge is responsible of the unusual stability properties of novel acylphosphatase from Escherichia coli.

    abstract::Acylphosphatase (AcP) activity in prokaryotes was classically attributed to some aspecific acid phosphatases. We identified an open reading frame for a putative AcP in the b0968 Escherichia coli gene and purified the recombinant enzyme after checking by RT-PCR that it was indeed expressed. EcoAcP has a predicted typic...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2006.11.033

    authors: Ramazzotti M,Parrini C,Stefani M,Manao G,Degl'Innocenti D

    更新日期:2006-12-22 00:00:00

  • Focus on histone variant H2AX: to be or not to be.

    abstract::Phosphorylation of histone variant H2AX at serine 139, named gammaH2AX, has been widely used as a sensitive marker for DNA double-strand breaks (DSBs). gammaH2AX is required for the accumulation of many DNA damage response (DDR) proteins at DSBs. Thus it is believed to be the principal signaling protein involved in DD...

    journal_title:FEBS letters

    pub_type: 杂志文章,评审

    doi:10.1016/j.febslet.2010.05.021

    authors: Yuan J,Adamski R,Chen J

    更新日期:2010-09-10 00:00:00

  • Mapping the residues of protein kinase CK2 alpha subunit responsible for responsiveness to polyanionic inhibitors.

    abstract::The quadruple mutation of the whole basic cluster, K74KKK77 conserved in the catalytic subunits of protein kinase CK2 and implicated in substrate recognition, not only abolishes inhibition by heparin but even induces with some peptide substrates an up to 5-fold stimulation by heparin in the 0.5-5 micrograms/ml concent...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(95)01542-6

    authors: Vaglio P,Sarno S,Marin O,Meggio F,Issinger OG,Pinna LA

    更新日期:1996-02-12 00:00:00

  • Apoptosis repressor with caspase recruitment domain (ARC) is expressed in cancer cells and localizes to nuclei.

    abstract::Apoptosis repressor with caspase recruitment domain is expressed at high levels in brain and myogenic tissues, consistent with a role to inhibit apoptosis in the terminally differentiated cells. Expression of ARC in cancers is not known. In this study, we reported that ARC was highly expressed in various non-myogenic ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2005.03.040

    authors: Wang M,Qanungo S,Crow MT,Watanabe M,Nieminen AL

    更新日期:2005-04-25 00:00:00

  • The binding interface of kindlin-2 and ILK involves Asp344/Asp352/Thr356 in kindlin-2 and Arg243/Arg334 in ILK.

    abstract::Focal adhesion (FA) proteins, kindlin-2 and integrin-linked kinase (ILK), regulate cell adhesion and migration. ILK interacts with and promotes kindlin-2 targeting to FAs. Leu353 and Leu357 in kindlin-2 have been reported to be important for the interaction between kindlin-2 and ILK. However, the binding interface bet...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1002/1873-3468.12938

    authors: Guan SY,Chng CP,Ong LT,Tan HF,Alex Law SK,Tan SM

    更新日期:2018-01-01 00:00:00

  • Structure-dependent functional properties of human defensin 5.

    abstract::The mucosal epithelium secretes a variety of antimicrobial peptides that act as part of the innate immune system to protect against invading microbes. Here, we describe the functional properties of human defensin (HD) 5, the major antimicrobial peptide produced by Paneth cells in the ileum, in relation to its structur...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2006.12.036

    authors: de Leeuw E,Burks SR,Li X,Kao JP,Lu W

    更新日期:2007-02-06 00:00:00

  • Rat brain Na+ channel mRNAs in non-excitable Schwann cells.

    abstract::The expression of rat brain voltage-sensitive Na+ channel mRNAs in Schwann cells was examined using in situ hybridization cytochemistry and RT-PCR. The mRNAs of rat brain Na+ channel subtype II and III, but not subtype I, were detected in cultured Schwann cells from sciatic nerve and in intact sciatic nerve, which con...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(94)00807-8

    authors: Oh Y,Black JA,Waxman SG

    更新日期:1994-08-22 00:00:00

  • Evidence for the archaebacterial-type conformation about the bond between the beta-ionone ring and the polyene chain of the chromophore retinal in chlamyrhodopsin.

    abstract::Previous studies using retinal analogs (Wada, A., Sakai, M., Kinumi, T., Tsujimoto, K., Yamauchi, M. and Ito, M. (1994) J. Org. Chem. 59, 6992-6997; Wada, A., Sakai, M., Imamoto, Y., Shichida., Y., Yoshizawa, T. and Ito, M. (1993) Chem. Pharm. Bull. 41, 793-795) revealed that both retinochrome and visual pigments shar...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(98)01004-7

    authors: Sakamoto M,Wada A,Akai A,Ito M,Goshima T,Takahashi T

    更新日期:1998-09-04 00:00:00

  • A light-sensitive mechanism differently regulates transcription and transcript stability of omega3 fatty-acid desaturases (FAD3, FAD7 and FAD8) in soybean photosynthetic cell suspensions.

