Abstract
Chemically modified nucleic acids have become crucial tools across a diverse range of sciences. They are extensively used not only as diagnostic and therapeutic agents to modulate gene expression or impede protein function by binding a specific RNA sequence or target protein but also in synthetic biology, particularly in the context of artificial genetic polymers (XNAs). In order to enable maximum scope for all in vivo applications, it is pivotal for oligonucleotides to form thermodynamically and metabolically stable helical structures via self- or cross-pairing with natural complements. In this respect, the discovery of hexitol nucleic acid (HNA), consisting of a phosphorylated 1,5-anhydrohexitol backbone and natural nucleobases, has driven many significant advances in these areas, and especially in the last decade, numerous novel approaches have emerged that overstepped the molecular and functional boundaries of extant biopolymers. Herein, we discuss the more recent progress that has been made to synthesize HNA as well as related six-membered nucleic acids [altritol nucleic acid (ANA), FHNA (3′-fluorohexitol nucleic acid), cyclohexene nucleic acid (CeNA), and 2′-fluoro cyclohexene nucleic acid (F-CeNA)] involving optimized and novel chemical and enzymatic methods, and we highlight a number of selected examples of in vitro and in vivo biological and biomedical applications in which such synthetic polymers played a crucial role. Despite most of these efforts are still at their early stages, the influence of these modified nucleic acids in medicine and biotechnology is destined to increase, especially judging from their impressive and unique abilities.
The Figure 2, 3, 7 and 9 were created using BioRender.com and the figures 4, 5, 6 and 8 were partially created using BioRender.com.
Similar content being viewed by others
References
Abramov M, Herdewijn P (2007) Synthesis of altritol nucleoside phosphoramidites for oligonucleotide synthesis. Curr Protoc Nucleic Acid Chem 30:1.18.11–1.18.21
Abramov M, Schepers G, Van Aerschot A, Van Hummelen P, Herdewijn P (2008) HNA and ANA high-affinity arrays for detections of DNA and RNA single-base mismatches. Biosens Bioelectron 23:1728–1732
Adams D, Gonzalez-Duarte A, O’Riordan WD, Yang C-C, Ueda M, Kristen AV, Tournev I, Schmidt HH, Coelho T, Berk JL, Lin K-P, Vita G, Attarian S, Planté-Bordeneuve V, Mezei MM, Campistol JM, Buades J, Brannagan TH, Kim BJ, Oh J, Parman Y, Sekijima Y, Hawkins PN, Solomon SD, Polydefkis M, Dyck PJ, Gandhi PJ, Goyal S, Chen J, Strahs AL, Nochur SV, Sweetser MT, Garg PP, Vaishnaw AK, Gollob JA, Suhr OB (2018) Patisiran, an RNAi therapeutic, for hereditary transthyretin amyloidosis. N Engl J Med 379:11–21
Aerschot Van A, Verheggen I, Hendrix C, Herdewijn P (1995) 1,5-Anhydrohexitol nucleic acids, a new promising antisense construct. Angew Chem Int Ed Eng 34:1338–1339
Allart B, Khan K, Rosemeyer H, Schepers G, Hendrix C, Rothenbacher K, Seela F, Van Aerschot A, Herdewijn P (1999) D-Altritol nucleic acids (ANA): hybridisation properties, stability, and initial structural analysis. Chem Eur J 5:2424–2431
Andersen MW, Daluge SM, Kerremans L, Herdewijn P (1996) The synthesis of modified D- and L-anhydrohexitol nucleosides. Tetrahedron Lett 37:8147–8150
