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Title: CRISPR–Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells

Journal Article · · Nucleic Acids Research
ORCiD logo [1];  [2];  [3]; ORCiD logo [1]; ORCiD logo [1];  [3];  [1];  [1];  [2];  [1];  [1];  [4]; ORCiD logo [2];  [3]; ORCiD logo [2];  [5]
  1. University of California, Berkeley, CA (United States)
  2. The Ohio State Univ., Columbus, OH (United States)
  3. Univ. of California, San Francisco, CA (United States). Gladstone Inst. of Genomic Immunology
  4. University of California, Berkeley, CA (United States); Univ. of California, San Francisco, CA (United States). Gladstone Inst. of Genomic Immunology
  5. University of California, Berkeley, CA (United States); Univ. of California, San Francisco, CA (United States). Gladstone Institutes; Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

DNA nanostructures are a promising tool to deliver molecular payloads to cells. DNA origami structures, where long single-stranded DNA is folded into a compact nanostructure, present an attractive approach to package genes; however, effective delivery of genetic material into cell nuclei has remained a critical challenge. Here, we describe the use of DNA nanostructures encoding an intact human gene and a fluorescent protein encoding gene as compact templates for gene integration by CRISPR-mediated homology-directed repair (HDR). Our design includes CRISPR–Cas9 ribonucleoprotein binding sites on DNA nanostructures to increase shuttling into the nucleus. We demonstrate efficient shuttling and genomic integration of DNA nanostructures using transfection and electroporation. These nanostructured templates display lower toxicity and higher insertion efficiency compared to unstructured double-stranded DNA templates in human primary cells. Furthermore, our study validates virus-like particles as an efficient method of DNA nanostructure delivery, opening the possibility of delivering nanostructures in vivo to specific cell types. Together, these results provide new approaches to gene delivery with DNA nanostructures and establish their use as HDR templates, exploiting both their design features and their ability to encode genetic information. This work also opens a door to translate other DNA nanodevice functions, such as biosensing, into cell nuclei.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
2470685
Journal Information:
Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 3 Vol. 50; ISSN 0305-1048
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English

References (51)

Smart Drug Delivery Nanocarriers with Self-Assembled DNA Nanostructures journal June 2013
DNA Origami Penetration in Cell Spheroid Tissue Models is Enhanced by Wireframe Design journal June 2021
A Tubular DNA Nanodevice as a siRNA/Chemo‐Drug Co‐delivery Vehicle for Combined Cancer Therapy journal December 2020
How We Make DNA Origami journal August 2017
UCSF Chimera?A visualization system for exploratory research and analysis journal January 2004
Daunorubicin-Loaded DNA Origami Nanostructures Circumvent Drug-Resistance Mechanisms in a Leukemia Model journal November 2015
Human Inborn Errors of Immunity: 2019 Update of the IUIS Phenotypical Classification journal January 2020
Nucleic acid junctions and lattices journal November 1982
Targeted delivery of CRISPR-Cas9 and transgenes enables complex immune cell engineering journal June 2021
Human IL2RA null mutation mediates immunodeficiency with lymphoproliferation and autoimmunity journal March 2013
Structural stability of DNA origami nanostructures under application-specific conditions journal January 2018
Nanofabrication based on DNA nanotechnology journal June 2019
DNA Nanocarriers: Programmed to Deliver journal December 2018
Electrotransfection of Polyamine Folded DNA Origami Structures journal September 2016
Exploring Nucleosome Unwrapping Using DNA Origami journal November 2016
Three-Dimensional DNA Origami as Programmable Anchoring Points for Bioreceptors in Fiber Optic Surface Plasmon Resonance Biosensing journal June 2018
Efficient Intracellular Delivery of RNase A Using DNA Origami Carriers journal March 2019
Chemical and Biophysical Modulation of Cas9 for Tunable Genome Engineering journal February 2016
Rapid Computational Analysis of DNA Origami Assemblies at Near-Atomic Resolution journal January 2021
Probing Nucleosome Stability with a DNA Origami Nanocaliper journal July 2016
DNA Origami as a Carrier for Circumvention of Drug Resistance journal August 2012
Programming Switchable Transcription of Topologically Constrained DNA journal May 2020
DNA Origami Delivery System for Cancer Therapy with Tunable Release Properties journal September 2012
DNA Origami as an In Vivo Drug Delivery Vehicle for Cancer Therapy journal June 2014
Synthesis from DNA of a molecule with the connectivity of a cube journal April 1991
Folding DNA to create nanoscale shapes and patterns journal March 2006
High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity journal August 2013
A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo journal February 2018
Engineering nucleic acid structures for programmable molecular circuitry and intracellular biocomputation journal September 2017
Magnesium-free self-assembly of multi-layer DNA objects journal January 2012
A primer to scaffolded DNA origami journal February 2011
A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum journal March 2013
Intracellular DNA recognition journal February 2010
A DNA origami-based aptamer nanoarray for potent and reversible anticoagulation in hemodialysis journal January 2021
Integrated computer-aided engineering and design for DNA assemblies journal April 2021
Reprogramming human T cell function and specificity with non-viral genome targeting journal July 2018
Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency journal December 2019
DNA origami journal January 2021
Dynamic DNA nanotechnology: toward functional nanoscale devices journal January 2020
Two design strategies for enhancement of multilayer–DNA-origami folding: underwinding for specific intercalator rescue and staple-break positioning journal January 2012
Sequence-dependent thermodynamics of a coarse-grained DNA model journal October 2012
DNA nanostructures coordinate gene silencing in mature plants journal March 2019
A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules journal August 2021
Rapid prototyping of 3D DNA-origami shapes with caDNAno journal June 2009
Follicular bronchiolitis as phenotype associated with CD25 deficiency journal January 2014
A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads journal February 2012
A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity journal June 2012
Programming Structured DNA Assemblies to Probe Biophysical Processes journal May 2019
Extending the Capabilities of Molecular Force Sensors via DNA Nanotechnology journal January 2020
An Effective Multi-Stage Liposomal DNA Origami Nanosystem for In Vivo Cancer Therapy journal December 2019
DNA Origami-Enabled Biosensors journal December 2020