Abstract
Triple helical nucleic acids are generated by the binding of a third oligonucleotide strand within the major groove of duplex DNA or RNA, where it makes specific interactions with exposed groups on the base pairs. They have been explored as gene-targeting agents, with potential as therapeutic agents, but have also found applications in generating switchable nanostructures and may have roles in biology through the action of some noncoding RNAs. The formation of triplexes containing natural nucleotides is limited by their relatively low affinity, slow binding kinetics, pH dependency, and the requirement for an oligopurine.oligopyrimidine duplex target. A large number of base, sugar, and backbone modifications have therefore been explored for generating triplexes at mixed-sequence targets with high affinity at neutral pH. This chapter summarizes these developments and outlines some of the recent proposals for the roles of triplexes in vivo and as components of nanostructure assemblies.
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References
Abulwerdi FA, Xu W, Ageeli AA, Yonkunas MJ, Arun G, Nam H, Schneekloth JS, Dayie TK, Spector D, Baird N, Le Grice SFJ (2019) Selective small-molecule targeting of a triple helix encoded by the long noncoding RNA MALAT1. ACS Chem Biol 14:223–235. https://doi.org/10.1021/acschembio.8b00807
Arya DP (2010) New approaches toward recognition of nucleic acid triple helices. Acc Chem Res 44:134–146. https://doi.org/10.1021/ar100113q
Asensio JL, Lane AN, Dhesi J, Bergqvist S, Brown T (1998) The contribution of cytosine protonation to the stability of parallel DNA triple helices. J Mol Biol 275:811–822. https://doi.org/10.1006/jmbi.1997.1520
Atsumi N, Ueno Y, Kanazaki M, Shuto S, Matsuda A (2002) Nucleosides and nucleotides. Part 214: thermal stability of triplexes containing 4′α-C-aminoalkyl-2′-deoxynucleosides. Bioorg Med Chem 10:2933–2939. https://doi.org/10.1016/S0968-0896(02)00141-4
Beal PA, Dervan PB (1992) Recognition of double helical DNA by alternate strand triple helix formation. J Am Chem Soc 114:4976–4982. https://doi.org/10.1021/ja00039a004
Bijapur J, Keppler MD, Bergqvist S, Brown T, Fox KR (1999) 5-(1-propargylamino)-2′-deoxyuridine (UP): a novel thymidine analogue for generating DNA triplexes with increased stability. Nucleic Acids Res 27:1802–1809. https://doi.org/10.1093/nar/27.8.1802
Brodyagin N, Kumpina I, Applegate J, Katkevics M, Rozners E (2021) Pyridazine nucleobase in triplex-forming PNA improves recognition of cytosine interruptions of polypurine tracts in RNA. ACS Chem Biol 16:872–881. https://doi.org/10.1021/acschembio.1c00044
Brown J (2020) Unraveling the structure and biological functions of RNA triple helices. WIREs RNA 11:e1598. https://doi.org/10.1002/wrna.1598
Brown PM, Madden C, Fox KR (1998) Triple-helix formation at different positions on nucleosomal DNA. Biochemistry 37:16139–16151. https://doi.org/10.1021/bi981768n
Brown JA, Valenstein ML, Yario TA, Tycowski KT, Steitz JA (2012) Formation of triple-helical structures by the 3′-end sequences of MALAT1 and MENβ noncoding RNAs. Proc Natl Acad Sci U S A 109:19202–19207. https://doi.org/10.1073/pnas.1217338109
