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Duart-Garcia C, Braunschweig MH. The Igf2as transcript is exported into cytoplasm and associated with polysomes. Biochem Genet 2012; 51:119-30. [PMID: 23108799 DOI: 10.1007/s10528-012-9547-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 09/12/2012] [Indexed: 11/27/2022]
Abstract
Murine insulin-like growth factor 2 antisense (Igf2as) transcripts originate from the opposite strand of the same Igf2 locus as the Igf2 sense mRNA. The Igf2, insulin 2 (Ins2), and H19 genes form a cluster of imprinted genes on chromosome 7. Loss of imprinting of IGF2 in humans is associated with Beckwith-Wiedemann syndrome and Silver-Russell syndrome, as well as with Wilm's tumor and colorectal cancer. We developed a RNA-FISH protocol to detect Igf2as and Igf2 transcripts. The results from the RNA-FISH were confirmed with quantitative real-time PCR and clearly indicate that the Igf2as transcripts are predominantly located in the cytoplasm of C2C12 cells. In a polysome association study, we showed that the Igf2as sedimented with polysomes in a sucrose gradient. The cellular localization of Igf2as transcripts together with polysome fractionation analysis provides compelling evidence that the Igf2as is protein coding.
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Affiliation(s)
- Carolina Duart-Garcia
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Berne, Switzerland
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Versteeg K, Zwilling D, Wang H, Church KM. Synthesis, structure, and sugar dynamics of a 2′-spiroisoxazolidine thymidine analog. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.08.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Cvetovich RJ. Hydrogen Peroxide Oxidation of Phosphite Triesters in Oligonucleotide Syntheses. Org Process Res Dev 2010. [DOI: 10.1021/op900044z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Raymond J. Cvetovich
- Department of Process Research, Merck Research Laboratories, Rahway, New Jersey 07065, U.S.A
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Chilibeck KA, Wu T, Liang C, Schellenberg MJ, Gesner EM, Lynch JM, MacMillan AM. FRET analysis of in vivo dimerization by RNA-editing enzymes. J Biol Chem 2006; 281:16530-5. [PMID: 16618704 DOI: 10.1074/jbc.m511831200] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Members of the ADAR (adenosine deaminase that acts on RNA) enzyme family catalyze the hydrolytic deamination of adenosine to inosine within double-stranded RNAs, a poorly understood process that is critical to mammalian development. We have performed fluorescence resonance energy transfer experiments in mammalian cells transfected with fluorophore-bearing ADAR1 and ADAR2 fusion proteins to investigate the relationship between these proteins. These studies conclusively demonstrate the homodimerization of ADAR1 and ADAR2 and also show that ADAR1 and ADAR2 form heterodimers in human cells. RNase treatment of cells expressing these fusion proteins changes their localization but does not affect dimerization. Taken together these results suggest that homo- and heterodimerization are important for the activity of ADAR family members in vivo and that these associations are RNA independent.
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Affiliation(s)
- Kaari A Chilibeck
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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Abstract
Multiple oligonucleotides of the same or different sequence, linked end-to-end in tandem can be synthesized in a single automated synthesis. A linker phosphoramidite [R. T. Pon and S. Yu (2004) Nucleic Acids Res., 32, 623–631] is added to the 5′-terminal OH end of a support-bound oligonucleotide to introduce a cleavable linkage (succinic acid plus sulfonyldiethanol) and the 3′-terminal base of the new sequence. Conventional phosphoramidites are then used for the rest of the sequence. After synthesis, treatment with ammonium hydroxide releases the oligonucleotides from the support and cleaves the linkages between each sequence. Mixtures of one oligonucleotide with both 5′- and 3′-terminal OH ends and other oligonucleotides with 5′-phosphorylated and 3′-OH ends are produced, which are deprotected and worked up as a single product. Tandem synthesis can be used to make pairs of PCR primers, sets of cooperative oligonucleotides or multiple copies of the same sequence. When tandem synthesis is used to make two self-complementary sequences, double-stranded structures spontaneously form after deprotection. Tandem synthesis of oligonucleotide chains containing up to six consecutive 20mer (120 bases total), various trinucleotide codons and primer pairs for PCR, or self-complementary strands for in situ formation of double-stranded DNA fragments has been demonstrated.
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Affiliation(s)
- Richard T Pon
- Department of Biochemistry and Molecular Biology, University of Calgary Calgary, AB, Canada T2N 4N1.