Atkins D, Miller M, De Bouvere B, van Aerschot A, Herdewijn P (2000) Evaluation of the cellular uptake of hexitol nucleic acids in HeLa cells. Pharmazie 55:615–617
Bain JD, Switzer C, Chamberlin AR, Benner SA (1992) Ribosome-mediated incorporation of a non-standard amino acid into a peptide through expansion of the genetic code. Nature 356:537–539
Bande O, Abu El Asrar R, Braddick D, Dumbre S, Pezo V, Schepers G, Pinheiro VB, Lescrinier E, Holliger P, Marlière P, Herdewijn P (2015) Isoguanine and 5-methyl-isocytosine bases, in vitro and in vivo. Chemistry 21:5009–5022
Böhringer M, Roth H-J, Hunziker J, Göbel M, Krishnan R, Giger A, Schweizer B, Schreiber J, Leumann C, Eschenmoser A (1992) Warum Pentose- und nicht Hexose-Nucleinsäuren??. Teil II. Oligonucleotide aus 2′,3′-Dideoxy-β-D-glucopyranosyl-Bausteinen (‘Homo-DNS’): Herstellung. Helv Chim Acta 75:1416–1477
Boudou V, Kerremans L, De Bouvere B, Lescrinier E, Schepers G, Busson R, Van Aerschot A, Herdewijn P (1999) Base pairing of anhydrohexitol nucleosides with 2,6-diaminopurine, 5-methylcytosine and uracil asbase moiety. Nucleic Acids Res 27:1450–1456
Bramsen JB, Laursen MB, Nielsen AF, Hansen TB, Bus C, Langkjaer N, Babu BR, Højland T, Abramov M, Van Aerschot A, Odadzic D, Smicius R, Haas J, Andree C, Barman J, Wenska M, Srivastava P, Zhou C, Honcharenko D, Hess S, Müller E, Bobkov GV, Mikhailov SN, Fava E, Meyer TF, Chattopadhyaya J, Zerial M, Engels JW, Herdewijn P, Wengel J, Kjems J (2009) A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity. Nucleic Acids Res 37:2867–2881
D’Alonzo D, Froeyen M, Schepers G, Di Fabio G, Van Aerschot A, Herdewijn P, Palumbo G, Guaragna A (2015) 1′,5′-Anhydro-l-ribo-hexitol adenine nucleic acids (α-l-HNA-A): synthesis and chiral selection properties in the Mirror image world. J Organomet Chem 80:5014–5022
De Fenza M, Eremeeva E, Troisi R, Yang H, Esposito A, Sica F, Herdewijn P, D’Alonzo D, Guaragna A (2020) Structure–Activity Relationship Study of a Potent α-Thrombin Binding Aptamer Incorporating Hexitol Nucleotides. Chem Eur J 26:9589–9597
De S, Jabgunde AM, Patil RS, De Jonghe S, Beigelman L, Herdewijn P (2018) Synthesis of protected amino hexitol nucleosides as building blocks for oligonucleotide synthesis. J Organomet Chem 83:15155–15169
Declercq R, Aerschot AV, Read RJ, Herdewijn P, Meervelt LV (2002) Crystal structure of double helical hexitol nucleic acids. J Am Chem Soc 124:928–933
Egli M, Pallan PS, Allerson CR, Prakash TP, Berdeja A, Yu J, Lee S, Watt A, Gaus H, Bhat B, Swayze EE, Seth PP (2011) Synthesis, improved antisense activity and structural rationale for the divergent RNA affinities of 3′-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides. J Am Chem Soc 133:16642–16649
Eremeeva E, Fikatas A, Margamuljana L, Abramov M, Schols D, Groaz E, Herdewijn P (2019) Highly stable hexitol based XNA aptamers targeting the vascular endothelial growth factor. Nucleic Acids Res 47:4927–4939
Eschenmoser A (1999) Chemical etiology of nucleic acid structure. Science 284:2118–2124
Fisher M, Abramov M, Van Aerschot A, Xu D, Juliano RL, Herdewijn P (2007) Inhibition of MDR1 expression with altritol-modified siRNAs. Nucleic Acids Res 35:1064–1074
