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Hybridization Experiments (hybridization + experiment)
Kinds of Hybridization Experiments Selected AbstractsOligonucleotides Containing 7-Deaza-2,-deoxyinosine as Universal Nucleoside: Synthesis of 7-Halogenated and 7-Alkynylated Derivatives, Ambiguous Base Pairing, and Dye Functionalization by the Alkyne,Azide ,Click' ReactionHELVETICA CHIMICA ACTA, Issue 7 2008Frank Seela Abstract Oligonucleotides containing 7-deaza-2,-deoxyinosine derivatives bearing 7-halogen substituents or 7-alkynyl groups were prepared. For this, the phosphoramidites 2b,2g containing 7-substituted 7-deaza-2,-deoxyinosine analogues 1b,1g were synthesized (Scheme,2). Hybridization experiments with modified oligonucleotides demonstrate that all 2,-deoxyinosine derivatives show ambiguous base pairing, as 2,-deoxyinosine does. The duplex stability decreases in the order Cd>Ad>Td>Gd when 2b,2g pair with these canonical nucleosides (Table,6). The self-complementary duplexes 5,-d(F7c7I-C)6, d(Br7c7I-C)6, and d(I7c7I-C)6 are more stable than the parent duplex d(c7I-C)6 (Table,7). An oligonucleotide containing the octa-1,7-diyn-1-yl derivative 1g, i.e., 27, was functionalized with the nonfluorescent 3-azido-7-hydroxycoumarin (28) by the Huisgen,Sharpless,Meldal cycloaddition ,click' reaction to afford the highly fluorescent oligonucleotide conjugate 29 (Scheme,3). Consequently, oligonucleotides incorporating the derivative 1g bearing a terminal CC bond show a number of favorable properties: i) it is possible to activate them by labeling with reporter molecules employing the ,click' chemistry. ii) Space demanding residues introduced in the 7-position of the 7-deazapurine base does not interfere with duplex structure and stability (Table,8). iii) The ambiguous pairing character of the nucleobase makes them universal probes for numerous applications in oligonucleotide chemistry, molecular biology, and nanobiotechnology. [source] Lineage-independent mosaic expression and regulation of the Ciona multidom gene in the ancestral notochordDEVELOPMENTAL DYNAMICS, Issue 7 2007Izumi Oda-Ishii Abstract The transcription factor Ciona Brachyury (Ci-Bra) plays an essential role in notochord development in the ascidian Ciona intestinalis. We characterized a putative Ci-Bra target gene, which we named Ci - multidom, and analyzed in detail its expression pattern in normal embryos and in embryos where Ci - Bra was misexpressed. Ci - multidom encodes a novel protein, which contains eight CCP domains and a partial VWFA domain. We show that an EGFP-multidom fusion protein localizes preferentially to the endoplasmic reticulum (ER), and is excluded from the nucleus. In situ hybridization experiments demonstrate that Ci - multidom is expressed in the notochord and in the anterior neural boundary (ANB). We found that the expression in the ANB is fully recapitulated by an enhancer element located upstream of Ci - multidom. By means of misexpression experiments, we provide evidence that Ci-Bra controls transcription of Ci - multidom in the notochord; however, while Ci-Bra is homogeneously expressed throughout this structure, Ci - multidom is transcribed at detectable levels only in a random subset of notochord cells. The number of notochord cells expressing Ci - multidom varies among different embryos and is independent of developmental stage, lineage, and position along the anterior,posterior axis. These results suggest that despite its morphological simplicity and invariant cell-lineage, the ancestral notochord is a mosaic of cells in which the gene cascade downstream of Brachyury is differentially modulated. Developmental Dynamics 236:1806,1819, 2007. © 2007 Wiley-Liss, Inc. [source] Nutrigenomics: a case study in the measurement of insect response to nutritional qualityENTOMOLOGIA EXPERIMENTALIS ET APPLICATA, Issue 1 2006Thomas A. Coudron Abstract Recent developments in the area of nutrigenomics hold the promise of providing valuable information about the impact of nutrition on a wide range of biochemical parameters by investigating how nutrition alters global gene expression patterns. Our goal is to use a nutrigenomics approach to identify insect molecular