    abstract::The omega3 fatty-acid desaturases: FAD7 and FAD8 (plastid) and FAD3 (reticular) are responsible for trienoic fatty-acid (TA) production in plants. The expression of these enzymes seemed to be regulated differently in response to light. Darkness leads to a decrease in total TA level. Under such conditions, FAD3 and FAD...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2006.07.087

    authors: Collados R,Andreu V,Picorel R,Alfonso M

    更新日期:2006-09-04 00:00:00

  • Restoration of hydroperoxide-dependent lipid peroxidation by 3-methylcholanthrene induction of cytochrome P-448 in hepatoma microsomes.

    abstract::Microsomal membranes from the slow-growing Morris hepatoma 9618A catalyze, in the presence of t-butyl hydroperoxide, lower rates of lipid peroxidation than rat liver microsomes. The cytochrome P-450 content of hepatoma microsomes is about 40% that of the liver. SKF 525-A, an inhibitor of mixed-function oxidase, produc...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(86)81132-2

    authors: Borrello S,Galeotti T,Palombini G,Minotti G

    更新日期:1986-12-15 00:00:00

  • Na(+)-dependent high affinity uptake of L-glutamate in primary cultures of human fibroblasts isolated from three different types of tissue.

    abstract::Cultured human fibroblasts isolated from embryonic muscle, skin and peripheral nerve tissues were found to accumulate [3H]L-glutamate by a Na(+)-dependent uptake process strongly inhibited by several glutamate/aspartate analogues including D- and L-aspartate, D- and L-threo-3-hydroxyaspartate and L-trans-pyrrolidine-2...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(94)80382-x

    authors: Balcar VJ,Shen J,Bao S,King NJ

    更新日期:1994-02-14 00:00:00

  • F-ATPase: specific observation of the rotating c subunit oligomer of EF(o)EF(1).

    abstract::The rotary motion in response to ATP hydrolysis of the ring of c subunits of the membrane portion, F(o), of ATP synthase, F(o)F(1), is still under contention. It was studied with EF(o)EF(1) (Escherichia coli) using microvideography with a fluorescent actin filament. To overcome the limited specificity of actin attachm...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(00)01436-8

    authors: Pänke O,Gumbiowski K,Junge W,Engelbrecht S

    更新日期:2000-04-21 00:00:00

  • Photoreceptors and olfactory cells express the same retinal guanylyl cyclase isoform in medaka: visualization by promoter transgenics.

    abstract::We examined the spatial expression patterns of two orphan receptor guanylyl cyclase genes OlGC4 and OlGC5 during embryogenesis of medaka and characterized the 5' flanking region required for tissue-specific expression of OlGC4 by introducing promoter-GFP fusion constructs into medaka embryos. Expression of OlGC5 is co...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(00)02109-8

    authors: Kusakabe T,Suzuki N

    更新日期:2000-10-20 00:00:00

  • Neopterin and 7,8-dihydroneopterin induce apoptosis in the rat alveolar epithelial cell line L2.

    abstract::The neopterin derivatives, neopterin and 7,8-dihydroneopterin, modulate the cellular oxidant-antioxidant balance as well as the expression of the inducible nitric oxide synthase (iNOS) gene. Since apoptosis can be induced by reactive oxygen intermediates and nitric oxide (NO) we investigated whether these neopterin de...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(96)01194-5

    authors: Schobersberger W,Hoffmann G,Hobisch-Hagen P,Bock G,Volkl H,Baier-Bitterlich G,Wirleitner B,Wachter H,Fuchs D

    更新日期:1996-11-18 00:00:00

  • tRNA concentration fine tunes protein solubility.

    abstract::Clusters of codons pairing to low-abundance tRNAs synchronize the translation with co-translational folding of single domains in multidomain proteins. Although proven with some examples, the impact of the ribosomal speed on the folding and solubility on a global, cell-wide level remains elusive. Here we show that upre...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2012.07.012

    authors: Fedyunin I,Lehnhardt L,Böhmer N,Kaufmann P,Zhang G,Ignatova Z

    更新日期:2012-09-21 00:00:00

  • Ghrelin inhibits insulin secretion through the AMPK-UCP2 pathway in beta cells.