Fisher M, Abramov M, Van Aerschot A, Rozenski J, Dixit V, Juliano RL, Herdewijn P (2009) Biological effects of hexitol and altritol-modified siRNAs targeting B-Raf. Eur J Pharmacol 606:38–44
Flores MVC, Atkins D, Stewart TS, van Aerschot A, Herdewijn P (1999) Antimalarial antisense activity of hexitol nucleic acids. Parasitol Res 85:864–866
Froeyen M, Wroblowski B, Esnouf R, De Winter H, Allart B, Lescrinier E, Herdewijn P (2000) Molecular-Dynamics Studies of Single-Stranded Hexitol, Altritol, Mannitol, and Ribose Nucleic Acids (HNA, MNA, ANA, and RNA, Resp.) and of the stability of HNA·RNA, ANA·RNA, and MNA·RNA duplexes. Helv Chim Acta 83:2153–2182
Gu P, Schepers G, Rozenski J, Van Aerschot A, Herdewijn P (2003) Base pairing properties of D- and L-cyclohexene nucleic acids (CeNA). Oligonucleotides 13:479–489
Gu P, Griebel C, Van Aerschot A, Rozenski J, Busson R, Gais H-J, Herdewijn P (2004) Synthesis of enantiomeric-pure cyclohexenyl nucleoside building blocks for oligonucleotide synthesis. Tetrahedron 60:2111–2123
Hean J, Crowther C, Ely A, Ul Islam R, Barichievy S, Bloom K, Weinberg MS, van Otterlo WA, de Koning CB, Salazar F, Marion P, Roesch EB, Lemaitre M, Herdewijn P, Arbuthnot P (2010) Inhibition of hepatitis B virus replication in vivo using lipoplexes containing altritol-modified antiviral siRNAs. Artif DNA PNA XNA 1:17–26
Hendrix C, Rosemeyer H, Verheggen I, Van Aerschot A, Seela F, Herdewijn P (1997a) 1′, 5′ -Anhydrohexitol oligonucleotides: synthesis, base pairing and recognition by regular oligodeoxyribonucleotides and oligoribonucleotides. Chem Eur J 3:110–120
Hendrix C, Rosemeyer H, De Bouvere B, Van Aerschot A, Seela F, Herdewijn P (1997b) 1′,5′-Anhydrohexitol oligonucleotides: hybridisation and strand displacement with oligoribonucleotides, interaction with RNase H and HIV reverse transcriptase. Chem Eur J 3:1513–1520
Herdewijn P (2010) Nucleic acids with a six-membered ‘carbohydrate’ mimic in the backbone. Chem Biodivers 7:1–59
Herdewijn P, Marlière P (2009) Toward safe genetically modified organisms through the chemical diversification of nucleic acids. Chem Biodivers 6:791–808
Hossain N, Wroblowski B, Van Aerschot A, Rozenski J, De Bruyn A, Herdewijn P (1998) Oligonucleotides composed of 2′-Deoxy-1′,5′-anhydro-d-mannitol nucleosides with a purine base moiety. J Organomet Chem 63:1574–1582
Kang H, Fisher MH, Xu D, Miyamoto YJ, Marchand A, Van Aerschot A, Herdewijn P, Juliano RL (2004) Inhibition of MDR1 gene expression by chimeric HNA antisense oligonucleotides. Nucleic Acids Res 32:4411–4419
Kestemont D, Renders M, Leonczak P, Abramov M, Schepers G, Pinheiro VB, Rozenski J, Herdewijn P (2018) XNA ligation using T4 DNA ligase in crowding conditions. Chem Commun 54:6408–6411
Kolb G, Reigadas S, Boiziau C, van Aerschot A, Arzumanov A, Gait MJ, Herdewijn P, Toulmé JJ (2005) Hexitol nucleic acid-containing aptamers are efficient ligands of HIV-1 TAR RNA. Biochemistry 44:2926–2933
Kozlov IA, Politis PK, Pitsch S, Herdewijn P, Orgel LE (1999a) A highly enantio-selective hexitol nucleic acid template for nonenzymatic oligoguanylate synthesis. J Am Chem Soc 121:1108–1109
