Relevant bibliographies by topics / RNA Cleavage

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'RNA Cleavage'

Author: Grafiati
Published: 4 June 2021
Last updated: 18 February 2022

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Journal articles on the topic "RNA Cleavage"

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Pantaleo, Vitantonio, György Szittya, and József Burgyán. "Molecular Bases of Viral RNA Targeting by Viral Small Interfering RNA-Programmed RISC." Journal of Virology 81, no. 8 (January 31, 2007): 3797–806. http://dx.doi.org/10.1128/jvi.02383-06.

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ABSTRACT RNA silencing is conserved in a broad range of eukaryotes and operates in the development and maintenance of genome integrity in many organisms. Plants have adapted this system for antiviral defense, and plant viruses have in turn developed mechanisms to suppress RNA silencing. RNA silencing-related RNA inactivation is likely based on target RNA cleavage or translational arrest. Although it is widely assumed that virus-induced gene silencing (VIGS) promotes the endonucleolytic cleavage of the viral RNA genome, this popular assumption has never been tested experimentally. Here we analyzed the viral RNA targeting by VIGS in tombusvirus-infected plants, and we show evidence that antiviral response of VIGS is based on viral RNA cleavage by RNA-induced silencing effector complex (RISC) programmed by virus-specific small interfering RNAs (siRNAs). In addition, we found that the RISC-mediated cleavages do not occur randomly on the viral genome. Indeed, sequence analysis of cloned cleavage products identified hot spots for target RNA cleavage, and the regions of specific RISC-mediated cleavages are asymmetrically distributed along the positive- and negative-sense viral RNA strands. In addition, we identified viral siRNAs containing high-molecular-mass protein complexes purified from the recovery leaves of the silencing suppressor mutant virus-infected plants. Strikingly, these large nucleoproteins cofractionated with microRNA-containing complexes, suggesting that these nucleoproteins are silencing related effector complexes.
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Desroches, Alexandre, and Jean-Bernard Denault. "Characterization of caspase-7 interaction with RNA." Biochemical Journal 478, no. 13 (July 16, 2021): 2681–96. http://dx.doi.org/10.1042/bcj20210366.

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Apoptosis is a regulated form of cell death essential to the removal of unwanted cells. At its core, a family of cysteine peptidases named caspases cleave key proteins allowing cell death to occur. To do so, each caspase catalytic pocket recognizes preferred amino acid sequences resulting in proteolysis, but some also use exosites to select and cleave important proteins efficaciously. Such exosites have been found in a few caspases, notably caspase-7 that has a lysine patch (K38KKK) that binds RNA, which acts as a bridge to RNA-binding proteins favoring proximity between the peptidase and its substrates resulting in swifter cleavage. Although caspase-7 interaction with RNA has been identified, in-depth characterization of this interaction is lacking. In this study, using in vitro cleavage assays, we determine that RNA concentration and length affect the cleavage of RNA-binding proteins. Additionally, using binding assays and RNA sequencing, we found that caspase-7 binds RNA molecules regardless of their type, sequence, or structure. Moreover, we demonstrate that the N-terminal peptide of caspase-7 reduces the affinity of the peptidase for RNA, which translates into slower cleavages of RNA-binding proteins. Finally, employing engineered heterodimers, we show that a caspase-7 dimer can use both exosites simultaneously to increase its affinity to RNA because a heterodimer with only one exosite has reduced affinity for RNA and cleavage efficacy. These findings shed light on a mechanism that furthers substrate recognition by caspases and provides potential insight into its regulation during apoptosis.
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Dorner, S., and A. Barta. "Probing Ribosome Structure by Europium-Induced RNA Cleavage." Biological Chemistry 380, no. 2 (February 1, 1999): 243–51. http://dx.doi.org/10.1515/bc.1999.032.

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AbstractDivalent metal ions are absolutely required for the structure and catalytic activities of ribosomes. They are partly coordinated to highly structured RNA, which therefore possesses high-affinity metal ion binding pockets. As metalion induced RNA cleavages are useful for characterising metal ion binding sites and RNA structures, we analysed europium (Eu3+) induced specific cleavages in both 16S and 23S rRNA ofE. coli. The cleavage sites were identified by primer extension and compared to those previously identified for calcium, lead, magnesium, and manganese ions. Several Eu3+cleavage sites, mostly those at which a general metal ion binding site had been already identified, were identical to previously described divalent metal ions. Overall, the Eu3+cleavages are most similar to the Ca2+cleavage pattern, probably due to a similar ion radius. Interestingly, several cleavage sites which were specific for Eu3+were located in regions implicated in the binding of tRNA and antibiotics. The binding of erythromycin and chloramphenicol, but not tetracycline and streptomycin, significantly reduced Eu3+cleavage efficiencies in the peptidyl transferase center. The identification of specific Eu3+binding sites near the active sites on the ribosome will allow to use the fluorescent properties of europium for probing the environment of metal ion binding pockets at the ribosome's active center.
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Westhof, E. "RNA CATALYSIS:Chemical Diversity in RNA Cleavage." Science 286, no. 5437 (October 1, 1999): 61–62. http://dx.doi.org/10.1126/science.286.5437.61.