Buchini S, Leumann CJ (2004) Stable and selective recognition of three base pairs in the parallel triple-helical DNA binding motif. Angew Chem Int Ed 43:3925–3928. https://doi.org/10.1002/anie.200460159
Burnett R, Melander C, Puckett JW, Son LS, Wells RD, Dervan PB, Gottesfeld JM (2006) DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA.TTC repeats in Friedreich’s ataxia. Proc Natl Acad Sci U S A 103:11497–11502. https://doi.org/10.1073/pnas.0604939103
Chandrasekaran AR, Rusling DA (2018) Triplex-forming oligonucleotides: a third strand for DNA nanotechnology. Nucleic Acids Res 46:1021–1037. https://doi.org/10.1093/nar/gkx1230
Cooney M, Czernuszewicz G, Postel EH, Flint SJ, Hogan ME (1988) Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro. Science 241:456–459. https://doi.org/10.1126/science.3293213
Cuenoud B, Casset F, Hüsken D, Natt F, Wolf RM, Altmann K-H, Martin P, Moser HE (1998) Dual recognition of double-stranded DNA by 2′-aminoethoxy-modified oligonucleotides. Angew Chem Int Ed 37:1288–1291. https://doi.org/10.1002/(SICI)1521-3773(19980518)37:9<1288
Cui H, Zhang T, Kong Y, Xing H, Wei B (2022) Controllable assembly of synthetic constructs with programmable ternary DNA interaction. Nucleic Acids Res 50:7188–7196. https://doi.org/10.1093/nar/gkac478
Doluca O, Boutorine AS, Filichev VV (2011) Triplex-forming twisted intercalating nucleic acids (TINAs): design rules, stabilization of antiparallel DNA triplexes and inhibition of G-quartet-dependent self-association. ChemBiolChem 12:2365–2374. https://doi.org/10.1002/cbic.201100354
Donlic A, Zafferani M, Padroni G, Puri M, Hargrove AE (2020) Regulation of MALAT1 triple helix stability and in vitro degradation by diphenylfurans. Nucleic Acids Res 48:7653–7664. https://doi.org/10.1093/nar/gkaa585
Escudé C, Garestier T, Hélène C (1999) Padlock oligonucleotides for duplex DNA based on sequence-specific triple helix formation. Proc Natl Acad Sci U S A 96:10603–10607. https://doi.org/10.1073/pnas.96.19.10603
Felsenfeld G, Davies DR, Rich A (1957) Formation of a three-stranded polynucleotide molecule. J Am Chem Soc 79:2023–2024. https://doi.org/10.1021/ja01565a074
Fox KR (2000) Targeting DNA with triplexes. Curr Med Chem 7:17–37. https://doi.org/10.2174/0929867003375506
Fox KR, Darby RAJ (2002) Triple helix-specific ligands. In: Demeunynck M, Bailly C, Wilson WD (eds) Small molecule DNA and RNA binders: from synthesis to nucleic acid complexes. WILEY-VCHVerlag GmbH, pp 360–383. https://doi.org/10.1002/3527601783.ch14
Fox KR, Brown T, Rusling DA (2018) DNA recognition by parallel triplex formation. In DNA-targeting molecules as therapeutic agents. In: Waring MJ (ed) The Royal Society of Chemistry, pp 1–32
Frank-Kamenetskii MD, Mirkin SM (1995) Triplex DNA structures. Annu Rev Biochem 64:65–95. https://doi.org/10.1146/annurev.bi.64.070195.000433
Gowers DM, Fox KR (1997) DNA triple helix formation at oligopurine sites containing multiple contiguous pyrimidines. Nucleic Acids Res 25:3787–3794. https://doi.org/10.1093/nar/25.19.3787
Gowers DM, Fox KR (1998) Triple helix formation at (AT)n adjacent to an oligopurine tract. Nucleic Acids Res 26:3626–3633. https://doi.org/10.1093/nar/26.16.3626
Greifenstein AA, Jo SY, Bierhoff H (2021) RNA:DNA triple helices: from peculiar structures to pervasive chromatin regulators. Essays Biochem 65:731–740. https://doi.org/10.1042/EBC20200089
