Further exploration of the imidazole pKaH motif in DNAzymes through NMR studies of sequence permutations

Anne-Mare de Vries
Persbericht

Further Exploration of the Imidazole pKaH Motif in DNAzymes through NMR studies of Sequence Permutations

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Bibliografie

1.      Van Gasse, B. (2012). Investigating the structure and stability of modified DNA duplexes with NMR spectroscopy. PhD. Ghent University.

2.      Gheerardijn, V. (2014). Functional nucleic acids as tools in catalysis. PhD. Ghent University.

3.      Buyst, D. (2015). Design and systematic study of imidazole based DNAzymes. PhD. Ghent University.

4.      Kirby, A. (1996). Enzyme mechanisms, models, and mimics. Angewandte Chemie-International Edition in English, 35(7), 707-724.

5.      Trends in pharmacological sciences, (2014). Beware of docking. [online] Available at: Cell.com [Accessed 21 Mar. 2016].

6.      Boehr, D., Nussinov, P. and Wright, P. (2009). The role of dynamic conformational ensembles in biomolecular recognition. Nature Chemical Biology, 5, 789-796.

7.      Dahm, R. (2005). Friedrich Miescher and the discovery of DNA. Developmental Biology, 278(2), 74-288.

8.      Crick, F. (1968). The origin of the genetic code. Journal of Molecular Biology, 38(3), 367-379.

9.      Nucleic Acids Book, (2005-2016). DNA duplex stability. [online] Available at: Atdbio.com/nucleic-acids-book. [Accessed 21 Mar. 2016].

10.  Neidle, S. (2008). Principles of Nucleic Acid Structure. Academic Press, Elsevier.

11.  Dickerson, R., H. Drew, et al. (1982). The anatomy of A-DNA, B-DNA, and Z-DNA. Science 216(4545), 475-485.

12.  Bochman, M., Paeschke K., et al. (2012). DNA secondary structures: stability and function of G-quadruplex structures. Nature Reviews. Genetics, 13(11), 770-780.

13.  Rich, A., Nordheim A., et al. (1984). The chemistry and biology of left handed Z-DNA. Annual Review of Biochemistry, 53, 791-846.

14.  Arnott, S. and D. Hukins (1972). Optimized parameters for A-DNA and B-DNA. Biochemical and Biophysical Research Communications, 47(6), 1504-&.

15.  Wing, R., H. Drew, et al. (1980). "Crystal-structure analysis of a complete turn of B-DNA. Nature, 287(5784), 755-758.

16.  Nanda, V. and R. Koder (2010). Designing artificial enzymes by intuition and computation. Nat Chem, 2(1), 15-24.

17.  Joyce, G. (1998). Nucleic acid enzymes: Playing with a fuller deck. Proceedings of the National Academy of Sciences of the United States of America, 95(11), 5845-5847.

18.  Perrin, D., Garestier T., et al. (2001). Bridging the gap between proteins and nucleic acids: A metal-independent RNAseA mimic with two protein-like functionalities. Journal of the American Chemical Society, 123(8), 1556-1563.

19.  Perrin, D., Garestier T., et al. (1999). Expanding the catalytic repertoire of nucleic acid catalysts: Simultaneous incorporation of two modified deoxyribonucleoside triphosphates bearing ammonium and imidazolyl functionalities. Nucleosides Nucleotides & Nucleic Acids 18(3), 377-391.

20.  Breaker, R. (1997). In vitro selection of catalytic polynucleotides. Chemical Reviews, 97(2), 371-390.

21.  Close, D. (2013). Calculated pKa’s of the DNA base radicals. The journal of physical chemistry, 117, 473-480.

22.  Fedor, M. and Williamson J. (2005). The catalytic diversity of RNAs. Nature Reviews. Molecular Cell Biology, 6(5), 399-412.

23.  Strobel, S. and Cochrane J. (2007). RNA Catalysis: Ribozymes, Ribosomes and Riboswitches. Current opinion in chemical biology, 11(6), 636-643.

24.  Nobel prizes, (2014). The Nobel Prize in Chemistry 1989 – Press Release. [online] Available at: Nobelprize.org. [Accessed. 11 Apr. 2016].

25.  Robertson, M. and Joyce G. (2012). The Origins of the RNA World. Cold Spring Harbor Perspectives in Biology, 4(5).

26.  Bernhardt, H. (2012). The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others). Biology Direct, 7.

27.  Cech, T.(2000). Structural biology - The ribosome is a ribozyme. Science, 289(5481), 878-879.

28.  Thompson, J. and Raines T. (1994). Value of general acid-base catalysis to ribonuclease-A. Journal of the American Chemical Society, 116(12), 5467-5468.

29.  Silverman, S. (2008). Catalytic DNA (deoxyribozymes) for synthetic applications - current abilities and future prospects. Chemical Communications, (30), 3467-3485.

30.  Lermer, L., Roupioz, et al. (2002). Toward an RNaseA mimic: a DNAzyme with imidazoles and cationic amines. Journal of the American Chemical Society, 124(34), 9960-9961.

