Selective nuclease digestion of messenger RNAs inside living cells via the short interfering RNA (siRNA)- triggered RNA interference pathway has become a mainstay in molecular biology to study gene function and holds promise for the development of new therapeutics. However, gaps in our understanding of the basic RNA interference mechanism and the ability of siRNAs to interact with intracellular RNA-binding proteins, particularly those involved in the innate immune response, limit the application of this promising new technology. Here we propose to develop new synthetic approaches to modified RNA oligonucleotides and to use the resulting molecules to carryout gene silencing with reduced undesirable off-target effects. This project has the following specific aims: 1) We will synthesize siRNAs bearing pendant alkyl groups projecting into either the major groove or the minor groove. The chemical modifications are designed to change the shape of the base while maintaining its ability to engage in Watson-Crick-like base pairing. These siRNA duplexes will be used to define the effects of nucleobase alkylation in gene silencing. The modifications are also expected to block sequence-dependent off-target effects mediated by Toll-like receptors and sequence- independent off-target effects from dsRBM proteins. 2) We hypothesize that anti-syn conformational changes in modified guanines will act as molecular switches to turn on (when Watson-Crick paired) or off (when Hoogsteen paired) steric blockades in the duplex RNA minor groove. We will investigate two alkylated guanine derivatives as switches, the common oxidized base lesion 8-oxoguanosine (8-oxoG) with added alkyl groups, and the acrolein alkylated purines. These modifications will be placed in the antisense strand using a Watson-Crick-paired sense strand for delivery;the antisense strand will be designed to target a complementary mRNA via Hoogsteen pairing to a purine at the site of modification. 3) We will evaluate the ability of modified siRNAs to engage in sequence-dependent and sequence-independent off-target effects in RNAi. Sequence-dependent effects will be assessed by analyzing modified siRNA duplexes containing immunostimulatory sequence motifs for their ability to stimulate immune responses in mice and in cultured murine immune cells including myeloid dendritic cells. Sequence-independent effects will be evaluated by determining the consequence of base modifications on the binding of cellular duplex RNA-binding proteins.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM080784-04
Application #
7790635
Study Section
Special Emphasis Panel (ZRG1-BST-Z (52))
Program Officer
Bender, Michael T
Project Start
2007-04-01
Project End
2012-03-31
Budget Start
2010-04-01
Budget End
2012-03-31
Support Year
4
Fiscal Year
2010
Total Cost
$254,605
Indirect Cost
Name
University of California Davis
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
047120084
City
Davis
State
CA
Country
United States
Zip Code
95618
Suter, Scott R; Ball-Jones, Alexi; Mumbleau, Madeline M et al. (2017) Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications. Org Biomol Chem 15:10029-10036
Zheng, Yuxuan; Beal, Peter A (2016) Synthesis and evaluation of an alkyne-modified ATP analog for enzymatic incorporation into RNA. Bioorg Med Chem Lett 26:1799-802
Suter, Scott R; Sheu-Gruttadauria, Jessica; Schirle, Nicole T et al. (2016) Structure-Guided Control of siRNA Off-Target Effects. J Am Chem Soc 138:8667-9
Valenzuela, Rachel A P; Onizuka, Kazumitsu; Ball-Jones, Alexi A et al. (2016) Guide Strand 3'-End Modifications Regulate siRNA Specificity. Chembiochem 17:2340-2345
Valenzuela, Rachel Anne P; Suter, Scott R; Ball-Jones, Alexi A et al. (2015) Base modification strategies to modulate immune stimulation by an siRNA. Chembiochem 16:262-7
Tran, Kiet; Arkin, Michelle R; Beal, Peter A (2015) Tethering in RNA: an RNA-binding fragment discovery tool. Molecules 20:4148-61
Onizuka, Kazumitsu; Harrison, Jason G; Ball-Jones, Alexi A et al. (2013) Short interfering RNA guide strand modifiers from computational screening. J Am Chem Soc 135:17069-77
Harrison, Jason G; Zheng, Yvonne B; Beal, Peter A et al. (2013) Computational approaches to predicting the impact of novel bases on RNA structure and stability. ACS Chem Biol 8:2354-9
Phelps, Kelly; Morris, Alexi; Beal, Peter A (2012) Novel modifications in RNA. ACS Chem Biol 7:100-9
Ibarra-Soza, José M; Morris, Alexi A; Jayalath, Prasanna et al. (2012) 7-Substituted 8-aza-7-deazaadenosines for modification of the siRNA major groove. Org Biomol Chem 10:6491-7

Showing the most recent 10 out of 18 publications