Peptide Nucleic Acids and Gene Editing: Perspectives on Structure and Repair

Unusual nucleic acid structures are salient triggers of endogenous repair and can occur in sequence-specific contexts. Peptide nucleic acids (PNAs) rely on these principles to achieve non-enzymatic gene editing. By forming high-affinity heterotriplex structures within the genome, PNAs have been used to correct multiple human disease-relevant mutations with low off-target effects. Advances in molecular design, chemical modification, and delivery have enabled systemic in vivo application of PNAs resulting in detectable editing in preclinical mouse models. In a model of β-thalassemia, treated animals demonstrated clinically relevant protein restoration and disease phenotype amelioration, suggesting a potential for curative therapeutic application of PNAs to monogenic disorders. This review discusses the rationale and advances of PNA technologies and their application to gene editing with an emphasis on structural biochemistry and repair.

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Using CRISPR-Cas9 for Therapeutic Protein Production (Review Article)

Asian Journal of Pharmacy Nursing and Medical Sciences ◽

10.24203/ajpnms.v9i1.6115 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Ashraf Ullah Khan ◽

Zabi Ullah

Keyword(s):

Nucleic Acids ◽

Protein Production ◽

Gene Editing ◽

Ex Vivo ◽

Somatic Cells ◽

Review Article ◽

Crispr Locus ◽

Target Effects ◽

Subsequent Integration

Existence of CRISPR/Cas9 systems in bacteria and archaea has been noted to be the reason for these organisms’ ability to disarm invading nucleic acids. Such immunity is noted to arise from the targeting of the invading nucleic acids by guiding RNAs (sgRNAs), their cleavage by Cas9 (an endonuclease), and their subsequent integration into CRISPR locus. Recent studies have shown that the CRISPR/Cas9 tool can be adopted for gene editing in eukaryotic cells and thus offering potential for its use to treat genetic conditions. In this review, CRISPR/Cas9 has been shown to be an effective genome-editing tool with studies showing efficacy in zygote editing, in-vivo editing of somatic cells and ex-vivo editing of somatic cells. Occurrence of off-target effects however make zygote editing in human cells ethically questionable due to possibility of introducing unwanted mutations that may be passed on to the progeny. Nevertheless, observations that such off-target effects arise mainly from the promiscuity of sgRNAs rather that errors in CRISPR/Cas9 system show promise for increased specificity by developing better sgRNAs. Such increased specificity will facilitate the adoption of CRISPR/Cas9 for clinical use in treatment of conditions such as β-thalassemia, cystic fibrosis, Duchenne muscular dystrophy and HIV.

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A universal discoidal nanoplatform for the intracellular delivery of PNAs

Nanoscale ◽

10.1039/c9nr03667a ◽

2019 ◽

Vol 11 (26) ◽

pp. 12517-12529 ◽

Cited By ~ 7

Author(s):

Armin Tahmasbi Rad ◽

Shipra Malik ◽

Lin Yang ◽

Tripat Kaur Oberoi-Khanuja ◽

Mu-Ping Nieh ◽

...

Keyword(s):

Nucleic Acids ◽

Gene Editing ◽

Peptide Nucleic Acids ◽

Intracellular Delivery

Peptide nucleic acids (PNAs) have gained considerable attention due to their remarkable potential in gene editing and targeting-based strategies.

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Advances in therapeutic application of CRISPR-Cas9

Briefings in Functional Genomics ◽

10.1093/bfgp/elz031 ◽

2019 ◽

Vol 19 (3) ◽

pp. 164-174 ◽

Cited By ~ 3

Author(s):

Jinyu Sun ◽

Jianchu Wang ◽

Donghui Zheng ◽

Xiaorong Hu

Keyword(s):

Gene Therapy ◽

Genome Editing ◽

Malignant Tumor ◽

Gene Editing ◽

Genome Engineering ◽

Therapeutic Application ◽

Adaptive Immune ◽

Efficient Gene

Abstract Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) is one of the most versatile and efficient gene editing technologies, which is derived from adaptive immune strategies for bacteria and archaea. With the remarkable development of programmable nuclease-based genome engineering these years, CRISPR-Cas9 system has developed quickly in recent 5 years and has been widely applied in countless areas, including genome editing, gene function investigation and gene therapy both in vitro and in vivo. In this paper, we briefly introduce the mechanisms of CRISPR-Cas9 tool in genome editing. More importantly, we review the recent therapeutic application of CRISPR-Cas9 in various diseases, including hematologic diseases, infectious diseases and malignant tumor. Finally, we discuss the current challenges and consider thoughtfully what advances are required in order to further develop the therapeutic application of CRISPR-Cas9 in the future.

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Peptide nucleic acids specifically cause antigene effects in vivo by systemic injection

Life Sciences ◽

10.1016/s0024-3205(02)01647-8 ◽

2002 ◽

Vol 71 (3) ◽

pp. 325-337 ◽

Cited By ~ 8

Author(s):

Beth M. McMahon ◽

Jennifer A. Stewart ◽

M.D. Bitner ◽

Abdul Fauq ◽

Daniel J. McCormick ◽

...

