1
|
Agramunt J, Tain J, Albiol F, Algora A, Caballero-Folch R, Calviño F, Cortes G, Dillmann I, Eronen T, Garcia A, Ganioglu E, Gelletly W, Gorelov D, Guadilla V, Hakala H, Jokinen A, Kankainen A, Montaner A, Marta M, Mendoza E, Moore I, Nobs C, Orrigo S, Penttila H, Reponen M, Rinta-Antila S, Riego A, Rubio B, Saastamoinen A, Salvador-Castiñeira P, Tarifeño-Saldivia A, Tolosa A, Valencia E. New accurate measurements of neutron emission probabilities for relevant fission products. EPJ Web Conf 2017. [DOI: 10.1051/epjconf/201714601004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
2
|
Kuuluvainen E, Hakala H, Havula E, Sahal Estimé M, Rämet M, Hietakangas V, Mäkelä TP. Cyclin-dependent kinase 8 module expression profiling reveals requirement of mediator subunits 12 and 13 for transcription of Serpent-dependent innate immunity genes in Drosophila. J Biol Chem 2014; 289:16252-61. [PMID: 24778181 DOI: 10.1074/jbc.m113.541904] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Cdk8 (cyclin-dependent kinase 8) module of Mediator integrates regulatory cues from transcription factors to RNA polymerase II. It consists of four subunits where Med12 and Med13 link Cdk8 and cyclin C (CycC) to core Mediator. Here we have investigated the contributions of the Cdk8 module subunits to transcriptional regulation using RNA interference in Drosophila cells. Genome-wide expression profiling demonstrated separation of Cdk8-CycC and Med12-Med13 profiles. However, transcriptional regulation by Cdk8-CycC was dependent on Med12-Med13. This observation also revealed that Cdk8-CycC and Med12-Med13 often have opposite transcriptional effects. Interestingly, Med12 and Med13 profiles overlapped significantly with that of the GATA factor Serpent. Accordingly, mutational analyses indicated that GATA sites are required for Med12-Med13 regulation of Serpent-dependent genes. Med12 and Med13 were also found to be required for Serpent-activated innate immunity genes in defense to bacterial infection. The results reveal a novel role for the Cdk8 module in Serpent-dependent transcription and innate immunity.
Collapse
Affiliation(s)
- Emilia Kuuluvainen
- From the Institute of Biotechnology, University of Helsinki, P. O. Box 56, 00014 Helsinki
| | - Heini Hakala
- From the Institute of Biotechnology, University of Helsinki, P. O. Box 56, 00014 Helsinki
| | - Essi Havula
- From the Institute of Biotechnology, University of Helsinki, P. O. Box 56, 00014 Helsinki, the Department of Biosciences, University of Helsinki, P. O. Box 65, 00014 Helsinki
| | - Michelle Sahal Estimé
- From the Institute of Biotechnology, University of Helsinki, P. O. Box 56, 00014 Helsinki
| | - Mika Rämet
- the Institute of Biomedical Technology, and BioMediTech, University of Tampere, 33014 Tampere, the Department of Pediatrics, Tampere University Hospital, 22521 Tampere, the Department of Pediatrics, Institute of Clinical Medicine, and Medical Research Center Oulu, University of Oulu, 90014 Oulu, and the Department of Children and Adolescents, Oulu University Hospital, 90029 Oulu, Finland
| | - Ville Hietakangas
- From the Institute of Biotechnology, University of Helsinki, P. O. Box 56, 00014 Helsinki, the Department of Biosciences, University of Helsinki, P. O. Box 65, 00014 Helsinki
| | - Tomi P Mäkelä
- From the Institute of Biotechnology, University of Helsinki, P. O. Box 56, 00014 Helsinki,
| |
Collapse
|
3
|
Arpalahti J, Jokilammi A, Hakala H, Lönnberg H. Depurination of (dien)Pt(II) complexes of purine deoxyribonucleosides. Comparison with the effects of (dien)Pd(II) ion complexing. J PHYS ORG CHEM 2004. [DOI: 10.1002/poc.610040507] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
4
|
Abstract
[reaction: see text] Novel nucleosidic phosphoramidite blocks were synthesized by a Mitsunobu reaction between 2'-deoxy-5'-O-(4,4'-dimethoxytrityl)uridine and a primary alcohol containing a conjugate group in its structure (a protected functional group, an organic dye, or a precursor of a lanthanide(III) chelate) followed by phosphitylation. They were used in machine-assisted DNA synthesis in the standard manner. A slightly modified deprotection procedure was used for the preparation of oligonucleotide conjugates tethered to lanthanide(III) chelates. For the latter application one non-nucleosidic block was also synthesized.