Hari Y, Obika S, Imanishi T (2012) Towards the sequence-selective recognition of double-stranded DNA containing pyrimidine-urine interruptions by triplex-forming oligonucleotides Eur. J Org Chem 2012:2875–2887. https://doi.org/10.1002/ejoc.201101821
Hennessy J, McGorman B, Molphy Z, Farrell NP, Singleton D, Brown T, Kellett A (2022) A click chemistry approach to targeted DNA crosslinking with cis-platinum(II)-modified triplex-forming oligonucleotides. Angew Chem Int Ed 61:e202110455. https://doi.org/10.1002/anie.202110455
Hu Y, Cecconello A, Idili A, Ricci F, Willner I (2017) Triplex DNA nanostructures: from basic properties to applications. Angew Chem Int Ed 56:15210–15233. https://doi.org/10.1002/anie.201701868
Idili A, Vallée-Bélisle A, Ricci F (2014) Programmable pH-triggered DNA nanoswitches. J Am Chem Soc 136:5836–5839. https://doi.org/10.1021/ja500619w
Ihara T, Ishii T, Araki N, Wilson AW, Jyo A (2009) Silver ion unusually stabilizes the structure of a parallel-motif DNA triplex. J Am Chem Soc 131:3826–3827. https://doi.org/10.1021/ja809702n
Ito T, Smith CL, Cantor CR (1992) Sequence-specific DNA purification by triplex affinity capture. Proc Natl Acad Sci U S A 89:495–498. https://doi.org/10.1073/pnas.89.2.49
James PL, Brown T, Fox KR (2003) Thermodynamic and kinetic stability of intermolecular triple helices containing different proportions of C+·GC and T·AT triplets. Nucleic Acids Res 31:5598–5606. https://doi.org/10.1093/nar/gkg782
Kishimoto Y, Fujii A, Nakagawa O, Obika S (2021) Enhanced duplex- and triplex-forming ability and enzymatic resistance of oligodeoxynucleotides modified by a tricyclic thymine derivative. Org Biomol Chem 19:8063–8074. https://doi.org/10.1039/d1ob01462e
Kunkler CN, Schiefelbein GE, O’Leary NJ, McCown PJ, Brown JA (2022) A single natural RNA modification can destabilize a U•A-T-rich RNA•DNA-DNA triple helix. RNA 28:172–1184. https://doi.org/10.1261/rna.079244.122
Le Doan T, Perrouault L, Praseuth D, Habhoub N, Decout JL, Thuong NT, Lhomme J, Hélène C (1987) Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-[α]-thymidylate covalently linked to an azidoproflavine derivative. Nucleic Acids Res 15:7749–7760. https://doi.org/10.1093/nar/15.19.7749
Leisegang MS et al (2022) HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex nature. Communications 13:6563. https://doi.org/10.1038/s41467-022-34252-2
Li H, Broughton-Head VJ, Peng G, Powers VEC, Ovens MJ, Fox KR, Brown T (2006) Triplex staples: DNA double-strand cross-linking at internal and terminal sites using psoralen-containing triplex-forming oligonucleotides. Bioconjug Chem 17:1561–1567. https://doi.org/10.1021/bc0601875
Li Y, Syed J, Sugiyama H (2016) RNA-DNA triplex formation by long noncoding RNAs. Cell Chem Biol 23:1325–1333. https://doi.org/10.1016/j.chembiol.2016.09.011
Li C, Zhou Z, Ren C, Deng Y, Peng F, Wang Q, Zhang H, Jiang Y (2022) Triplex-forming oligonucleotides as an anti-gene technique for cancer therapy. Front Pharmacol 13:1007723. https://doi.org/10.3389/fphar.2022.1007723
Lin P-Y, Chi R, Wu Y-L, Ho J-aA (2022) Applications of triplex DNA nanostructures in sensor development. Anal Bioanal Chem 414,:5217-5237:5217. https://doi.org/10.1007/s00216-022-04058-8
