Antisense oligonucleotides are now entering the clinic for hard-totreat diseases. New chemical modifications are urgently required to enhance their drug-like properties. We combine amide coupling with standard oligonucleotide synthesis to assemble backbone chimera gapmers that trigger an efficient RNase H response while improving serum life time and cellular uptake.Antisense oligonucleotides (ASOs) are short (B20mer) chemically modified oligomers that bind to their complementary RNA targets to modulate gene expression at the mRNA level. 1,2 Thus, ASOs can target proteins that are considered undruggable through conventional approaches. 3 As such, they hold enormous promise for hard-to-treat diseases as evidenced by a number of recently approved oligonucleotide (ON)-based drugs. [4][5][6] Chemical modifications are essential to improve the serum stability and pharmacodynamic properties of ASOs, as unmodified ONs are rapidly digested by nucleases in vivo 7,8 and suffer from poor cellular uptake and tissue distribution. 9 Whilst there have been considerable advances to modify ONs either at the nucleobase, sugar or backbone, a set of distinct chemical modifications to confer ideal drug-like properties has not yet been achieved. 10 Commonly used ribose modifications include 2 0 -F, 2 0 -OMe, 2 0 -O-(2-methoxyethyl) and locked nucleic acids, all of which have been shown to improve target affinity and serum stability. 11 The most commonly used phosphodiester (PO) mimic is the phosphorothioate (PS) linkage which is compatible with ribonuclease H (RNase H) activation, 12 a mechanism resulting in degradation of an mRNA upon formation of an ASO:mRNA heteroduplex. PS linkages also improve metabolic stability 13 and enhance pharmacodynamic properties through interactions with plasma proteins. 8,14,15 However, unspecific protein binding can contribute to the toxic potential of PS-ASOs 16,17 and the PS linkage is P-chiral resulting in a mixture of diastereomers (more than half a million isomers in Mipomersen 12,18 ). Moreover, inefficient cellular uptake remains a major challenge for ASO therapeutics. Therefore, the investigation of other artificial backbone linkages is urgently needed.Charge-neutral backbone modifications represent an interesting class of PO mimics. Among those, (thio)phosphonoacetate esters, 19 phosphotriesters 20 and alkyl phosphonates 21 can enhance cellular uptake by eliminating the PO negative charges. Moreover, incorporation of a single methylphosphonate can eliminate hepatotoxicity of PS-ASOs. 22 Phosphorodiamidate morpholino oligomers (PMOs) combine backbone and sugar modifications and enhance delivery through interactions with scavenger receptors, 23 but are not compatible with standard ON synthesis. All aforementioned PO mimics also suffer from increased steric complexity due to their P-chiral linkages.The absence of a chiral centre and the well-established solidphase peptide synthesis methods make the amide internucleoside linkage 24 (AM, Fig. 1A) a promising candidate for backbone surrogates. Within...

Oligonucleotides that target mRNA have great promise as therapeutic agents for life-threatening conditions but suffer from poor bioavailability, hence high cost. As currently untreatable diseases come within the reach of oligonucleotide therapies, new analogues are urgently needed to address this. With this in mind we describe reduced-charge oligonucleotides containing artificial LNA-amide linkages with improved gymnotic cell uptake, RNA affinity, stability and potency. To construct such oligonucleotides, five LNA-amide monomers (A, T, C, 5mC and G), where the 3′-OH is replaced by an ethanoic acid group, are synthesised in good yield and used in solid-phase oligonucleotide synthesis to form amide linkages with high efficiency. The artificial backbone causes minimal structural deviation to the DNA:RNA duplex. These studies indicate that splice-switching oligonucleotides containing LNA-amide linkages and phosphorothioates display improved activity relative to oligonucleotides lacking amides, highlighting the therapeutic potential of this technology.

Carbamate-LNA oligonucleotides have improved biophysical properties for theraputic applications.

Triazole linkages (TLs) are mimics of the phosphodiester bond in oligonucleotides with applications in synthetic biology and biotechnology. Here we report the RuAAC-catalyzed synthesis of a novel 1,5-disubstituted triazole (TL 2 ) dinucleoside phosphoramidite as well as its incorporation into oligonucleotides and compare its DNA polymerase replication competency with other TL analogues. We demonstrate that TL 2 has superior replication kinetics to these analogues and is accurately replicated by polymerases. Derived structure–biocompatibility relationships show that linker length and the orientation of a hydrogen bond acceptor are critical and provide further guidance for the rational design of artificial biocompatible nucleic acid backbones.