Collapse
Affiliation(s)
- J Hovinen
- PerkinElmer Life Sciences, Wallac Oy, P.O. Box 10, FIN-20101 Turku, Finland.
| | | |
Collapse
|
5
|
Salo H, Virta P, Hakala H, Prakash TP, Kawasaki AM, Manoharan M, Lönnberg H. Aminooxy functionalized oligonucleotides: preparation, on-support derivatization, and postsynthetic attachment to polymer support. Bioconjug Chem 1999; 10:815-23. [PMID: 10502348 DOI: 10.1021/bc990021m] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three novel phosphoramidites, each bearing a phthaloyl-protected aminooxy tail, were prepared and applied in automated oligonucleotide synthesis. After chain assembly, the phthaloyl protection was removed with hydrazinium acetate. Normal succinyl linker turned to be stable under these conditions, and hence the support-bound oligonucleotide could be converted to a pyrene oxime conjugates by reacting with pyrene carbaldehyde or cis-retinal. Standard ammonolytic deprotection then released the deprotected conjugate in solution. Alternatively, the crude aminooxy-tethered oligonucleotide was immobilized to microscopic polymer particles by reacting the aminooxy function with the particle-bound aldehyde or epoxide groups. These immobilized oligonuceotides were shown to serve properly as probes in a mixed phase hybridization assay.
Collapse
Affiliation(s)
- H Salo
- Department of Chemistry, University of Turku, FIN-20014 Turku,
| | | | | | | | | | | | | |
Collapse
|
6
|
Hakala H, Virta P, Salo H, Lönnberg H. Simultaneous detection of several oligonucleotides by time-resolved fluorometry: the use of a mixture of categorized microparticles in a sandwich type mixed-phase hybridization assay. Nucleic Acids Res 1998; 26:5581-8. [PMID: 9837986 PMCID: PMC148034 DOI: 10.1093/nar/26.24.5581] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Porous, uniformly sized (50 micrometer) glycidyl methacrylate/ethylene dimethacrylate particles (SINTEF) were used as a solid phase to construct a sandwich type hybridization assay that allowed simultaneous detection of up to six oligonucleotides from a single sample. The assay was based on categorization of the particles by two organic prompt fluorophores, viz. fluorescein and dansyl, and quantification of the oligonucleotide hybridization by time-resolved fluorometry. Accordingly, allele-specific oligodeoxyribonucleotide probes were assembled on the particles by conventional phosphoramidite strategy using a non-cleavable linker, and the category defining fluorescein and/or dansyl tagged building blocks were inserted in the 3'-terminal sequence. An oligonucleotide bearing a photoluminescent europium(III) chelate was hybridized to the complementary 3'-terminal sequence of the target oligonucleotide, and the resulting duplex was further hybridized to the particle-bound allele-specific probes via the 5'-terminal sequence of the target. After hybridization each individual particle was subjected to three different fluorescence intensity measurements. The intensity of the prompt fluorescence signals of fluorescein and dansyl defined the particle category, while the europium(III) chelate emission quantified the hybridization. The length of the complementary region between the target oligonucleotide and the particle-bound probe was optimized to achieve maximal selectivity. Furthermore, the kinetics of hybridization and the effect of the concentration of the target oligomer on the efficiency of hybridization were evaluated. By this approach the possible presence of a three base deletion (DeltaF508), point mutation (G542X) and point deletion (1078delT) related to cystic fibrosis could unequivocally be detected from a single sample.
Collapse
Affiliation(s)
- H Hakala
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
| | | | | | | |
Collapse
|
7
|
Hakala H, Mäki E, Lönnberg H. Detection of oligonucleotide hybridization on a single microparticle by time-resolved fluorometry: quantitation and optimization of a sandwich type assay. Bioconjug Chem 1998; 9:316-21. [PMID: 9576805 DOI: 10.1021/bc9701860] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Uniformly sized (50 micro m) porous glycidyl methacrylate/ethylene dimethacrylate particles (SINTEF) were used as the solid phase in a sandwich type mixed-phase hybridization assay based on time-resolved fluorescence detection on a single particle. These particles were coated with oligodeoxyribonucleotide probes by conventional phosphoramidite chain assembly. An oligodeoxyribonucleotide bearing a photoluminescent europium(III) chelate, ¿2,2',2",2"'-¿¿4'-¿4"'-[(4, 6-dichloro-1,3,5-triazin-2-yl)amino]phenyl¿-2,2':6',2"-terpyrid ine-6, 6"-diyl¿bis(methylenenitrilo)¿tetrakis(acetato)¿eur opi um(III), was hybridized to a complementary sequence of the target oligonucleotide, and the resulting duplex was further hybridized to the particle-bound probes. The latter binding was quantified by time-resolved measurement of the emission signal of a single particle. Kinetics of hybridization and the effect of the concentration of the target oligomer and the fluorescently tagged probe on the efficiency of hybridization were studied. The intensity of the emission signal was linearly related to the concentration of the target oligomer over a range of 5 orders of magnitude. The length of the complementary region between the target oligomer and the particle-bound probe was varied, and the effect of point mutations and deletions on the hybridization efficiency was determined in each case. The maximal selectivity was observed with 10-16-base pair complementary sequences, the optimal length depending on the oligonucleotide loading on the particle. Discrimination between the complete matches and point mismatches was unequivocal, a single point mutation and/or deletion decreasing the efficiency of hybridization by more than 2 orders of magnitude.
