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DNA baskets for the targeted delivery of siRNA

Amanda Zirzow, MIkhail Skoblov, Andre Marakhonov, Maria Emelianenko, Alexandre Vetcher, Vikas Chandhoke, Zobair M. Younossi

This is a collaborative project between

Molecular and Microbiology Department, College of Science,George Mason University, Fairfax, VA

Research Center for Medical Genetics, RAMS, Moscow

Department of Mathematics, College of Science, George Mason University, Fairfax, VA

The paper describing the basics of this technology has been recently accepted to International Journal of Nano and Biomaterials (IJNBM)

Silencing of gene expression by siRNA holds a promise both for a drug target discovery and as a therapy. Major bottlenecks of siRNA technology include ‘off-target’ silencing effects and problems with siRNA degradation before delivery. We propose a two-fold approach aimed at curtailing described shortcomings. First, before pre-clinical tests each siRNA shall be matched to comprehensive redundancy minimiser (CRM) curated database that contain comprehensively mapped all unique sequences (‘targets’) 9 nt to 15 nt in size within human transcriptome. Second, we propose to deliver siRNA within DNA-wrapped RNA-containing nanoparticle formed by partial dsRNA-DNA triplex. The DNA core will be chemically modified to promote triplex formation/folding. In these binary nanoparticles, DNA will serve as the biodegradable ‘basket’ that could be custom designed in order to enhance its interaction with the particular siRNA duplex. We also propose to covalently bind DNA basket to targeting peptides ensuring addressed delivery of the therapeutic nanoparticle.

Figure 1. ‘DNA baskets’ for siRNA delivery. (A) simplest implementation of the biodegradable DNA baskets slowing down the kinetics of the degradation of siRNA (B) targeting of the DNA basket to the tissue of interest may be achieved by the crosslinking of DNA with various proteins and protein fragments affine to the surface receptors of the target cells (C) branching DNA structures stably locked at physiological temperatures are sterically capable of encapsulating siRNA molecules (D) parts of the DNA molecules within DNA-siRNA nanoparticles could be engineered to form dsRNA-DNA triplexes.