Lubitz I, Zikich D, Kotlyar A (2010) Specific high-affinity binding of thiazole orange to triplex and G-quadruplex DNA. Biochemistry 49:3567–3574. https://doi.org/10.1021/bi1000849
Maldonado R, Längst G (2020) Analyzing RNA–DNA triplex formation in chromatin. In: Ørom U (ed) RNA-chromatin interactions. Methods in molecular biology, vol 2161. Humana, New York. https://doi.org/10.1007/978-1-0716-0680-3_17
Maldonado R, Schwartz U, Silberhorn E, Längst G (2019) Nucleosomes stabilize ssRNA-dsDNA triple helices in human cells. Mol Cell 73:1243–1254. https://doi.org/10.1016/j.molcel.2019.01.007
Mayer A, Häberli A, Leumann CJ (2005) Synthesis and triplex forming properties of pyrrolidino pseudoisocytidine containing oligodeoxynucleotides org. Biomol Chem 3:1653–1658. https://doi.org/10.1039/B502799C
Miao S, Bhunia D, Devari S, Liang Y, Munyaradzi O, Rundell S, Bong D (2021) Bifacial PNAs destabilize MALAT1 by 3′ A-tail displacement from the U-rich internal loop. ACS Chem Biol 16:1600–1609. https://doi.org/10.1021/acschembio.1c00575
Mirkin SM, Lyamichev VI, Drushlyak KN, Dobrynin VN, Filippov SA, Frank-Kamenetskii MD (1987) DNA H form requires a homopurine–homopyrimidine mirror repeat. Nature 330:495–497. https://doi.org/10.1038/330495a0
Moser HE, Dervan PB (1987) Sequence-specific cleavage of double helical DNA by triple helix formation. Science 238:645–650. https://doi.org/10.1126/science.3118
Muse O, Zengeya T, Mwaura J, Hnedzko D, McGee DW, Grewer CT, Rozners E (2013) Sequence selective recognition of double-stranded RNA at physiologically relevant conditions using PNA-peptide conjugates. ACS Chem Biol 8:1683–1686. https://doi.org/10.1021/cb400144x
Nielsen PE (2001) Targeting double stranded DNA with peptide nucleic acid (PNA). Curr Med Chem 8:545–550. https://doi.org/10.2174/0929867003373373
Notomi R, Sasaki S, Taniguchi Y (2022) Development of novel C-nucleoside analogues for the formation of antiparallel-type triplex DNA with duplex DNA that includes TA and dUA base pairs. Nucleic Acids Res 50:12071–12081. https://doi.org/10.1093/nar/gkac1110
Obika S, Hari Y, Sekiguchi M, Imanishi T (2002) Stable oligonucleotide-directed triplex formation at target sites with CG interruptions: strong sequence-specific recognition by 2′,4′-bridged nucleic-acid-containing 2-pyridones under physiological conditions. Chem Eur J 8:4796–4802. https://doi.org/10.1002/1521-3765
Ohkubo A, Yamada K, Ito Y, Yoshimura K, Miyauchi K, Kanamori T, Masaki Y, Seio K, Yuasa H, Sekine M (2015) Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs. Nucleic Acids Res 43:5675–5686. https://doi.org/10.1093/nar/gkv496
Osborne SD, Powers VEC, Rusling DA, Lack O, Fox KR, Brown T (2004) Selectivity and affinity of triplex-forming oligonucleotides containing 2′-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine for recognizing AT base pairs in duplex DNA. Nucleic Acids Res 32:4439–4447. https://doi.org/10.1093/nar/gkh776
Patel HP, Lu L, Blaszak RT, Bissler JJ (2004) PKD1 intron 21: triplex DNA formation and effect on replication. Nucleic Acids Res 32:41460–41468. https://doi.org/10.1093/nar/gkh312
Patterson A, Caprio F, Valle A, Moscone D, Plaxco KW, Palleschi G, Ricci F (2010) Using triplex-forming oligonucleotide probes for the reagentless, electrochemical detection of double-stranded DNA. Anal Chem 82:9109–9115. https://doi.org/10.1021/ac1024528