markers that could be used as early indicators of insect responses to different nutritional sources. Such molecular markers could be chosen for degree of expression and evaluated for suitability as nutritional biomarkers by examining developmental and generational expression. Ideal markers would be highly expressed, manifested in the first generation within one developmental stage, and consistent over many generations. Our objective for the current study was to illustrate the potential discovery of molecular markers using Perillus bioculatus (F.) (Heteroptera: Pentatomidae), when reared on an optimal vs. suboptimal diet, and analyze the presence of differentially expressed genes resulting from those treatments. In this paper we present preliminary results of microarray and subtractive hybridization experiments that represent the feasibility of using nutrigenomics to assist in analyzing insect responses to nutritional changes and dietary quality with the intent of stimulating further studies in this area. [source] Localization of nAChR subunit mRNAs in the brain of Macaca mulattaEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 10 2000Zhi-Yan Han Abstract We present here a systematic mapping of nAChR subunit mRNAs in Macaca mulatta brain. A fragment, from the transmembrane segments MIII to MIV of Macaca neuronal nAChR subunits was cloned, and shown to exhibit high identity (around 95%) to the corresponding human subunits. Then, specific oligodeoxynucleotides were synthesized for in situ hybridization experiments. Both ,4 and ,2 mRNA signals were widely distributed in the brain, being stronger in the thalamus and in the dopaminergic cells of the mesencephalon. Most brain nuclei displayed both ,4 and ,2 signals with the exception of some basal ganglia regions and the reticular thalamic nucleus which were devoid of ,4 signal. ,6 and ,3 mRNA signals were selectively concentrated in the substantia nigra and the medial habenula. The strongest signals for ,3 or ,4 mRNAs were found in the epithalamus (medial habenula and pineal gland), whereas there were no specific ,3 or ,4 signals in mesencephalic dopaminergic nuclei. ,5 and ,7 mRNA signals were found in several brain areas, including cerebral cortex, thalamus and substantia nigra, although at a lower level than ,4 and ,2. The distribution of ,3, ,4, ,5, ,6, ,7, ,2, ,3 and ,4 subunit mRNAs in the monkey is substantially similar to that observed in rodent brain. Surprisingly, ,2 mRNA signal was largely distributed in the Macaca brain, at levels comparable with those of ,4 and ,2. This observation represents the main difference between rodent and Macaca subunit mRNA distribution and suggests that, besides ,4,2*, ,2,2* nAChRs constitute a main nAChR isoform in primate brain. [source] N -acyl-homoserine lactone-mediated quorum-sensing in Azospirillum: an exception rather than a ruleFEMS MICROBIOLOGY ECOLOGY, Issue 2 2006Ludovic Vial Abstract Forty Azospirillum strains were tested for their ability to synthesize N -acyl-homoserine lactones (AHLs). AHL production was detected for four strains belonging to the lipoferum species and isolated from a rice rhizosphere. AHL molecules were structurally identified for two strains: Azospirillum lipoferum TVV3 produces 3O,C8 -HSL (N -3-oxo-octanoyl-homoserine-lactone), C8 -HSL (N -3-octanoyl-homoserine-lactone), 3O,C10 -HSL (N -3-oxo-decanoyl-homoserine-lactone), 3OH,C10 -HSL (N -3-hydroxy-decanoyl-homoserine-lactone) and C10 -HSL (N -3-decanoyl-homoserine-lactone), whereas A. lipoferum B518 produced 3O,C6 -HSL (N -3-oxo-hexanoyl-homoserine-lactone), C6 -HSL (N -3-hexanoyl-homoserine-lactone), 3O,C8 -HSL, 3OH,C8 -HSL and C8 -HSL. Genes involved in AHL production were characterized for A. lipoferum TVV3 by generating a genomic library and complementing an AHL-deficient strain with sensor capabilities. Those genes, designated alpI and alpR, were found to belong to the luxI and luxR families, respectively. When cloned in a suitable heterologous host, alpI and alpR could direct the synthesis of the five cognate AHLs present in A. lipoferum TVV3. These two adjacent genes were found to be located on a 85kb plasmid. Southern hybridization experiments with probes alpI/R indicated