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Altman, Sidney, Madeline Baer, Cecilia Guerrier-Takada, and Agustin Vioque. "Enzymatic cleavage of RNA by RNA." Trends in Biochemical Sciences 11, no. 12 (December 1986): 515–18. http://dx.doi.org/10.1016/0968-0004(86)90086-1.

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Altman, Sidney. "Enzymatic cleavage of RNA by RNA." Bioscience Reports 10, no. 4 (August 1, 1990): 317–37. http://dx.doi.org/10.1007/bf01117232.

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Suhasini, Avvaru N., and Ravi Sirdeshmukh. "Transfer RNA Cleavages by Onconase Reveal Unusual Cleavage Sites." Journal of Biological Chemistry 281, no. 18 (February 23, 2006): 12201–9. http://dx.doi.org/10.1074/jbc.m504488200.

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Rusk, Nicole. "Another player for RNA-guided RNA cleavage." Nature Methods 14, no. 3 (March 2017): 222–23. http://dx.doi.org/10.1038/nmeth.4213.

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Saleem, M., and L. E. Pelcher. "Site-specific cleavage of tobacco mosaic virus RNA: A study of factors influencing the cleavage." Canadian Journal of Biochemistry and Cell Biology 63, no. 5 (May 1, 1985): 382–86. http://dx.doi.org/10.1139/o85-055.

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DNA oligomer directed ribonuclease H (RNase H) methodology is applied to specifically cleave tobacco mosaic virus (TMV) RNA. Using a synthetic DNA oligomer P(dT8)dCdC, complementary to a region from nucleotide 5545 to nucleotide 5554 at the 3′ end of TMV RNA, we have cleaved the RNA at the site of polynucleotides complementary to the DNA oligomer. Factors such as secondary structure of the RNA, concentrations of DNA oligomer, RNase H and magnesium ions in the reaction mixture, and time of incubation were optimized for the RNase H cleavage of TMV RNA – DNA oligomer complex. Denaturation of TMV RNA with 50% dimethyl sulphoxide at 50 °C is essential for the site-specific cleavage.
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Ryan, Kevin. "Pre-mRNA 3’ Cleavage is Reversibly Inhibited in Vitro by Cleavage Factor Dephosphorylation." RNA Biology 4, no. 1 (January 2007): 26–33. http://dx.doi.org/10.4161/rna.4.1.4365.

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Dissertations / Theses on the topic "RNA Cleavage"

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Forster, Anthony Carlyle. "Self-cleavage of plant pathogenic RNAs." Title page, contents and summary only, 1987. http://web4.library.adelaide.edu.au/theses/09PH/09phf7331.pdf.

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Mitchell, Michelle Hall. "Understanding structural mechanisms of endolytic RNA cleavage enzymes." Tallahassee, Florida : Florida State University, 2009. http://etd.lib.fsu.edu/theses/available/etd-07102009-145044.

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Thesis (Ph. D.)--Florida State University, 2009.
Advisor: Hong Li, Florida State University, College of Arts and Sciences, Institute of Molecular Biophysics. Title and description from dissertation home page (viewed on Oct. 26, 2009). Document formatted into pages; contains vi, 68 pages. Includes bibliographical references.
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Jin, Yan. "In vitro and in vivo studies of DNA cleavage and targeted cleavage of HIV REV response element RNA by metallopeptides." Columbus, Ohio : Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1155606670.

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Marriott, Robert Edward. "Accelerated cleavage of phosphate esters." Thesis, University of Cambridge, 1994. https://www.repository.cam.ac.uk/handle/1810/272476.

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Hurst, Phillip C. "Lanthanum(III)-promoted cleavage of RNA and cyclic nucleotides." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape11/PQDD_0015/NQ44460.pdf.

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Barman, Jharna. "Targeting RNA by the Antisense Approach and a Close Look at RNA Cleavage Reaction." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8272.

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Ruan, Wenjie. "Evolution of two modes of intrinsic RNA polymerase transcript cleavage." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-136940.

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Jennebach, Stefan. "RNA polymerase I domain architecture and basis of rRNA cleavage." Diss., lmu, 2012. http://nbn-resolving.de/urn:nbn:de:bvb:19-146779.