31.  Breaker, R. and Joyce G. (1994). A DNA enzyme that cleaves RNA. Chemistry & Biology 1(4), 223-229.

32.  Breslow, R. and Chung S. (1989). A novel synthesis of substituted imidazoles, and a reexamination of a purported chymotrypsin model. Tetrahedron Letters, 30(33), 4353-4356.

33.  Santoro, S.and Joyce G. (1997). A general purpose RNA-cleaving DNA enzyme. Proceedings of the National Academy of Sciences of the United States of America, 94(9), 4262-4266.

34.  Raines, R. (1998). Ribonuclease A. Chemical Reviews, 98(3), 1045-1065.

35.  Razkin, J., Nilsson H., et al. (2007). Catalysis of the cleavage of uridine 3'-2,2,2-trichloroethylphosphate by a designed Helix-Loop-Helix motif peptide. Journal of the American Chemical Society, 129(47), 14752-14758.

36.  Buyst, D., Gheerardijn, V. et al. (2015). Identification of a pKa-regulating motif stabilizing imidazole-modified double-stranded DNA. Nucleic Acids Research, 43(1), 51-62.

37.  Holmes, S. C and Gait, M. (2005). Syntheses and oligonucleotide incorporation of nucleoside analogues containing pendant imidazolyl or amino functionalities - The search for sequence-specific artificial ribonucleases. European Journal of Organic Chemistry, 2005(24), 5171-5183.

38.  Beaucage, S. and Caruthers, M. (1981). Deoxynucleoside phosphoramidites – a new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Letters, 22(20), 1859-1862.

39.  Blackburn, G., Gait, M., Loakes, D. and Williams, D. (2006). Nucleic acids in chemistry and biology. 3rd ed. Cambridge: The Royal Society of Chemistry.

40.  Nucleic Acids Book, (2005-2016). The phosphoramidite method. [online] Available at: Atdbio.com/nucleic-acids-book. [Accessed 28 Sep. 2016].

41.  Vargeese, C., Carter J., et al. (1998). Efficient activation of nucleoside phosphoramidites with 4,5-dicyanoimidazole during oligonucleotide synthesis. Nucleic Acids Research, 26(4), 1046-1050.

42.  Mergny, J. and Lacroix L. (2003). Analysis of thermal melting curves. Oligonucleotides, 13(6), 515-537.

43.  Boelens, R., Scheek, R. et al. (1985). Sequential assignment of imono-proton and amino-proton resonances in H-1-NMR spectra of oligonucleotides by two-dimensional NMR-spectroscopy – Application to a LAC operator fragment. Journal of Magnetic Resonance, 62(3), 378-386.

44.  Wütrich, K. (1986). NMR of Proteins and Nucleic Acids. New York, Wiley Interscience.

45.  Weiss, M., Patel, D. et al. (1984). Two dimentional H-1-NMR of the lambda-operator site OL1- A sequential assignment strategy and its application. Proceedings of the National Academy of Sciences of the United States of America-Biological Sciences, 81(1), 130-134.

46.  Ash, E., Sudmeier, J. et al. (2000). Unusual H-1 NMR chemical shifts support (His) C-epsilon 1-H center dot center dot center dot O = C H-bond, Proposal for reaction-driven ring flip mechanism in serine protease catalysis. Proceedings of the National Academy of Sciences of the United States of America, 97(19), 10371-10376.

47.  Robillar.G and Shulman, R. (1972). High-resolution nuclear magnetic-resonance study of histidine-aspartate hydrogen-bond in chemotrypsin and chymotrypsinogen. Journal of Molecular Biology, 71(2), 507-&.

48.  Cruz-Gallardo, I., Del Conte, R. et al. (2015). A Non-Invasive NMR Method Based on Histidine Imidazoles to Analyze the pH-Modulation of Protein-Nucleic Acid Interfaces. Chemistry-a European Journal, 21(20), 7588-7595.

49.  Silverstein, T. (2012). Fitting Imidazole 1H NMR Titration Data to the Henderson–Hasselbalch Equation. Journal of Chemical Education, 89(11), 1474-1475.

50.  Calladine, C. and Drew, H. (1986). Principles of sequence dependent flexure of DNA. Journal of Molecular Biology, 192(4), 907-918.

51.  Andrus, A. and Kuimelis, G. (2001). Overview of Purification and Analysis of Synthetic Nucleic Acids in Current Protocols in Nucleic Acid Chemistry. John Wiley & Sons, Inc.

52.  Vranken, W., et al. (2005).The CCPN data model for NMR spectroscopy: Development of a software pipeline. Proteins-Structure Function and Bioinformatics, 59(4), 687-696.

53.   James, T. (2000), Current Protocols in Nucleic Acid Chemistry. John Wiley & Sons, Inc.

54.   Bruker AVANCE, (2003). Beginners Guide. [online] Available at: https://www.auburn.edu. [Accessed. 14 May 2016].

Universiteit of Hogeschool
Master of Science in Chemistry
Publicatiejaar
2016
Promotor(en)
Prof. Dr. J. C. Martins
Kernwoorden
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