that genes involved in AHL production in the three other AHL-producing strains were not closely related to alpI and alpR. This study demonstrates that AHL-based quorum-sensing is not widespread among the genus Azospirillum and could be found only in some A. lipoferum strains. [source] Vibrio owensii sp. nov., isolated from cultured crustaceans in AustraliaFEMS MICROBIOLOGY LETTERS, Issue 2 2010Ana Cano-Gómez Abstract Two bacterial strains (DY05T and 47666-1) were isolated in Queensland, Australia, from diseased cultured crustaceans Panulirus ornatus and Penaeus monodon, respectively. On the basis of 16S rRNA gene sequence identity, the strains were shown to belong to the Harveyi clade of the genus Vibrio. Multilocus sequence analysis using five housekeeping genes (rpoA, pyrH, topA, ftsZ and mreB) showed that the strains form a monophyletic group with 94.4% concatenated sequence identity to the closest species. DNA,DNA hybridization experiments showed that strains DY05T and 47666-1 had 76% DNA similarity to each other, but <70% to their closest neighbours Vibrio harveyi LMG 4044T (,55%), Vibrio campbellii LMG 11216T (,52%) and Vibrio rotiferianus LMG 21460T (,46%). Strains DY05T and 47666-1 could be differentiated from their relatives on the basis of several phenotypic characteristics. The major fatty acids were C15:0 iso 2-OH and/or C16:1,7, C16:0, C18:1,7 and C14:0. Based on the polyphasic evidence presented here, it can be concluded that strains DY05T and 47666-1 belong to the same novel species of the genus Vibrio, for which the name Vibrio owensii sp. nov. is proposed. The type strain is DY05T (=JCM 16517T=ACM 5300T). [source] Usefulness of R72H PCR assay for differentiation between Vibrio parahaemolyticus and Vibrio alginolyticus species: validation by DNA,DNA hybridizationFEMS MICROBIOLOGY LETTERS, Issue 1 2002Annick Robert-Pillot Abstract We compared the efficiencies of biochemical methods and polymerase chain reaction (PCR) for the identification of Vibrio parahaemolyticus strains. The 122 isolates studied, identified by biochemical tests as V. parahaemolyticus or Vibrio alginolyticus, were tested by R72H PCR assay. The results obtained with the two methods were consistent for 90% of the strains studied. PCR amplification of the R72H fragment generated two unique amplicons, 387 bp and 320 bp in length. For 11% of the strains from seawater, the results of biochemical identification did not correlate with PCR results. DNA,DNA hybridization experiments provided evidence that some strains identified as V. alginolyticus in biochemical tests should be considered members of the V. parahaemolyticus species. We therefore suggest that biochemical tests are not accurate enough for the identification of V. parahaemolyticus isolates and we demonstrate that amplification of the R72H fragment, whether the amplicon is 320 bp or 387 bp long, is a powerful tool for the reliable identification of V. parahaemolyticus. [source] Molecular analysis of tetracycline resistance in Salmonella enterica subsp. enterica serovars Typhimurium, Enteritidis, Dublin, Choleraesuis, Hadar and Saintpaul: construction and application of specific gene probesJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2000G. Frech A total of 65 epidemiologically unrelated tetracycline-resistant isolates of the six Salmonella enterica subsp. enterica (Salm.) serovars Dublin, Choleraesuis, Typhimurium, Enteritidis, Hadar and Saintpaul were investigated for the presence of tetracycline resistance genes. For this, specific gene probes of the tetracycline resistance genes (tet) of the hybridization classes A, B, C, D, E and G were constructed by cloning PCR-amplified internal segments of the respective tet structural genes. These gene probes were sequenced and used in hybridization experiments with plasmid DNA or endonuclease digested whole cell DNA as targets. Only tet(A) genes were detected on plasmids in all Salm. Dublin isolates as well as in single isolates of Salm. Choleraesuis and Salm. Typhimurium. Genes of the hybridization classes B, C, D and G, but also in some cases those of class A, were located in the chromosomal DNA of the corresponding Salmonella isolates. Restriction fragment length