Collapse
Affiliation(s)
- H Hakala
- Department of Chemistry, University of Turku, Finland
| | | | | |
Collapse
|
8
|
Lövgren T, Heinonen P, Lehtinen P, Hakala H, Heinola J, Harju R, Takalo H, Mukkala VM, Schmid R, Lönnberg H, Pettersson K, Iitiä A. Sensitive bioaffinity assays with individual microparticles and time-resolved fluorometry. Clin Chem 1997; 43:1937-43. [PMID: 9342016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Future immunoassays and nucleic acid hybridization assays will be performed in miniaturized formats that utilize microchips or microparticles. This will require a sensitive detection technology that allows spatial resolution. By using fluorescent europium chelates and time-resolved microfluorometry, one can detect 11,000 europium molecules on individual microparticles. In a miniaturized noncompetitive immunoassay of prostate-specific antigen (PSA), we quantitatively detected 5 ng/L (0.05 amol per particle) of the analyte on an individual microparticle with excellent precision over the whole measurement range (CV <10%). Using a hybridization assay, we also could detect the deltaF508 mutation for cystic fibrosis on individual microparticles. Consequently, fluorescent lanthanide chelate labels and time-resolved microfluorometry qualify as the next generation of technology in this field.
Collapse
Affiliation(s)
- T Lövgren
- Department of Biotechnology, University of Turku, Finland.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Hakala H, Heinonen P, Iitiä A, Lönnberg H. Detection of oligonucleotide hybridization on a single microparticle by time-resolved fluorometry: hybridization assays on polymer particles obtained by direct solid phase assembly of the oligonucleotide probes. Bioconjug Chem 1997; 8:378-84. [PMID: 9177844 DOI: 10.1021/bc970033c] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Oligodeoxyribonucleotides were assembled by conventional phosphoramidite chemistry on uniformly sized (50 microns) porous glycidyl methacrylate/ethylene dimethacrylate (SINTEF) and compact polystyrene (Dynosphere) particles, the aminoalkyl side chains of which were further derivatized with DMTrO-acetyl groups. The linker was completely resistant toward ammonolytic deprotection of the base moieties. The quality of oligonucleotides was assessed by repeating the synthesis on the same particles derivatized with a cleavable ester linker. The ability of the oligonucleotide-coated particles to bind complementary sequences via hybridization was examined by following the attachment of oligonucleotides bearing a photoluminescent europium(III) chelate to the particles. The fluorescence emission was measured directly on a single particle. The effects of the following factors on the kinetics and efficiency of hybridization were studied: number of particles in a given volume of the assay solution, loading of oligonucleotide on the particle, concentration of the target oligonucleotide in solution, length of the hybridizing sequence, presence of noncomplementary sequences, and ionic strength. The fluorescence signal measured on a single particle after hybridization was observed to be proportional to the concentration of the target oligonucleotide in solution over a concentration range of 5 orders of magnitude.
Collapse
Affiliation(s)
- H Hakala
- Department of Chemistry, University of Turku, Finland.
| | | | | | | |
Collapse
|
10
|
Hakala H, Lönnberg H. Time-resolved fluorescence detection of oligonucleotide hybridization on a single microparticle: covalent immobilization of oligonucleotides and quantitation of a model system. Bioconjug Chem 1997; 8:232-7. [PMID: 9095365 DOI: 10.1021/bc9700143] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Several alternative methods have been described for the immobilization of oligodeoxyribonucleotides to uniformly sized glycidyl methacrylate/ethylene dimethacrylate particles. Hybridization of complementary oligodeoxyribonucleotides labeled with photoluminescent europium(III) chelates to these particle-bound oligonucleotide probes was followed by subjecting a single microparticle to a time-resolved fluorescence measurement. The hybridization was further quantified by releasing the europium ion to a fluorescence enhancement solution and determining its concentration against europium(III) chloride standards. Both the efficiency and kinetics of the hybridization were observed to depend markedly on the linker employed to tether the oligonucleotide probes to the particles. These effects and those of the experimental conditions, such as oligonucleotide concentration in solution, oligonucleotide density on particles, and number of particles in a given volume of assay solution, are discussed.
Collapse
Affiliation(s)
- H Hakala
- Department of Chemistry, University of Turku, Finland
| | | |
Collapse
|