Kozlov IA, Politis PK, Van Aerschot A, Busson R, Herdewijn P, Orgel LE (1999b) Nonenzymatic synthesis of RNA and DNA oligomers on hexitol nucleic acid templates: the importance of the A structure. J Am Chem Soc 121:2653–2656
Kozlov IA, Zielinski M, Allart B, Kerremans L, Van Aerschot A, Busson R, Herdewijn P, Orgel LE (2000) Nonenzymatic template-directed reactions on altritol oligomers, preorganized analogues of oligonucleotides. Chemistry 6:151–155
Kumar P, Degaonkar R, Guenther DC, Abramov M, Schepers G, Capobianco M, Jiang Y, Harp J, Kaittanis C, Janas MM, Castoreno A, Zlatev I, Schlegel MK, Herdewijn P, Egli M, Manoharan M (2020) Chimeric siRNAs with chemically modified pentofuranose and hexopyranose nucleotides: altritol-nucleotide (ANA) containing GalNAc-siRNA conjugates: in vitro and in vivo RNAi activity and resistance to 5′-exonuclease. Nucleic Acids Res 48:4028–4040
Lagoja IM, Marchand A, Van Aerschot A, Herdewijn P (2003) Synthesis of 1,5-Anhydrohexitol building blocks for oligonucleotide synthesis. Curr Protoc Nucleic Acid Chem 14:1.9.1–1.9.22
Lavrik IN, Avdeeva ON, Dontsova OA, Froeyen M, Herdewijn PA (2001) Translational properties of mHNA, a messenger RNA containing anhydrohexitol nucleotides. Biochemistry 40:11777–11784
Le BT, Chen S, Abramov M, Herdewijn P, Veedu RN (2016) Evaluation of anhydrohexitol nucleic acid, cyclohexenyl nucleic acid and d-altritol nucleic acid-modified 2′-O-methyl RNA mixmer antisense oligonucleotides for exon skipping in vitro. Chem Commun 52:13467–13470
Lescrinier E, Esnouf R, Schraml J, Busson R, Heus H, Hilbers C, Herdewijn P (2000) Solution structure of a HNA-RNA hybrid. Chem Biol 7:719–731
Maier T, Przylas I, Strater N, Herdewijn P, Saenger W (2005) Reinforced HNA backbone hydration in the crystal structure of a decameric HNA/RNA hybrid. J Am Chem Soc 127:2937–2943
Maiti M, Nauwelaerts K, Lescrinier E, Herdewijn P (2011) Structural and binding study of modified siRNAs with the Argonaute 2 PAZ domain by NMR spectroscopy. Chemistry 17:1519–1528
Malyshev DA, Dhami K, Lavergne T, Chen T, Dai N, Foster JM, Corrêa Jr IR, Romesberg FE (2014) A semi-synthetic organism with an expanded genetic alphabet. Nature 509:385–388
Marlière P, Patrouix J, Döring V, Herdewijn P, Tricot S, Cruveiller S, Bouzon M, Mutzel R (2011) Chemical evolution of a bacterium’s genome. Angew Chem Int Ed Eng 50:7109–7114
Mehta AP, Li H, Reed SA, Supekova L, Javahishvili T, Schultz PG (2016a) Replacement of 2′-deoxycytidine by 2′-deoxycytidine analogues in the E. coli genome. J Am Chem Soc 138:14230–14233
Mehta AP, Li H, Reed SA, Supekova L, Javahishvili T, Schultz PG (2016b) Replacement of thymidine by a modified base in the Escherichia coli genome. J Am Chem Soc 138:7272–7275
Migawa MT, Prakash TP, Vasquez G, Seth PP, Swayze EE (2013) Synthesis and biophysical properties of constrained d-Altritol nucleic acids (cANA). Org Lett 15:4316–4319
Mutschler H, Taylor AI, Porebski BT, Lightowlers A, Houlihan G, Abramov M, Herdewijn P, Holliger P (2018) Random-sequence genetic oligomer pools display an innate potential for ligation and recombination. elife 7:e43022
Nauwelaerts K, Lescrinier E, Sclep G, Herdewijn P (2005) Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides. Nucleic Acids Res 33:2452–2463