polymorphisms (RFLPs) of tet gene carrying fragments were detected in chromosomally tetracycline-resistant isolates. These RFLPs might represent valuable additional tools for the identification and characterization of tetracycline-resistant Salmonella isolates. [source] Altered expression of transcripts for ,-tubulin and an unidentified gene in the spinal cord of phenyl saligenin phosphate treated hens (Gallus gallus)JOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY, Issue 5 2003Jonathan H. Fox Abstract Phenyl saligenin phosphate (PSP) induces a central-peripheral distal axonopathy in domestic fowl that develops 7,21 days after a single exposure. Neurotoxic esterase (NTE) is the initial molecular target for this neurotoxicity. PSP has to covalently bind to NTE and chemically "age" for induction of axonopathy. It was hypothesized that exposure to PSP results in early changes in spinal cord gene expression that do not occur with phenylmethylsulfonyl fluoride, a non-neuropathic compound that also inhibits NTE, or DMSO controls. Targeted display was used to screen ,15,000 gel bands. Three candidate genes were identified, but only the transcript designated P1 showed decreased expression following PSP exposure (2 mg/kg i.m.) in subsequent Northern blot and in situ hybridization experiments in samples taken <48 h after exposure. Additional experiments revealed that a ,2.5 kb ,-tubulin transcript had decreased expression at 12,48 h after PSP exposure, with maximum change at 48 h (33%, p = 0.0479). A ,4.5 kb ,-tubulin transcript had increased expression at 12 h (38%, p = 0.0125) and decreased expression at 48 h (28%, p = 0.0576). In situ hybridization on spinal cord revealed neuronal expression of P1 and ,-tubulin transcripts. Decreased expression of transcripts for P1 and ,-tubulin was present at 12 and 48 h, respectively. This decrease occurred in all neurons, not just those whose axons degenerate. Results suggest that (1) in PSP-induced OPIDN (organophosphorus-induced delayed neurotoxicity) some gene transcript expression changes are associated with initiation of axonopathy, and (2) PSP modulates spinal cord gene expression in neuronal types that do not undergo axonal degeneration. © 2003 Wiley Periodicals, Inc. J Biochem Mol Toxicol 17:263,271, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.10088 [source] Modular changes of cis-regulatory elements from two functional Pit1 genes in the duplicated genome of Cyprinus carpioJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 3 2006G. Kausel Abstract The pituitary-specific transcription factor Pit1 is involved in its own regulation and in a network of transcriptional regulation of hypothalamo-hypophyseal factors including prolactin (PRL) and growth hormone (GH). In the ectotherm teleost Cyprinus carpio, Pit1 plays an important role in regulation of the adaptive response to seasonal environmental changes. Two Pit1 genes exist in carp, a tetraploid vertebrate and transcripts of both genes were detected by RT-PCR analysis. Powerful comparative analyses of the 5,-flanking regions revealed copy specific changes comprising modular functional units in the naturally evolved promoters. These include the precise replacement of four nucleotides around the transcription start site embedded in completely conserved regions extending upstream of the TATA-box, an additional transcription factor binding site in the 5,-UTR of gene-I and, instead, duplication of a 9 bp element in gene-II. Binding of nuclear factors was assessed by electro mobility shift assays using extracts from rat pituitary cells and carp pituitary. Binding was confirmed at one conserved Pit1, one conserved CREB and one consensus MTF1. Interestingly, two functional Pit1 sites and one putative MTF1 binding site are unique to the Pit1 gene-I. In situ hybridization experiments revealed that the expression of gene-I in winter carp was significantly stronger than that of gene-II. Our data suggest that the specific control elements identified in the proximal regulatory region are physiologically relevant for the function of the duplicated Pit1 genes in carp and highlight modular changes in the architecture of two Pit1 genes that evolved for at least 12 MYA in the same organism. J. Cell. Biochem. 