Abstract
Triplex-forming oligonucleotides (TFOs) are capable of coordinating genome modification in a targeted, site-specific manner, causing mutagenesis or even coordinating homologous recombination events. Here, we describe the use of TFOs such as peptide nucleic acids for targeted genome modification. We discuss this method and its applications and describe protocols for TFO design, delivery, and evaluation of activity in vitro and in vivo.
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References
Pauling L, Corey RB (1953) A proposed structure for the nucleic acids. Proc Natl Acad Sci U S A 39(2):84–97
Felsenfeld G, Rich A (1957) Studies on the formation of two- and three-stranded polyribonucleotides. Biochim Biophys Acta 26(3):457–468
Nielsen PE, Egholm M, Buchardt O (1994) Peptide nucleic acid (PNA). A DNA mimic with a peptide backbone. Bioconjug Chem 5(1):3–7
Nielsen PE (1999) Peptide nucleic acid. A molecule with two identities. Acc Chem Res 32(7):624–630
He G et al (2009) Strand invasion of extended, mixed-sequence B-DNA by gammaPNAs. J Am Chem Soc 131(34):12088–12090
Rapireddy S, Bahal R, Ly DH (2011) Strand invasion of mixed-sequence, double-helical B-DNA by gamma-peptide nucleic acids containing G-clamp nucleobases under physiological conditions. Biochemistry 50(19):3913–3918
Bahal R et al (2012) Sequence-unrestricted, Watson-Crick recognition of double helical B-DNA by (R)-miniPEG-gammaPNAs. Chembiochem 13(1):56–60
Kumar R et al (1998) The first analogues of LNA (locked nucleic acids): phosphorothioate-LNA and 2'-thio-LNA. Bioorg Med Chem Lett 8(16):2219–2222
Koshkin AA et al (1998) LNA (Locked Nucleic Acids): synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron 54(14):3607–3630
Petersen M et al (2000) The conformations of locked nucleic acids (LNA). J Mol Recognit 13(1):44–53
Vester B, Wengel J (2004) LNA (locked nucleic acid): high-affinity targeting of complementary RNA and DNA. Biochemistry 43(42):13233–13241
Egholm M et al (1995) Efficient pH-independent sequence-specific DNA binding by pseudoisocytosine-containing bis-PNA. Nucleic Acids Res 23(2):217–222
Bentin T, Larsen HJ, Nielsen PE (2003) Combined triplex/duplex invasion of double-stranded DNA by “tail-clamp” peptide nucleic acid. Biochemistry 42(47):13987–13995
Kaihatsu K et al (2003) Extending recognition by peptide nucleic acids (PNAs): binding to duplex DNA and inhibition of transcription by tail-clamp PNA-peptide conjugates. Biochemistry 42(47):13996–14003
Lohse J, Dahl O, Nielsen PE (1999) Double duplex invasion by peptide nucleic acid: a general principle for sequence-specific targeting of double-stranded DNA. Proc Natl Acad Sci U S A 96(21):11804–11808
Sazani P et al (2001) Nuclear antisense effects of neutral, anionic and cationic oligonucleotide analogs. Nucleic Acids Res 29(19):3965–3974
Koppelhus U et al (2008) Improved cellular activity of antisense peptide nucleic acids by conjugation to a cationic peptide-lipid (CatLip) domain. Bioconjug Chem 19(8):1526–1534
Rogers FA et al (2004) Peptide conjugates for chromosomal gene targeting by triplex-forming oligonucleotides. Nucleic Acids Res 32(22):6595–6604
Faria M et al (2000) Targeted inhibition of transcription elongation in cells mediated by triplex-forming oligonucleotides. Proc Natl Acad Sci U S A 97(8):3862–3867
Birg F et al (1990) Inhibition of simian virus 40 DNA replication in CV-1 cells by an oligodeoxynucleotide covalently linked to an intercalating agent. Nucleic Acids Res 18(10):2901–2908
Maher LJ III, Wold B, Dervan PB (1989) Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation. Science 245(4919):725–730
Havre PA et al (1993) Targeted mutagenesis of DNA using triple helix-forming oligonucleotides linked to psoralen. Proc Natl Acad Sci U S A 90(16):7879–7883
Takasugi M et al (1991) Sequence-specific photo-induced cross-linking of the two strands of double-helical DNA by a psoralen covalently linked to a triple helix-forming oligonucleotide. Proc Natl Acad Sci U S A 88(13):5602–5606
Vasquez KM et al (1996) High-efficiency triple-helix-mediated photo-cross-linking at a targeted site within a selectable mammalian gene. Biochemistry 35(33):10712–10719
Wang G, Seidman MM, Glazer PM (1996) Mutagenesis in mammalian cells induced by triple helix formation and transcription-coupled repair. Science 271(5250):802–805
Chin JY et al (2008) Correction of a splice-site mutation in the beta-globin gene stimulated by triplex-forming peptide nucleic acids. Proc Natl Acad Sci U S A 105(36):13514–13519
Schleifman EB et al (2011) Targeted disruption of the CCR5 gene in human hematopoietic stem cells stimulated by peptide nucleic acids. Chem Biol 18(9):1189–1198
Rogers FA et al (2012) Targeted gene modification of hematopoietic progenitor cells in mice following systemic administration of a PNA-peptide conjugate. Mol Ther 20(1):109–118
McNeer NA et al (2012) Systemic delivery of triplex-forming PNA and donor DNA by nanoparticles mediates site-specific genome editing of human hematopoietic cells in vivo. Gene Ther 20(6):658–669