Nauwelaerts K, Fisher M, Froeyen M, Lescrinier E, Van Aerschot A, Xu D, DeLong R, Kang H, Juliano RL, Herdewijn P (2007) Structural characterization and biological evaluation of small interfering RNAs containing cyclohexenyl nucleosides. J Am Chem Soc 129:9340–9348
Ng EW, Shima DT, Calias P, Cunningham Jr ET, Guyer DR, Adamis AP (2006) Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nat Rev Drug Discov 5:123–132
Ni S, Zhuo Z, Pan Y, Yu Y, Li F, Liu J, Wang L, Wu X, Li D, Wan Y, Zhang L, Yang Z, Zhang B-T, Lu A, Zhang G (2021) Recent progress in aptamer discoveries and modifications for therapeutic applications. ACS Appl Mater Interfaces 13:9500–9519
Ovaere M, Herdewijn P, Van Meervelt L (2011) The crystal structure of the CeNA:RNA hybrid ce(GCGTAGCG):r(CGCUACGC). Chemistry 17:7823–7830
Ovaere M, Sponer J, Sponer JE, Herdewijn P, Van Meervelt L (2012) How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid:ribonucleic acid duplex. Nucleic Acids Res 40:7573–7583
Pezo V, Liu FW, Abramov M, Froeyen M, Herdewijn P, Marlière P (2013) Binary genetic cassettes for selecting XNA-Templated DNA synthesis in vivo. Angew Chem Int Ed 52:8139–8143
Pezo V, Schepers G, Lambertucci C, Marlière P, Herdewijn P (2014) Probing ambiguous base-pairs by genetic transformation with XNA templates. Chembiochem 15:2255–2258
Pinheiro VB, Taylor AI, Cozens C, Abramov M, Renders M, Zhang S, Chaput JC, Wengel J, Peak-Chew S-Y, McLaughlin SH, Herdewijn P, Holliger P (2012) Synthetic genetic polymers capable of heredity and evolution. Science 336:341–344
Pochet S, Kaminski PA, Van Aerschot A, Herdewijn P, Marlière P (2003) Replication of hexitol oligonucleotides as a prelude to the propagation of a third type of nucleic acid in vivo. C R Biol 326:1175–1184
Renders M, Dumbre S, Abramov M, Kestemont D, Margamuljana L, Largy E, Cozens C, Vandenameele J, Pinheiro VB, Toye D, Frère J-M, Herdewijn P (2019) Kinetic analysis of N-alkylaryl carboxamide hexitol nucleotides as substrates for evolved polymerases. Nucleic Acids Res 47:2160–2168
Rietmeyer L, Li De La Sierra-Gallay I, Schepers G, Dorchêne D, Iannazzo L, Patin D, Touzé T, van Tilbeurgh H, Herdewijn P, Ethève-Quelquejeu M, Fonvielle M (2022) Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis. Nucleic Acids Res 50:11415–11425
Robeyns K, Herdewijn P, Van Meervelt L (2008a) Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC. J Am Chem Soc 130:1979–1984
Robeyns K, Herdewijn P, Van Meervelt L (2008b) Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(CGCGAATTCGCG). Nucleic Acids Res 36:1407–1414
Robeyns K, Herdewijn P, Van Meervelt L (2010) Direct observation of two cyclohexenyl (CeNA) ring conformations in duplex DNA. Artif DNA PNA XNA 1:2–8
Rohner E, Yang R, Foo KS, Goedel A, Chien KR (2022) Unlocking the promise of mRNA therapeutics. Nat Biotechnol 40:1586–1600
Samson C, Legrand P, Tekpinar M, Rozenski J, Abramov M, Holliger P, Pinheiro VB, Herdewijn P, Delarue M (2020) Structural studies of HNA substrate specificity in mutants of an archaeal DNA polymerase obtained by directed evolution. Biomol Ther 10:1647
Seth PP, Yu J, Jazayeri A, Pallan PS, Allerson CR, Østergaard ME, Liu F, Herdewijn P, Egli M, Swayze EE (2012) Synthesis and antisense properties of fluoro cyclohexenyl nucleic acid (F-CeNA), a nuclease stable mimic of 2′-Fluoro RNA. J Organomet Chem 77:5074–5085