99: 905,921, 2006. © 2006 Wiley-Liss, Inc. [source] Postzygotic incompatibilities between the pupfishes, Cyprinodon elegans and Cyprinodon variegatus: hybrid male sterility and sex ratio biasJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 6 2006C. TECH Abstract I examined the intrinsic postzygotic incompatibilities between two pupfishes, Cyprinodon elegans and Cyprinodon variegatus. Laboratory hybridization experiments revealed evidence of strong postzygotic isolation. Male hybrids have very low fertility, and the survival of backcrosses into C. elegans was substantially reduced. In addition, several crosses produced female-biased sex ratios. Crosses involving C. elegans females and C. variegatus males produced only females, and in backcrosses involving hybrid females and C. elegans males, males made up approximately 25% of the offspring. All other crosses produced approximately 50% males. These sex ratios could be explained by genetic incompatibilities that occur, at least in part, on sex chromosomes. Thus, these results provide strong albeit indirect evidence that pupfish have XY chromosomal sex determination. The results of this study provide insight on the evolution of reproductive isolating mechanisms, particularly the role of Haldane's rule and the ,faster-male' theory in taxa lacking well-differentiated sex chromosomes. [source] A simple and rapid technique for the detection of Epstein-Barr virus DNA in HIV-associated oral hairy leukoplakia biopsiesJOURNAL OF ORAL PATHOLOGY & MEDICINE, Issue 3 2000M. J. E. M. F. Mabruk Abstract: A method of generating nucleic acid probes by polymerase chain reaction (PCR) for the detection of Epstein,Barr virus (EBV)-DNA by in situ hybridization in oral hairy leukoplakia (OHL) lesions is described. This method has the advantage over older methods of being cheaper, quicker and retaining sensitivity and specificity. Purified PCR products of Epstein-Barr virus DNA of 110 bp and 328 bp were labelled with biotin by nick translation or random primer labelling and were compared in in situ hybridization experiments with probes prepared by incorporation of biotin-labelled nucleotides in the PCR reaction mixture, with EBV viral DNA as a template. These probes were applied to 18 OHL tongue biopsies known to be positive for EBV-DNA, using a commercially available biotin-labelled BamHI "V" fragment EBV-DNA probe. To determine the specificity of the probes, we applied them to 20 normal tongue tissue samples and to 12 biopsies taken from keratotic tongue lesions from patients without risk factors for HIV infection and known to be negative for EBV-DNA. Clear positive signals for EBV-DNA were detected in all 18 cases of OHL biopsies using the amplimer of 328 bp labelled by PCR and random primer labelling. However, nick translation labelling was less efficient and sensitive. All control specimens were negative for EBV-DNA. [source] Population Dynamics of Pseudomonas syringae pv. tomato Strains on Tomato Cultivars Rio Grande and Rio Grande- Pto under Field ConditionsJOURNAL OF PHYTOPATHOLOGY, Issue 4 2009David K. Willis Abstract We examined the effects of the Pto resistance locus on the population dynamics of Pseudomonas syringae pv. tomato (Pst) strains in field experiments with the nearly isogenic tomato lines Rio Grande (RG, susceptible to Pst races 0 and 1) and Rio Grande-Pto (RG-Pto, resistant to Pst race 0, susceptible to Pst race 1). Pst strain SM78-1Smr (race 0) grew well under field conditions and caused ample bacterial speck disease on susceptible RG plants. In contrast, strain DC3000 failed to establish large populations when inoculated onto field grown RG plants. Mean population sizes of SM78-1Smr were 4,5 orders of magnitude larger on RG than RG-Pto plants indicating that RG-Pto plants were highly effective in attenuating pathogen population development. Most of the sampled leaflets from RG-Pto field plots harboured small numbers of SM78-1Smr. However, population sizes SM78-1Smr as large as 105,106 CFU were found on a few leaflets. Bacteria isolated from these leaflets had phenotypes characteristic of Pst race 1 strains. In growth chamber plant assays, the bacterial