    abstract::Ghrelin inhibits insulin secretion partly via induction of IA-2beta. However, the orexigenic effect of ghrelin is mediated by the AMP-activated protein kinase (AMPK)-uncoupling protein 2 (UCP2) pathway. Here, we demonstrate that ghrelin's inhibitory effect on insulin secretion also occurs through the AMPK-UCP2 pathway...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2010.02.069

    authors: Wang Y,Nishi M,Doi A,Shono T,Furukawa Y,Shimada T,Furuta H,Sasaki H,Nanjo K

    更新日期:2010-04-16 00:00:00

  • Impacts of deletion and ichthyosis prematurity syndrome-associated mutations in fatty acid transport protein 4 on the function of RPE65.

    abstract::The retinal pigment epithelium-specific 65 kDa (RPE65) isomerase plays a pivotal role in photoreceptor survival and function. RPE65-catalyzed synthesis of 11-cis-retinol from all-trans-retinyl esters in the visual cycle is negatively regulated, through a heretofore unknown mechanism, by the fatty acid transport protei...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1002/1873-3468.13633

    authors: Li S,Green JF,Jin M

    更新日期:2020-02-01 00:00:00

  • Inhibition of ICE-family cysteine proteases rescues murine lymphocytes from lipoxygenase inhibitor-induced apoptosis.

    abstract::Two lipophilic derivatives of caffeic acid which inhibit lipoxygenase, caffeic acid phenethyl ester (CAPE) and N,N'-dicyclohexyl-O-(3,4-dihydroxycinnamoyl)-isourea (DCHCU), reduced the proliferative response of murine splenocytes to concanavalin A in vitro. Both CAPE and DCHCU induced apoptosis in murine thymocyte cul...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(96)01111-8

    authors: Mirzoeva OK,Yaqoob P,Knox KA,Calder PC

    更新日期:1996-11-04 00:00:00

  • Phospholipid phase transitions in homogeneous nanometer scale bilayer discs.

    abstract::Nanoscale protein supported phospholipid bilayer discs, or Nanodiscs, were produced for the purpose of studying the phase transition behavior of the incorporated lipids. Nanodiscs and vesicles were prepared with two phospholipids, dipalmitoyl phosphatidylcholine and dimyristoyl phosphatidylcholine, and the phase trans...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(03)01400-5

    authors: Shaw AW,McLean MA,Sligar SG

    更新日期:2004-01-02 00:00:00

  • Transduction of Cu,Zn-superoxide dismutase mediated by an HIV-1 Tat protein basic domain into mammalian cells.

    abstract::A human Cu,Zn-superoxide dismutase (Cu,Zn-SOD) gene was fused with a gene fragment encoding the nine amino acid transactivator of transcription (Tat) protein transduction domain (RKKRRQRRR) of HIV-1 in a bacterial expression vector to produce a genetic in-frame Tat-SOD fusion protein. The expressed and purified Tat-SO...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(00)02215-8

    authors: Kwon HY,Eum WS,Jang HW,Kang JH,Ryu J,Ryong Lee B,Jin LH,Park J,Choi SY

    更新日期:2000-11-24 00:00:00

  • Clp upregulates transcription of engA gene encoding a virulence factor in Xanthomonas campestris by direct binding to the upstream tandem Clp sites.

    abstract::In Xanthomonas campestris, the causative agent of black rot in crucifers, the endoglucanase level is greatly decreased in the mutant deficient in Clp, a homologue of cyclic AMP receptor protein (CRP). It is established that Clp has the same DNA binding specificity as CRP at positions 5, 6, and 7 (GTG motif) of the DNA...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2005.05.023

    authors: Hsiao YM,Liao HY,Lee MC,Yang TC,Tseng YH

    更新日期:2005-07-04 00:00:00

  • DNA polyintercalation: comparison of DNA binding properties of an acridine dimer and trimer.

    abstract::The DNA binding characteristics of a mono-, di- and trimeric derivative of 9-aminoacridine were studied. The length of the linking carboxamidoalkyl chains was selected to allow bis- or tris-intercalation according to the excluded-site model. Measurements of DNA unwinding angle using closed circular DNA showed that the...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(84)80302-6

    authors: Gaugain B,Markovits J,Le Pecq JB,Roques BP

    更新日期:1984-04-24 00:00:00

  • High levels of rhodopsin phosphorylation in missense mutations of C-terminal region of rhodopsin.

    abstract::Rhodopsin phosphorylation was investigated using synthetic C-terminal peptides from rhodopsin. The peptides were phosphorylated by expressed rhodopsin kinase (RK) in the presence of a photolyzed truncated rhodopsin at the C-terminus. No peptide phosphorylation was detected under dark or in conditions in which RK was i...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(97)00957-5

    authors: Ohguro H

    更新日期:1997-08-25 00:00:00