National Institute for Research and Development of
Isotopic and Molecular Technologies (INCDTIM)

In silico optimization of CRISPR/Cas9-Gold nanovehicle design

Project financed by UEFISCDI

Project Type: Postdoctoral research projects

Project Code: PN-III-P1-1.1-PD-2019-0292

Contract No.: PD 37

Project Duration: 01.09.2020 – 31.08.2022

Principal Investigator:

Dr. Alexandra FARCAS

INCDTIM – National Institute for Research and Development of Isotopic and Molecular Technologies,

Molecular and Biomolecular Physics Department

67-103 Donat St., Box 700, RO-400293 Cluj-Napoca, Romania

e-mail: alexandra.farcas@itim-cj.ro

phone: (+40)264-584037, ext. 177

Project abstract

CRISPR/Cas9 gene editing is a novel and versatile technology that correct disease-causing errors in the genomes, with multiple and broad applications in medical, agricultural and pharmaceutical industries. The major obstacle in implementing CRISPR/Cas9-based therapeutics is to develop nanovehicles that can target genetic mutations in a specific manner. Gold nanoparticles (GNP) functionalized with synthetic oligonucleotides combine the optoelectronic properties of the gold core with the particular properties of oligonucleotides, for instance selectivity and specificity. Furthermore, functionalized GNPs have been previously used in vivo for delivery of CRISPR/Cas9 to successfully repair gene mutations causing muscular dystrophy. However, prior to clinical applications, safe and efficient CRISPR/Cas9-Gold-based delivery vehicles should be designed based on a deep understanding of the underlying molecular mechanisms. In this proposal, we intend to computationally optimize such a design in two steps. First, we will optimize the DNA loading on a range of GNP sizes in nanoparticle-oligonucleotide conjugates. In the second stage, we will perform a thorough in silico investigation of GNP-oligonucleotide conjugates complexed with Cas9 ribonucleoprotein as delivery nanovehicles.

Objectives

The specific objectives of the project are:

O1 Optimization of DNA loading on a range of GNP sizes in nanoparticle-oligonucleotide conjugates.

O2 In silico investigation of GNP-oligonucleotide conjugates complexed with Cas9 ribonucleoprotein as potential delivery nanovehicles.

Team

Dr. Alexandra FARCAS

PhD in Physics

Scientific Researcher
National Institute for Research and Development of Isotopic and Molecular Technologies

Prof. Dr. Simion ASTILEAN

Department of Biomolecular Physics Faculty of Physics,
Babes-Bolyai University
Head of NanoBioPhotonics and
Laser Microspectroscopy Center

Equipment

Workstation Supermicro SYS-7039A-i

Processor 2 x Intel Xeon 4210 10 Core/20 Core HT, 2.2GHz
RAM 64GB DDR4, 2933 MHz, ECC
Storage 1 x SSD 240GB SATA 6Gb/s, 1 x HDD 2TB SATA 6 Gb/s
GPU 2 x GeForce RTX 2080 Ti, 11GB GDDR6

1 workstation acquired through the project

Workstation Supermicro SYS-7039A-i

Processor 2 x Intel Xeon 4210 10 Core/20 Core HT, 2.2GHz
RAM 64GB DDR4, 2933 MHz, ECC
Storage 1 x SSD 240GB SATA 6Gb/s, 1 x HDD 2TB SATA 6 Gb/s
GPU 2 x GeForce RTX 2080 Ti, 11GB GDDR6

1 workstation acquired through the project

Network Attached Storage, NAS DS420j

NAS DS420j CPU Quad-core 1.4GHz, RAM 1 GB DDR4
CAPACITY 16 TB (2 x HDD 8TB), Max 64 TB (16 TB HDD x 4)
CONECTIVITY: USB 3.0 LAN 1GbE
RAID: RAID 0, 1, 5, 6, 10, JBOD