Postepska-Igielska A, Blank-Giwojna A, Grummt I (2020) Analysis of RNA-DNA triplex structures in vitro and in vivo. In RNA-chromatin interactions (ed. Orom, UAV). Methods Mol Biol 2161:229–246. https://doi.org/10.1007/978-1-0716-0680-3_16
Pozza MD, Abdullrahman A, Cardin CJ, Gasser G, Hall JP (2022) Three’s a crowd – stabilisation, structure, and applications of DNA triplexes. Chem Sci 13:10193–10215. https://doi.org/10.1039/D2SC01793H
Pyne ALB, Noy A, Main KHS, Velasco-Berrelleza V, Piperakis VM, Mitchenall LA, Cugliandolo FM, Beton JG, Stevenson CEM, Hoogenboom BW, Bates AD, Maxwell A, Harris SA (2021) Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides. Nat Commun 12:1053. https://doi.org/10.1038/s41467-021-21243-y
Rhee S, Han Z-j, Liu K, Miles HT, Davies DR (1999) Structure of a triple helical DNA with a triplex-duplex junction. Biochemistry 38:16810–16815. https://doi.org/10.1021/bi991811m
Roberts RW, Crothers DM (1992) Stability and properties of double and triple helices: dramatic effects of RNA or DNA backbone composition. Science 258:1463–1466. https://doi.org/10.1126/science.1279808
Roberts RW, Crothers DM (1996) Prediction of the stability of DNA triplexes. Proc Natl Acad Sci U S A 93:4320–4325. https://doi.org/10.1073/pnas.93.9.4320
Rusling DA (2021) Triplex-forming properties and enzymatic incorporation of a base-modified nucleotide capable of duplex DNA recognition at neutral pH. Nucleic Acids Res 49:7256–7266. https://doi.org/10.1093/nar/gkab572
Rusling DA, Powers VEC, Ranasinghe RT, Wang Y, Osborne SD, Brown T, Fox KR (2005) Four base recognition by triplex-forming oligonucleotides at physiological pH. Nucleic Acids Res 33:3025–3032. https://doi.org/10.1093/nar/gki625
Rusling DA, Broughton-Head VJ, Tuck A, Khairallah H, Osborne SD, Brown T, Fox KR (2008) Kinetic studies on the formation of DNA triplexes containing the nucleoside analogue 2’-O-(2-aminoethyl)-5-(3-amino-1-propynyl)uridine. Org Biomol Chem 6:122–129. https://doi.org/10.1039/b713088k
Rusling DA, Nandhakumar IS, Brown T, Fox KR (2012) Triplex-directed recognition of a DNA nanostructure assembled by crossover strand exchange. ACS Nano 6:3604–3613. https://doi.org/10.1021/nn300718z
Ruszkowska A, Ruszkowski M, Hulewicz JP, Dauter Z, Brown JA (2020) Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples. Nucleic Acids Res 48:3304–3314. https://doi.org/10.1093/nar/gkz1222
Ryan CA, Brodyagin N, Lok J, Rozners E (2021) The 2-aminopyridine nucleobase improves triple-helical recognition of RNA and DNA when used instead of pseudoisocytosine in peptide nucleic acids. Biochemistry 60:1919–1925. https://doi.org/10.1021/acs.biochem.1c00275
Schmitz KM, Mayer C, Postepska A, Grummt I (2010) Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev 24:2264–2269. https://doi.org/10.1101/gad.590910
Semerad CL, Maher III LJ (1994) Exclusion of RNA strands from a purine motif triple helix. Nucleic Acids Res 22:5321–5325. https://doi.org/10.1093/nar/22.24.5321
Strobel SA, Doucette-Stamm LA, Riba L, Housman DE, Dervan PB (1991) Site-specific cleavage of human chromosome 4 mediated by triple-helix formation. Science 254:1639–1642. https://doi.org/10.1126/science.18362