strains grew well and caused typical speck lesions on RG-Pto plants. The strains appeared to be race-shift mutants of SM SM78-1Smr. Interestingly, results from DNA hybridization experiments demonstrated that the race-shift mutants were deleted for the avirulence gene, avrPto but not for avrPtoB. [source] Genome-wide analysis of the general stress response in Bacillus subtilisMOLECULAR MICROBIOLOGY, Issue 4 2001Chester W. Price Bacteria respond to diverse growth-limiting stresses by producing a large set of general stress proteins. In Bacillus subtilis and related Gram-positive pathogens, this response is governed by the ,B transcription factor. To establish the range of cellular functions associated with the general stress response, we compared the transcriptional profiles of wild and mutant strains under conditions that induce ,B activity. Macroarrays representing more than 3900 annotated reading frames of the B. subtilis genome were hybridized to 33P-labelled cDNA populations derived from (i) wild-type and sigB mutant strains that had been subjected to ethanol stress; and (ii) a strain in which ,B expression was controlled by an inducible promoter. On the basis of their significant ,B -dependent expression in three independent experiments, we identified 127 genes as prime candidates for members of the ,B regulon. Of these genes, 30 were known previously or inferred to be ,B dependent by other means. To assist in the analysis of the 97 new genes, we constructed hidden Markov models (HMM) that identified possible ,B recognition sequences preceding 21 of them. To test the HMM and to provide an independent validation of the hybridization experiments, we mapped the ,B -dependent messages for seven representative genes. For all seven, the 5, end of the message lay near typical ,B recognition sequences, and these had been predicted correctly by the HMM for five of the seven examples. Lastly, all 127 gene products were assigned to functional groups by considering their similarity to known proteins. Notably, products with a direct protective function were in the minority. Instead, the general stress response increased relative message levels for known or predicted regulatory proteins, for transporters controlling solute influx and efflux, including potential drug efflux pumps, and for products implicated in carbon metabolism, envelope function and macromolecular turnover. [source] Affinity of corpora amylacea for oligonucleotides: Sequence dependency and proteinaceous binding motifNEUROPATHOLOGY, Issue 4 2006Ioan A. Balea Corpora amylacea (CA) have an affinity to nucleic acids as shown by in situ hybridization experiments. However, little is known about the specificity of this interaction, as well as the mechanism involved. We investigated the ability of different probes of digoxigenin-labeled oligonucleotides corresponding to some specific neuronal receptors, both sense and antisense, to bind to CA from human autopsy brain tissue. The bound nucleotides were detected with antidigoxigenin antibody and the signal was further amplified using the tyramide signal amplification system. The affinity of binding varies with the sequence of nucleotides. The most intense signal is produced by the adenosine-2A receptor antisense probe and the least intense signal is produced by the N-methyl-D-aspartate receptor sense probe. The affinity of binding for the same probe does not depend on the localization of CA in the central nervous system. Complete staining loss by proteinase K pretreatment in higher concentrations shows that the binding motif is partially proteinaceous. The circumferential but not the punctate internal staining is diminished by mild amylglucosidase pretreatment, suggesting a process of progressive apposition and condensation. [source] Detection of Water Buffalo Sex Chromosomes in Spermatozoa by Fluorescence in situ HybridizationREPRODUCTION IN DOMESTIC ANIMALS, Issue 5 2003T Révay Contents In order to identify X- and Y-bearing spermatozoa in water buffalo by fluorescence in situ hybridization (FISH), some available probes of closely related species were examined. An X- and Y-specific probe set, made from flow sorted yak chromosomes, labelled in somatic