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Dey I, Rath PC. A novel rat genomic simple repeat DNA with RNA-homology shows triplex (H-DNA)-like structure and tissue-specific RNA expression. Biochem Biophys Res Commun 2005; 327:276-86. [PMID: 15629459 DOI: 10.1016/j.bbrc.2004.12.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Indexed: 11/17/2022]
Abstract
Mammalian genome contains a wide variety of repetitive DNA sequences of relatively unknown function. We report a novel 227 bp simple repeat DNA (3.3 DNA) with a d{(GA)7A(AG)7} dinucleotide mirror repeat from the rat (Rattus norvegicus) genome. 3.3 DNA showed 75-85% homology with several eukaryotic mRNAs due to (GA/CU)n dinucleotide repeats by nBlast search and a dispersed distribution in the rat genome by Southern blot hybridization with [32P]3.3 DNA. The d{(GA)7A(AG)7} mirror repeat formed a triplex (H-DNA)-like structure in vitro. Two large RNAs of 9.1 and 7.5 kb were detected by [32P]3.3 DNA in rat brain by Northern blot hybridization indicating expression of such simple sequence repeats at RNA level in vivo. Further, several cDNAs were isolated from a rat cDNA library by [32P]3.3 DNA probe. Three such cDNAs showed tissue-specific RNA expression in rat. pRT 4.1 cDNA showed strong expression of a 2.39 kb RNA in brain and spleen, pRT 5.5 cDNA showed strong expression of a 2.8 kb RNA in brain and a 3.9 kb RNA in lungs, and pRT 11.4 cDNA showed weak expression of a 2.4 kb RNA in lungs. Thus, genomic simple sequence repeats containing d(GA/CT)n dinucleotides are transcriptionally expressed and regulated in rat tissues. Such d(GA/CT)n dinucleotide repeats may form structural elements (e.g., triplex) which may be sites for functional regulation of genomic coding sequences as well as RNAs. This may be a general function of such transcriptionally active simple sequence repeats widely dispersed in mammalian genome.
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Affiliation(s)
- Indranil Dey
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India
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Abstract
RNA interference (RNAi) is a powerful biological process for specific silencing of gene expression in diversified eukaryotic cells and has tremendous potential for functional genomics, drug discovery through in vivo target validation, and development of novel gene-specific medicine. The future success of this technology relies on identifying appropriate chemical modifications to improve stability, potency and in vivo cellular delivery. The present review summarizes the role of the chemist's toolbox in this emerging technology.
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Affiliation(s)
- Muthiah Manoharan
- Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, Massachusetts 02142, USA.
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Potter CV, Corkill M, Dean JL, Kybett AP, Kidd R, James M, Saxton H. Comment: 2004’s fastest organic and biomolecular chemistry! NEW J CHEM 2004. [DOI: 10.1039/b417567k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Potter CV, Freshwater J, Dean JL, Kybett AP, Kidd R, James M, Saxton H. Comment: 2004’s fastest organic and biomolecular chemistry! Chem Soc Rev 2004; 33:567-72. [PMID: 15592621 DOI: 10.1039/b417566m] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In January 2003, the Royal Society of Chemistry launched Organic & Biomolecular Chemistry (OBC)--a journal promising to provide high quality research from all aspects of synthetic, physical and biomolecular organic chemistry. The journal was set to build upon the foundations laid down by its predecessor publications (J. Chem. Soc., Perkin Trans. 1 and J. Chem. Soc., Perkin Trans. 2) as well as complement the subject coverage already published in prestigious general chemistry journals such as Chemical Communications and Chemical Society Reviews. Nearly two years on, just how is the programme developing and what can the community expect to see from the Royal Society of Chemistry (RSC)?
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Affiliation(s)
- Caroline V Potter
- Royal Society of Chemistry, Thomas Graham House, Cambridge, UK CB4 0WF.
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Potter CV, Thomas S, Dean JL, Kybett AP, Kidd R, James M, Saxton H. Comment: 2004’s fastest organic and biomolecular chemistry! Chem Commun (Camb) 2004:2781-6. [PMID: 15599407 DOI: 10.1039/b417565b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In January 2004, the Royal Society of Chemistry launched Organic & Biomolecular Chemistry (OBC) - a journal promising to provide high quality research from all aspects of synthetic, physical and biomolecular organic chemistry. The journal was set to build upon the foundations laid down by its predecessor publications (J. Chem. Soc., Perkin Trans. 1 and J. Chem. Soc., Perkin Trans. 2) as well as complement the subject coverage already published in prestigious general chemistry journals such as Chemical Communications and Chemical Society Reviews. Nearly two years on, just how is the programme developing and what can the community expect to see from the Royal Society of Chemistry (RSC)?
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Affiliation(s)
- Caroline V Potter
- Royal Society of Chemistry, Thomas Graham House, Cambridge, UK CB4 0WF.
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Potter CV, McCann G, Dean JL, Kybett AP, Kidd R, James M, Canning M. Comment: 2004’s fastest organic and biomolecular chemistry! ACTA ACUST UNITED AC 2004. [DOI: 10.1039/b417514j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Potter CV, Dean JL, Kybett AP, Kidd R, James M, Canning M. Comment: 2004’s fastest organic and biomolecular chemistry! Org Biomol Chem 2004; 2:3535-40. [PMID: 15592609 DOI: 10.1039/b417338b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In January 2003, the Royal Society of Chemistry launched Organic & Biomolecular Chemistry (OBC)--a journal promising to provide high quality research from all aspects of synthetic, physical and biomolecular organic chemistry. The journal was set to build upon the foundations laid down by its predecessor publications (J. Chem. Soc., Perkin Trans. 1 and J. Chem. Soc., Perkin Trans. 2) as well as complement the subject coverage already published in prestigious general chemistry journals such as Chemical Communications and Chemical Society Reviews. Nearly two years on, just how is the programme developing and what can the community expect to see from the Royal Society of Chemistry (RSC)?
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Affiliation(s)
- Caroline V Potter
- Royal Society of Chemistry, Thomas Graham House, Cambridge, UK CB4 0WF.
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