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Sheldon, Candice Claire. "Hammerhead mediated self-cleavage of plant pathogenic RNAs /." Title page, contents and summary only, 1992. http://web4.library.adelaide.edu.au/theses/09PH/09phs544.pdf.

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Chambers, A. "RNA 3' cleavage and polyadenylation in oocytes, eggs and embryos of Xenopus laevis." Thesis, University of Warwick, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.380275.

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Books on the topic "RNA Cleavage"

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Guo, Hans Chung-Teh. Characterization of RNA cleavage mediated by the Neurospora VS RNA ribozyme. Ottawa: National Library of Canada = Bibliothèque nationale du Canada, 1993.

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Chambers, Alistair. RNA 3' cleavage and polyadenylation in oocytes, eggs and embryos of "Xenopus laevis". [s.l.]: typescript, 1986.

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service), ScienceDirect (Online, ed. RNA turnover in eukaryotes: Nucleases, pathways and analysis of mRNA decay. San Diego, Calif: Academic, 2008.

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Nicholson, Allen W. Ribonucleases. Berlin, Heidelberg: Springer-Verlag Berlin Heidelberg, 2011.

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Livingston, Schuyler, Benjamin Young, Martin Markowitz, Poonam Mathur, and Bruce L. Gilliam. HIV Virology. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190493097.003.0017.

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HIV is a member of the lentivirus subfamily of retroviruses. Two distinct groups of viruses are pathogenic in humans: HIV-1 and HIV-2. Both are transmitted sexually and known to cause immunodeficiency disease. HIV enters the cell through use of the CD4 receptor and chemokine co-receptors, primarily CCR5 and CXCR4. The viral genome is transcribed from RNA to DNA by reverse transcriptase and integrated into the host genome by integrase. The HIV genome encodes 15 proteins, comprising three categories: structural, regulatory, and accessory. After budding from the host cell, the virus matures into its infectious form through cleavage of viral precursor proteins by protease.
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Book chapters on the topic "RNA Cleavage"

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Gagnon, Keith T., and E. Stuart Maxwell. "Assessing Intermolecular RNA:RNA Interactions Within a Ribonucleoprotein Complex Using Heavy Metal Cleavage Mapping." In RNA-RNA Interactions, 125–34. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1896-6_9.

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Kirsebom, Leif A., and Jerzy Ciesiolka. "Pb2+-Induced Cleavage of RNA." In Handbook of RNA Biochemistry, 269–84. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2014. http://dx.doi.org/10.1002/9783527647064.ch13.

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Vlassov, V. V., and A. V. Vlassov. "Cleavage of RNA by Imidazole." In Artificial Nucleases, 49–60. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-642-18510-6_5.

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Kierzek, R. "Structural Considerations Concerning Cleavage of RNA." In Artificial Nucleases, 33–48. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-642-18510-6_4.

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Sheldon, C. C., A. C. Jeffries, C. Davies, and R. H. Symons. "RNA Self-Cleavage by the Hammerhead Structure." In Nucleic Acids and Molecular Biology, 227–42. Berlin, Heidelberg: Springer Berlin Heidelberg, 1990. http://dx.doi.org/10.1007/978-3-642-84150-7_14.

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Heidrich, Corina G., and Christian Berens. "Probing RNA Structure and Ligand Binding Sites on RNA by Fenton Cleavage." In Handbook of RNA Biochemistry, 301–18. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2014. http://dx.doi.org/10.1002/9783527647064.ch15.

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Zheng, Dinghai, and Bin Tian. "RNA-Binding Proteins in Regulation of Alternative Cleavage and Polyadenylation." In Systems Biology of RNA Binding Proteins, 97–127. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1221-6_3.

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Ponchon, Luc, Geneviève Beauvais, Sylvie Nonin-Lecomte, and Frédéric Dardel. "Selective RNase H Cleavage of Target RNAs from a tRNA Scaffold." In Recombinant and In Vitro RNA Synthesis, 9–18. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-113-4_2.

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Lee, Gwangrog. "Single-Molecule Studies of Exonucleases: Following Cleavage Actions One Step at a Time." In Biophysics of RNA-Protein Interactions, 57–84. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9726-8_4.

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Miyoshi, Keita, Hiroshi Uejima, Tomoko Nagami-Okada, Haruhiko Siomi, and Mikiko C. Siomi. "In vitro RNA Cleavage Assay for Argonaute-Family Proteins." In Methods in Molecular Biology™, 29–43. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-191-8_3.

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Conference papers on the topic "RNA Cleavage"

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Schmidt, Christian, Rüdiger Welz, and Sabine Müller. "Ribozyme mediated RNA double cleavage." In XIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 1999. http://dx.doi.org/10.1135/css199902197.