metaphases of water buffalo the whole X and Y, respectively, except their centromere regions. A cattle Y-chromosome repeat sequence (BC1.2) showed strong signal on the telomere region of the buffalo Y-chromosome, demonstrating the evolutionary conservation of this locus in water buffalo. In hybridization experiments with spermatozoa from five buffaloes, the yak X-Y paint set demonstrated clear signals in more than 92% (46.8% X and 45.8% Y) of the cells. Using the cattle Y-chromosome specific BC1.2 probe, clear hybridization signal was detected in more than 48% of the cells. Statistical analysis showed that there was no significant difference between bulls or from the expected 50 : 50 ratio of X- and Y-bearing cells. The probes presented here are reliable to assess separation of X- and Y-bearing spermatozoa. [source] Association of ANA, a Member of the Antiproliferative Tob Family Proteins, with a Cafl Component of the CCR4 Transcriptional Regulatory ComplexCANCER SCIENCE, Issue 6 2001Yutaka Yoshida A 35-kDa protein, ANA, belongs to an emerging family of antiproliferative proteins consisting of Tob, Tob2, ANA/BTG3, PC3B, PC3/TIS21/BTG2, and BTG1. All of these, except ANA and PC3B, have been shown to interact with the CCR4 transcription factor-associated protein Cafl. Here we show that ANA also associates with Cafl, ANA being the preferred partner of Cafl among the Tob family proteins. Although ANA is likely to interact with Cafl at its amino-terminal hall', which is conserved among the family members, our data suggest that the carboxyl-terminal half of ANA plays a role in the interaction. Finally, in situ hybridization experiments revealed that expression of Caf1 overlaps at least in part with that of ANA. Thus, ANA could function through its interaction with Caf1. [source] DNA and RNA-Controlled Switching of Protein Kinase ActivityCHEMBIOCHEM, Issue 4 2009Lars Röglin Dr. Abstract Constrained: The readily programmable nucleic acid mediated recognition is used to constrain a phosphopeptide that was flanked by PNA segments. RNA-based switching allows control over the activity of target enzymes such as the protein kinase Src. It might thus be feasible to transduce changes of the concentration of selected RNA molecules to changes of the activity of signal transduction proteins. Protein switches use the binding energy gained upon recognition of ligands to modulate the conformation and binding properties of protein segments. We explored whether the programmable nucleic acid mediated recognition might be used to design or mimic constraints that limit the conformational freedom of peptide segments. The aim was to design nucleic acid,peptide conjugates in which the peptide portion of the conjugate would change the affinity for a protein target upon hybridization. This approach was used to control the affinity of a PNA,phosphopeptide conjugate for the signal transduction protein Src kinase, which binds the cognate phosphopeptides in a linear conformation. Peptide,nucleic acid arms were attached to known peptide binders. The chimeric molecules were studied in three modes: 1) as single strands, 2) constrained by intermolecular hybridization (duplex formation) and 3) constrained by intramolecular hybridization (hairpin formation). Of note, duplexes that were designed to accommodate bulged peptide structures (for example, in hairpins or bulges) had lower binding affinities than duplexes in which the peptide was allowed to adopt a more relaxed conformation. Greater than 90-fold differences in binding affinities were observed. It was, thus, feasible to make use of DNA hybridization to reversibly switch from no to almost complete inhibition of Src-SH2,peptide binding, and vice versa. A series of DNA and PNA-based hybridization experiments revealed the importance of charges and conformational effects. Nucleic acid mediated switching was extended to the use of RNA; this enabled a regulation of the enzymatic activity of the Src kinase. The proof-of-principle results demonstrate for the first time that PNA,peptide chimeras can transduce changes of the concentration of a given RNA molecule to changes of the activity of a signal transduction enzyme. [source] | ||||||||||||||||