Therapeutic agents such as small interfering siRNAs, ribozymes, and anti-sense RNAs show significant potential in new molecular approaches to down-regulate specific gene expression in cancerous or viral- infected cells. The development of safe, efficient, specific and non-pathogenic nano-particles for the packaging and delivery of multifunctional therapeutic RNAs is thus highly desirable. While programmable RNA self-assembly has been shown to potentially provide a solution towards that goal, the underlying principles for the design and engineering of multifunctional nano-structures based on RNA have still to be delineated. The long-term goal of this proposal is to contribute to the development of fully controllable and versatile bio-materials based on RNA and nucleic acid analogs for use in the study of biology, disease diagnosis, or therapy. In order to achieve this challenge, this project aims at generating stimuli-responsive programmable three-dimensional (3D) supra-molecular assemblies with control over their geometry, topology, directionality and addressability and able to respond to the cues of the environment. For instance, programmable, addressable and multifunctional 3D nano-cages that allow precise immobilization in 3D space of various functional therapeutic modules with catalytic or recognition properties will be synthesized and characterized by biochemical and biophysical methods such as AFM and cryo electron microscopy. Some of these RNA nano-devices will be engineered to switch reversibly between distinct supra-molecular shapes in response to small target compounds. The principles underlying the engineering of concerted and transient, time-activated complex functions as well as the enhancement of the chemical stability of these assemblies using RNA structural mimics like locked-in nucleic acid (LNA) will be investigated. This work will provide new insights in the control of self-assembly processes involving large population of RNA molecules and will pave the way towards the design of complex RNA-based nano-machines with strong potential in biology and medicine. It is anticipated that this project will establish the fundamental assembly and functional principles for the design and development of versatile responsive vehicles for therapeutic RNAs that will be suitable for in vivo applications and amenable to industrial-scale development in the future.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM079604-04
Application #
7802308
Study Section
Special Emphasis Panel (ZRG1-BCMB-H (50))
Program Officer
Lewis, Catherine D
Project Start
2007-04-15
Project End
2012-03-31
Budget Start
2010-04-01
Budget End
2011-03-31
Support Year
4
Fiscal Year
2010
Total Cost
$276,707
Indirect Cost
Name
University of California Santa Barbara
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
094878394
City
Santa Barbara
State
CA
Country
United States
Zip Code
93106
Afonin, Kirill A; Schultz, Danielle; Jaeger, Luc et al. (2015) Silver nanoclusters for RNA nanotechnology: steps towards visualization and tracking of RNA nanoparticle assemblies. Methods Mol Biol 1297:59-66
Dabkowska, Aleksandra P; Michanek, Agnes; Jaeger, Luc et al. (2015) Assembly of RNA nanostructures on supported lipid bilayers. Nanoscale 7:583-96
Afonin, Kirill A; Kasprzak, Wojciech; Bindewald, Eckart et al. (2014) Computational and experimental characterization of RNA cubic nanoscaffolds. Methods 67:256-65
Afonin, Kirill A; Viard, Mathias; Koyfman, Alexey Y et al. (2014) Multifunctional RNA nanoparticles. Nano Lett 14:5662-71
Afonin, Kirill A; Viard, Mathias; Martins, Angelica N et al. (2013) Activation of different split functionalities on re-association of RNA-DNA hybrids. Nat Nanotechnol 8:296-304
Grabow, Wade W; Zhuang, Zhuoyun; Shea, Joan-Emma et al. (2013) The GA-minor submotif as a case study of RNA modularity, prediction, and design. Wiley Interdiscip Rev RNA 4:181-203
Afonin, Kirill A; Lin, Yen-Ping; Calkins, Erin R et al. (2012) Attenuation of loop-receptor interactions with pseudoknot formation. Nucleic Acids Res 40:2168-80
Afonin, Kirill A; Kireeva, Maria; Grabow, Wade W et al. (2012) Co-transcriptional assembly of chemically modified RNA nanoparticles functionalized with siRNAs. Nano Lett 12:5192-5
Grabow, Wade W; Zhuang, Zhuoyun; Swank, Zoe N et al. (2012) The right angle (RA) motif: a prevalent ribosomal RNA structural pattern found in group I introns. J Mol Biol 424:54-67
Afonin, Kirill A; Grabow, Wade W; Walker, Faye M et al. (2011) Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine. Nat Protoc 6:2022-34

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