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Mikkola, Satu, Ulla Kaukinen, Izabella Zagorowska, and Harri Lönnberg. "The cleavage of RNA phosphodiester bonds by metal ions." In XIIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2002. http://dx.doi.org/10.1135/css200205121.

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Tennilä, Tuula, Pirkko Muhonen, Elena Azhayeva, H. Kalervo Väänänen, Alex Azhayev, and Tiina Laitala-Leinonen. "RNA interference tolerates 2'-fluoro modifications at the Argonaute2 cleavage site." In XIVth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2008. http://dx.doi.org/10.1135/css200810465.

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Lönnberg, Tuomas, Mia Helkearo, Attila Jancsó, and Tamás Gajda. "Modeling the general acid/base catalyzed RNA cleavage of small ribozymes." In XVth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2011. http://dx.doi.org/10.1135/css201112268.

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Wang, Qi, Satu Mikkola, Zoltan Jori, Mia Helkearo, and Harri Lönnberg. "Bimetallic Ca2+ and Zn2+ complexes of BISDIEN: Potential catalysts of RNA cleavage." In XIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 1999. http://dx.doi.org/10.1135/css199902222.

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Wang, Qi, Attila Jancsó, Teija Niittymäki, Päivi Poijärvi-Virta, Kaisa Ketomäki, Pasi Virta, Ewelina Leino, et al. "Base and sequence selective cleavage of RNA phosphodiester bonds by Zn(II) azacrown chelates." In XIVth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2008. http://dx.doi.org/10.1135/css200810063.

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Welz, Rüdiger, and Sabine Müller. "Polyamine dependent RNA cleavage: Investigations on the function of spermine in hairpin ribozyme catalysis." In XIIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2002. http://dx.doi.org/10.1135/css200205251.

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Fokina, Alesya, Daria Novopashina, Mariya Meschaninova, Jean-Christophe François, and Alya Venyaminova. "3'-Modified oligo(2'-O-methylribonucleotides) improve cleavage of long structured RNA by DNAzyme 10-23." In XIVth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2008. http://dx.doi.org/10.1135/css200810420.

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Liu, Chung Y., Dominic Chung, Earl Davie, and Leonard Chess. "FORMER STUDIES OF FIBRINOGEN NEW YORK I : ANALYSIS OF HE GENUINIC C DISORDER for the deletion OF MINO ACID SEQUENCE 9-72 OF THE Bβ CHAIN." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644697.

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Fibrinogens New York I and la (NY-I and NY-la) have been purified from blood plasma samples of a^ sister and a brother in a white family with thrombotic tendency. Both are heterozygous and contain both thrombin-clottable fibrinogen with two normal Bβ-chains and thrombin-nonclottable fibrinogen with two abnormal Bβ chains. The abnormal β-chains result- fran deletions of ammo acid residues 9-72, which are encoded exactly by exon II of the gene. To study the genomic disorder for this deletion, gencmic DNAs were isolated respectively from leukocytes of NY-la, NY-Ib (a nonaffected brother), and four normal individuals outside the NY-I family, and analysed in Southern blotting experiments with a human gencmic DNA probe containing exons I-V. Digestion of various DNAs were performed with two different restriction enzymes, and these digestions were analyzed respectively by agrose electroptoresis.Digestion with Hind III reveals 3 cleavage sites (one site in intron A near exon II)witn formation of two fragments of equal size (2 bands : 3.1kb and 3.1 kb) in normal, NY-la and NY-Id, but an extra fragment (one band = 6.0 kb) in NY-Ia.Digestion with Pvu II reveals 3 cleavage sites (one site in exonII) with formation of two fragments (2 bands : 7.5 kb and 2.9kb)m normal, NY-Ia and NY-Ib, but an extra fragment (one band - 5.7 kb) in NY-Ia. These results show that one Hind III and one Pvu II cleavage sites which are present in the normal allele are absent in the abnormal allele of NY-Ia. Thus, these studies indicate that generic disorder is associated with the patient (NY-Ia) with a thrombotic tendency, and further suggest that the genomic defect in the aonormal allele is near the junction of intron A and exon II. A possible mechanism for this genomic disorder is due to that an inverse double crossover have taken place in a region covering this junction, resulting in m abnormal RNA-splicing site in this junction. Thus, exon II is eliminated with intron A during RNA processing and absent in the abnormal rnRNA. Accordingly, the β(9-72) amino acid sequence disappears from one abnromal β-chains.
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Mikkola, Satu, Izabela Zagorowska, and Harri Lönnberg. "The effect of the secondary structure of RNA on the reactivity of its phosphodiester bonds: The cleavage of phosphodiester bonds within hairpin loops in the presence and absence of metal ion catalysts." In XIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 1999. http://dx.doi.org/10.1135/css199902006.

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