The oligonucleoside boranophosphates (BH3--ODN) are a new class of phosphorus modified oligonucleotides that differ chemically from natural DNA in that a borane (BH-) group replaces one of the non-bridging oxygens in the phosphodiester backbone. BH3--ODN are more lipophilic and much more resistant to nucleases than natural DNA; they form Watson-Crick duplexes, and activate the Rnase H-mediated cleavage of complementary RNA. The boranophosphates join the natural phosphodiester, the (mono-and di-) thioates, and the more-nuclease-susceptible 2'-F-arabinonucleic acids, as the only classes of oligonucleotides that by themselves can orchestrate mRNA degradation in RNA/oligonucleotide hybrids via the enzyme RNase H. Despite recent improvements in the utility of antisense oligonucleotides in vivo, further progress is still needed. The goals of the proposed work are: (1) To synthesize a set of borano phosphate oligonucleotides and mixed-backbone chimeras targeted against the ras gene; (2) To evaluate the potential of BH3--ODN and chimeras to activate Tnase H1; (3) To evaluate biophysical properties of BH3--ODN including the thermodynamics, structure, and kinetics of their hybridization with RNA oligonucleotides and to study the kinetics of hydrolysis of RNA in BH3--ODN /RNA/Rnase H complexes. (4) To examine penetration of BH3-ODN and localization in cells, and other pharmacological properties; and (5) to probe the sequence and structural requirements for Rnase H specificity through our chemistry. The boranophosphates provide a new platform for probing the subtle effects of structure and sequence on RNase H catalysis. Our overall goals are to better understand the unique chemical and biological properties of boranophosphate oligonucleotides and gain further insight into the mechanism of action of RNase H and antisense agents. This information should allow us to design more potent antisense drugs for treating cancer and viral diseases.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM057693-06
Application #
6700766
Study Section
Bio-Organic and Natural Products Chemistry Study Section (BNP)
Program Officer
Lograsso, Philip
Project Start
1998-05-01
Project End
2007-01-31
Budget Start
2004-02-01
Budget End
2006-01-31
Support Year
6
Fiscal Year
2004
Total Cost
$315,700
Indirect Cost
Name
Duke University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
044387793
City
Durham
State
NC
Country
United States
Zip Code
27705
Xu, Zhihong; Shaw, Barbara Ramsay (2015) Synthesis, Hydrolysis, and Protonation-Promoted Intramolecular Reductive Breakdown of Potential NRTIs: Stavudine ?-P-Borano-?-P-N-l-tryptophanyltriphosphates. Molecules 20:18808-26
Shaw, Barbara Ramsay; Moussa, Laura; Sharaf, Mariam et al. (2008) Boranophosphate siRNA-aptamer chimeras for tumor-specific downregulation of cancer receptors and modulators. Nucleic Acids Symp Ser (Oxf) :655-6
Liu, Hongyan; Hashmi, Syed N; Shaw, Barbara Ramsay (2007) Synthesis of 9-fluorenemethyl boranophosphonodiphosphate via an H-phosphonate approach. Nucleosides Nucleotides Nucleic Acids 26:1455-7
Li, Ping; Sergueeva, Zinaida A; Dobrikov, Mikhail et al. (2007) Nucleoside and oligonucleoside boranophosphates: chemistry and properties. Chem Rev 107:4746-96
Hall, Allison H S; Wan, Jing; Spesock, April et al. (2006) High potency silencing by single-stranded boranophosphate siRNA. Nucleic Acids Res 34:2773-81
Li, Ping; Xu, Zhihong; Liu, Hongyan et al. (2005) Synthesis of alpha-P-modified nucleoside diphosphates with ethylenediamine. J Am Chem Soc 127:16782-3
Khan, Shoeb I; Dobrikov, Mikhail I; Shaw, Barbara Ramsay (2005) Synthesis of 5-ethynyl-2'-deoxyuridine-5'-boranomono phosphate as a potential thymidylate synthase inhibitor. Nucleosides Nucleotides Nucleic Acids 24:1047-9
Wang, Joy Xin; Sergueev, Dmitri S; Shaw, Barbara Ramsay (2005) The effect of a single boranophosphate substitution with defined configuration on the thermal stability and conformation of a DNA duplex. Nucleosides Nucleotides Nucleic Acids 24:951-5
Wan, Jing; Shaw, Barbara Ramsay (2005) Incorporation of ribonucleoside 5'-(alpha-P-borano)triphosphates into a 20-mer RNA by T7 RNA polymerase. Nucleosides Nucleotides Nucleic Acids 24:943-6
Summers, Jack S; Base, Karel; Boukhalfa, Hakim et al. (2005) Use of phosphorus ligand NMR probes to investigate electronic and second-sphere solvent effects in ligand substitution reactions at manganese(II) and manganese(III). Inorg Chem 44:3405-11

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