Yin H et al (2010) Optimization of peptide nucleic acid antisense oligonucleotides for local and systemic dystrophin splice correction in the mdx mouse. Mol Ther 18(4):819–827
Roberts J et al (2006) Efficient and persistent splice switching by systemically delivered LNA oligonucleotides in mice. Mol Ther 14(4):471–475
Singhal G et al (2011) DNA triplex-mediated inhibition of MET leads to cell death and tumor regression in hepatoma. Cancer Gene Ther 18(7):520–530
Cogoi S et al (2004) Antiproliferative activity of a triplex-forming oligonucleotide recognizing a Ki-ras polypurine/polypyrimidine motif correlates with protein binding. Cancer Gene Ther 11(7):465–476
Shen C et al (2003) Targeting bcl-2 by triplex-forming oligonucleotide—a promising carrier for gene-radiotherapy. Cancer Biother Radiopharm 18(1):17–26
Taniguchi Y, Sasaki S (2012) An efficient antigene activity and antiproliferative effect by targeting the Bcl-2 or survivin gene with triplex forming oligonucleotides containing a W-shaped nucleoside analogue (WNA-betaT). Org Biomol Chem 10(41):8336–8341
Onyshchenko MI et al (2009) Stabilization of G-quadruplex in the BCL2 promoter region in double-stranded DNA by invading short PNAs. Nucleic Acids Res 37(22):7570–7580
Ebbinghaus SW et al (1993) Triplex formation inhibits HER-2/neu transcription in vitro. J Clin Invest 92(5):2433–2439
Rogers FA et al (2002) Site-directed recombination via bifunctional PNA-DNA conjugates. Proc Natl Acad Sci U S A 99(26):16695–16700
Lonkar P et al (2009) Targeted correction of a thalassemia-associated beta-globin mutation induced by pseudo-complementary peptide nucleic acids. Nucleic Acids Res 37(11):3635–3644
McNeer NA et al (2011) Nanoparticles deliver triplex-forming PNAs for site-specific genomic recombination in CD34+ human hematopoietic progenitors. Mol Ther 19(1):172–180
Vasquez KM, Narayanan L, Glazer PM (2000) Specific mutations induced by triplex-forming oligonucleotides in mice. Science 290(5491):530–533
Chin JY, Schleifman EB, Glazer PM (2007) Repair and recombination induced by triple helix DNA. Front Biosci 12:4288–4297
Chin JY, Glazer PM (2009) Repair of DNA lesions associated with triplex-forming oligonucleotides. Mol Carcinog 48(4):389–399
Vasquez KM et al (2002) Human XPA and RPA DNA repair proteins participate in specific recognition of triplex-induced helical distortions. Proc Natl Acad Sci U S A 99(9):5848–5853
Faruqi AF et al (2000) Triple-helix formation induces recombination in mammalian cells via a nucleotide excision repair-dependent pathway. Mol Cell Biol 20(3):990–1000
Datta HJ et al (2001) Triplex-induced recombination in human cell-free extracts. Dependence on XPA and HsRad51. J Biol Chem 276(21):18018–18023
Knauert MP et al (2005) Distance and affinity dependence of triplex-induced recombination. Biochemistry 44(10):3856–3864
Kim KH, Nielsen PE, Glazer PM (2006) Site-specific gene modification by PNAs conjugated to psoralen. Biochemistry 45(1):314–323
Christensen L et al (1995) Solid-phase synthesis of peptide nucleic acids. J Pept Sci 1(3):175–183
Maurisse R et al (2010) Comparative transfection of DNA into primary and transformed mammalian cells from different lineages. BMC Biotechnol 10:9
Luo D et al (1999) Controlled DNA delivery systems. Pharm Res 16(8):1300–1308
Blum JS, Saltzman WM (2008) High loading efficiency and tunable release of plasmid DNA encapsulated in submicron particles fabricated from PLGA conjugated with poly-L-lysine. J Control Release 129(1):66–72
Woodrow KA et al (2009) Intravaginal gene silencing using biodegradable polymer nanoparticles densely loaded with small-interfering RNA. Nat Mater 8(6):526–533
Babar IA et al (2012) Nanoparticle-based therapy in an in vivo microRNA-155 (miR-155)-dependent mouse model of lymphoma. Proc Natl Acad Sci U S A 109(26):E1695–E1704
Fahmy TM et al (2005) Surface modification of biodegradable polyesters with fatty acid conjugates for improved drug targeting. Biomaterials 26(28):5727–5736
Fields RJ et al (2012) Surface modified poly(beta amino ester)-containing nanoparticles for plasmid DNA delivery. J Control Release 164(1):41–48
Vasquez KM et al (1999) Chromosomal mutations induced by triplex-forming oligonucleotides in mammalian cells. Nucleic Acids Res 27(4):1176–1181
Gunther EJ et al (1995) Mutagenesis by 8-methoxypsoralen and 5-methylangelicin photoadducts in mouse fibroblasts: mutations at cross-linkable sites induced by offoadducts as well as cross-links. Cancer Res 55(6):1283–1288
Schleifman EB, Chin JY, Glazer PM (2008) Triplex-mediated gene modification. Methods Mol Biol 435:175–190
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Ricciardi, A.S., McNeer, N.A., Anandalingam, K.K., Saltzman, W.M., Glazer, P.M. (2014). Targeted Genome Modification via Triple Helix Formation. In: Wajapeyee, N. (eds) Cancer Genomics and Proteomics. Methods in Molecular Biology, vol 1176. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0992-6_8
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DOI: https://doi.org/10.1007/978-1-4939-0992-6_8
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Print ISBN: 978-1-4939-0991-9
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