DNA recognition and induced genome modification by a hydroxymethyl-γ tail-clamp peptide nucleic acid

Stanley N Oyaghire; Elias Quijano; J Dinithi R Perera; Hanna K Mandl; W Mark Saltzman; Raman Bahal; Peter M Glazer

doi:10.1016/j.xcrp.2023.101635

DNA recognition and induced genome modification by a hydroxymethyl-γ tail-clamp peptide nucleic acid

Cell Rep Phys Sci. 2023 Oct 18;4(10):101635. doi: 10.1016/j.xcrp.2023.101635.

Authors

Stanley N Oyaghire^{1

2}, Elias Quijano^{3

4

2}, J Dinithi R Perera¹, Hanna K Mandl⁴, W Mark Saltzman^{4

5

6

7}, Raman Bahal⁸, Peter M Glazer^{1

3

9}

Affiliations

¹ Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA.
² These authors contributed equally.
³ Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
⁴ Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA.
⁵ Department of Chemical & Environmental Engineering, Yale University, New Haven, CT 06511, USA.
⁶ Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA.
⁷ Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA.
⁸ Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA.
⁹ Lead contact.

Abstract

Peptide nucleic acids (PNAs) can target and stimulate recombination reactions in genomic DNA. We have reported that γPNA oligomers possessing the diethylene glycol γ-substituent show improved efficacy over unmodified PNAs in stimulating recombination-induced gene modification. However, this structural modification poses a challenge because of the inherent racemization risk in O-alkylation of the precursory serine side chain. To circumvent this risk and improve γPNA accessibility, we explore the utility of γPNA oligomers possessing the hydroxymethyl-γ moiety for gene-editing applications. We demonstrate that a γPNA oligomer possessing the hydroxymethyl modification, despite weaker preorganization, retains the ability to form a hybrid with the double-stranded DNA target of comparable stability and with higher affinity than that of the diethylene glycol-γPNA. When formulated into poly(lactic-co-glycolic acid) nanoparticles, the hydroxymethyl-γPNA stimulates higher frequencies (≥ 1.5-fold) of gene modification than the diethylene glycol γPNA in mouse bone marrow cells.

Abstract

Grants and funding