Keyword(s):

Nucleic Acids ◽

Peptide Nucleic Acids ◽

Systemic Injection

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Hydroxyproline-Based DNA Mimics: A Review on Synthesis and Properties

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc20060929 ◽

2006 ◽

Vol 71 (7) ◽

pp. 929-955 ◽

Cited By ~ 10

Author(s):

Vladimir A. Efimov ◽

Oksana G. Chakhmakhcheva

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Phosphonic Acid ◽

Peptide Nucleic Acids ◽

Biological Properties ◽

High Potential ◽

Physicochemical And Biological Properties

With the aim to improve physicochemical and biological properties of natural oligonucleotides, many types of DNA analogues and mimics are designed on the basis of hydroxyproline and its derivatives, and their properties are evaluated. Among them, two types of DNA mimics representing hetero-oligomers constructed from alternating monomers of phosphono peptide nucleic acids and monomers on the base of trans-1-acetyl-4-hydroxy-L-proline (HypNA-pPNAs) and oligomers constructed from monomers containing (2S,4R)-1-acetyl-4-hydroxypyrrolidine-2-phosphonic acid backbone (pHypNAs) are of particular interest. In a set of in vitro and in vivo assays, it was shown that HypNA-pPNAs and pHypNAs demonstrated a high potential for the use in nucleic acid based diagnostics, isolation of nucleic acids and antisense experiments. A review with 53 references.

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Specific gene blockade shows that peptide nucleic acids readily enter neuronal cells in vivo

FEBS Letters ◽

10.1016/s0014-5793(97)01575-5 ◽

1998 ◽

Vol 421 (3) ◽

pp. 280-284 ◽

Cited By ~ 64

Author(s):

Beth M Tyler ◽

Daniel J McCormick ◽

Clark V Hoshall ◽

Christopher L Douglas ◽

Karen Jansen ◽

...

Keyword(s):

Nucleic Acids ◽

Peptide Nucleic Acids ◽

Neuronal Cells ◽

Specific Gene

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Exploring miR-9 Involvement in Ciona intestinalis Neural Development Using Peptide Nucleic Acids

International Journal of Molecular Sciences ◽

10.3390/ijms21062001 ◽

2020 ◽

Vol 21 (6) ◽

pp. 2001

Author(s):

Silvia Mercurio ◽

Silvia Cauteruccio ◽

Raoul Manenti ◽

Simona Candiani ◽

Giorgio Scarì ◽

...

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Neural Development ◽

Peptide Nucleic Acids ◽

Model Organism ◽

Ciona Intestinalis ◽

Transcriptional Level ◽

Regulate Gene Expression

The microRNAs are small RNAs that regulate gene expression at the post-transcriptional level and can be involved in the onset of neurodegenerative diseases and cancer. They are emerging as possible targets for antisense-based therapy, even though the in vivo stability of miRNA analogues is still questioned. We tested the ability of peptide nucleic acids, a novel class of nucleic acid mimics, to downregulate miR-9 in vivo in an invertebrate model organism, the ascidian Ciona intestinalis, by microinjection of antisense molecules in the eggs. It is known that miR-9 is a well-conserved microRNA in bilaterians and we found that it is expressed in epidermal sensory neurons of the tail in the larva of C. intestinalis. Larvae developed from injected eggs showed a reduced differentiation of tail neurons, confirming the possibility to use peptide nucleic acid PNA to downregulate miRNA in a whole organism. By identifying putative targets of miR-9, we discuss the role of this miRNA in the development of the peripheral nervous system of ascidians.

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crisprSQL: a novel database platform for CRISPR/Cas off-target cleavage assays

Nucleic Acids Research ◽

10.1093/nar/gkaa885 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D855-D861

Author(s):

Florian Störtz ◽

Peter Minary

Keyword(s):

Gene Editing ◽

Target Prediction ◽

Current Version ◽

Therapeutic Gene ◽

Guide Rnas ◽

Rodent Cell ◽

Ongoing Development ◽

Database Platform ◽

Target Effects

Abstract With ongoing development of the CRISPR/Cas programmable nuclease system, applications in the area of in vivo therapeutic gene editing are increasingly within reach. However, non-negligible off-target effects remain a major concern for clinical applications. Even though a multitude of off-target cleavage datasets have been published, a comprehensive, transparent overview tool has not yet been established. Here, we present crisprSQL (http://www.crisprsql.com), an interactive and bioinformatically enhanced collection of CRISPR/Cas9 off-target cleavage studies aimed at enriching the fields of cleavage profiling, gene editing safety analysis and transcriptomics. The current version of crisprSQL contains cleavage data from 144 guide RNAs on 25,632 guide-target pairs from human and rodent cell lines, with interaction-specific references to epigenetic markers and gene names. The first curated database of this standard, it promises to enhance safety quantification research, inform experiment design and fuel development of computational off-target prediction algorithms.

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