Sun B-W, Babu BR, Sørensen MD, Zakrzewska K, Wengel J, Sun J-S (2004) Sequence and pH effects of LNA-containing triple helix-forming oligonucleotides: physical chemistry, biochemistry, and modeling studies. Biochemistry 43:4160–4169. https://doi.org/10.1021/bi036064e
Taniguchi Y, Magata Y, Osuki T, Notomi R, Wang L, Okamura H, Sasaki S (2020) Development of novel C-nucleoside analogues for the formation of antiparallel-type triplex DNA with duplex DNA that includes TA and dUA base pairs. Org Biomol Chem 18:2845–2851. https://doi.org/10.1039/d0ob00420k
Tateishi-Karimata H, Sugimoto N (2021) Roles of non-canonical structures of nucleic acids in cancer and neurodegenerative diseases. Nucleic Acids Res 49:7839–7855. https://doi.org/10.1093/nar/gkab580
Torigoe H, Hari Y, Sekiguchi Y, Obika S, Imanishi T (2001) 2′-O,4′-C-methylene bridged nucleic acid modification promotes pyrimidine motif triplex DNA formation at physiological pH: thermodynamic and kinetic studies. J Biol Chem 276:2354–2360. https://doi.org/10.1074/jbc.M007783200
Torigoe H, Sasaki K, Katayama T (2009) Thermodynamic and kinetic effects of morpholino modification on pyrimidine motif triplex nucleic acid formation under physiological condition. J Biol Chem 146:173–183. https://doi.org/10.1093/jb/mvp059
Wang L, Taniguchi T, Okamura H, Sasaki S (2018) Modification of the aminopyridine unit of 2′-deoxyaminopyridinyl-pseudocytidine allowing triplex formation at CG interruptions in homopurine sequences. Nucleic Acids Res 46:8679–8688. https://doi.org/10.1093/nar/gky704
Warwick T, Seredinski S, Krause NM, Bains JK, Althaus L, Oo JA, Bonetti A, Dueck A, Engelhardt S, Schwalbe H, Leisegang MS, Schulz MH, Brandes RP (2022) A universal model of RNA·DNA:DNA triplex formation accurately predicts genome-wide RNA DNA interactions. Brief Bioinform 23:1–12. https://doi.org/10.1093/bib/bbac445
Wells RD (2008) DNA triplexes and Friedreich ataxia. FASEB J 22:1625–1634. https://doi.org/10.1096/fj.07-097857
Wilusz JE, JnBaptiste CK, Lu LY, Kuhn CD, Joshua-Tor L, Sharp PA (2012) A triple helix stabilizes the 3′ ends of long noncoding RNAs that lack poly(A) tails. Genes Dev 26:2392–2407. https://doi.org/10.1101/gad.204438.112
Wittung P, Nielsen P, Nordén B (1997) Extended DNA-recognition repertoire of peptide nucleic acid (PNA): PNA−dsDNA triplex formed with cytosine-rich homopyrimidine PNA. Biochemistry 36:7973–7979. https://doi.org/10.1021/bi963136b
Yang S, Liu W, Wang R (2019) Control of the stepwise assembly–disassembly of DNA origami nanoclusters by pH stimuli-responsive DNA triplexes. Nanoscale 11:18026–18030. https://doi.org/10.1039/c9nr05047g
Zhang J, Fakharzadeh A, Pan F, Roland C, Sagui C (2020a) Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich’s ataxia: DNA triplexes and RNA/DNA hybrids. Nucleic Acids Res 48:9899–9917. https://doi.org/10.1093/nar/gkaa665
Zhang Y, Long Y, Kwoh CK (2020b) Deep learning based DNA:RNA triplex forming potential prediction. BMC Bioinformatics 21:522. https://doi.org/10.1186/s12859-020-03864-0
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Fox, K.R. (2023). Targeting DNA with Triplexes. In: Sugimoto, N. (eds) Handbook of Chemical Biology of Nucleic Acids. Springer, Singapore. https://doi.org/10.1007/978-981-16-1313-5_88-1
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