Taylor AI, Pinheiro VB, Smola MJ, Morgunov AS, Peak-Chew S, Cozens C, Weeks KM, Herdewijn P, Holliger P (2015) Catalysts from synthetic genetic polymers. Nature 518:427–430
Taylor AI, Beuron F, Peak-Chew S-Y, Morris EP, Herdewijn P, Holliger P (2016) Nanostructures from synthetic genetic polymers. Chembiochem 17:1107–1110
Van Aerschot A, Meldgaard M, Schepers G, Volders F, Rozenski J, Busson R, Herdewijn P (2001) Improved hybridisation potential of oligonucleotides comprising O-methylated anhydrohexitol nucleoside congeners. Nucleic Acids Res 29:4187–4194
Vandermeeren M, Préveral S, Janssens S, Geysen J, Saison-Behmoaras E, Van Aerschot A, Herdewijn P (2000) Biological activity of hexitol nucleic acids targeted at Ha-ras and intracellular adhesion molecule-1 mRNA. Biochem Pharmacol 59:655–663
Vanmeert M, Razzokov J, Mirza MU, Weeks SD, Schepers G, Bogaerts A, Rozenski J, Froeyen M, Herdewijn P, Pinheiro VB, Lescrinier E (2019) Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins. Nucleic Acids Res 47:7130–7142
Verbeure B, Lescrinier E, Wang J, Herdewijn P (2001) RNase H mediated cleavage of RNA by cyclohexene nucleic acid (CeNA). Nucleic Acids Res 29:4941–4947
Verheggen I, Vanaerschot A, Toppet S, Snoeck R, Janssen G, Balzarini J, Declercq E, Herdewijn P (1993) SYNTHESIS AND ANTIHERPES VIRUS ACTIVITY OF 1,5-ANHYDROHEXITOL NUCLEOSIDES. J Med Chem 36:2033–2040
Wang J, Verbeure B, Luyten I, Lescrinier E, Froeyen M, Hendrix C, Rosemeyer H, Seela F, Van Aerschot A, Herdewijn P (2000) Cyclohexene nucleic acids (CeNA): serum stable oligonucleotides that activate RNase H and increase duplex stability with complementary RNA. J Am Chem Soc 122:8595–8602
Wang J, Morral J, Hendrix C, Herdewijn P (2001) A straightforward stereoselective synthesis of d- and l-5-Hydroxy-4-hydroxymethyl-2-cyclohexenylguanine. J Organomet Chem 66:8478–8482
Winter HD, Lescrinier E, Aerschot AV, Herdewijn P (1998) Molecular dynamics simulation to investigate differences in minor groove hydration of HNA/RNA hybrids as compared to HNA/DNA complexes. J Am Chem Soc 120:5381–5394
Zhou J, Abramov M, Liu F, Amrane S, Bourdoncle A, Herdewijn P, Mergny J-L (2013) Effects of six-membered carbohydrate rings on structure, stability, and kinetics of G-Quadruplexes. Chem Eur J 19:14719–14725
Zhu Y, Zhu L, Wang X, Jin H (2022) RNA-based therapeutics: an overview and prospectus. Cell Death Dis 13:644
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Section Editor information
Rights and permissions
Copyright information
© 2023 Springer Nature Singapore Pte Ltd.
About this entry
Cite this entry
Groaz, E., Herdewijn, P. (2023). Hexitol Nucleic Acid (HNA): From Chemical Design to Functional Genetic Polymer. In: Sugimoto, N. (eds) Handbook of Chemical Biology of Nucleic Acids. Springer, Singapore. https://doi.org/10.1007/978-981-16-1313-5_15-1
Download citation
DOI: https://doi.org/10.1007/978-981-16-1313-5_15-1
Received:
Accepted:
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-16-1313-5
Online ISBN: 978-981-16-1313-5
eBook Packages: Springer Reference Chemistry and Mat. ScienceReference Module Physical and Materials ScienceReference Module Chemistry, Materials and Physics