Chiral communications exist in secondary structures of foldamers and copolymers via a network of noncovalent interactions within effective intermolecular force (IMF) range. It is not known whether long-range chiral communication exists between macromolecular tertiary structures such as peptide coiled-coils beyond the IMF distance. Harnessing the high sensitivity of single-molecule force spectroscopy, we investigate the chiral interaction between covalently linked DNA duplexes and peptide coiled-coils by evaluating the binding of a diastereomeric pair of three DNA-peptide conjugates. We find that right-handed DNA triple helices well accommodate peptide triple coiled-coils of the same handedness, but not with the left-handed coiled-coil stereoisomers. This chiral communication is effective in a range (<4.5 nm) far beyond canonical IMF distance. Small-angle X-ray scattering and molecular dynamics simulation indicate that the interdomain linkers are tightly packed via hydrophobic interactions, which likely sustains the chirality transmission between DNA and peptide domains. Our findings establish that long-range chiral transmission occurs in tertiary macromolecular domains, explaining the presence of homochiral pairing of superhelices in proteins.

Attachmento fc ationic moieties to oligonucleotides (ONs) promises not only to increase the binding affinity of antisense ONs by reducing charger epulsion between the two negatively charged strandso faduplex, but also to augment their in vivo stability against nucleases.I nt his study, polyamine functionality was introduced into ONs by means of 2'-amino-LNAs caffolds. The resulting ONs exhibited efficient binding towardsssDNA, ssRNA and dsDNA targets, and the 2'-amino-LNA analogue carrying at riaminated linker showed them ostp ronouncedd uplex-and triplex-stabilizing effect. Molecular modelling revealed that favourable conformationala nd electrostatic effects led to salt-bridge formation between positivelyc harged polyamine moieties and the Watson-Hoogsteen groove of the dsDNA targets, resulting in the observed triplex stabilization. All the investigated monomers showedi ncreased resistance against 3'-nucleolytic digestion relative to the non-functionalized controls.

Off-target effects remain as ignificant challengei n the therapeutic use of gapmer antisense oligonucleotides (AONs). Over the yearsv arious modificationsh ave been synthesizeda nd incorporated into AONs,h owever,p recise control of RNase H-induced cleavage and target sequences electivity has yet to be realized.H erein, the synthesis of the uracil and cytosine derivatives of anovel class of 2'-deoxy-2'fluoro-3'-C-hydroxymethyl-b-d-lyxo-configured nucleotides has been accomplisheda nd the targetm oleculesh ave been incorporated into AONs. Experiments on exonucleased egradation showed improvedn ucleolytic stability relative to the unmodified control.U pon the introduction of one or two of the novel 2'-fluoro-3'-C-hydroxymethyl nucleotides as modificationsi nt he gapr egion of ag apmer AON was associated with efficient RNase H-mediated cleavage of the RNA strand of the corresponding AON:RNA duplex. Notably,atailored single cleavage event could be engineered depending on the positioning of as ingle modification. The effect of single mismatched base pairs was scanned along the full gap regiond emonstrating that the modificatione nables ar emarkable specificity of RNase Hc leavage. Ac ell-basedm odel systemw as used to demonstrate the potential of gapmer AONs containing the novel modification to mediate gene silencing.Supporting information and the ORCID identification number(s) for the author(s) of this article can be found under: https://doi.

Antisense oligonucleotides (ASOs) have the ability of binding to endogenous nucleic acid targets, thereby inhibiting the gene expression. Although ASOs have great potential in the treatment of many diseases, the search for favorable toxicity profiles and distribution has been challenging and consequently impeded the widespread use of ASOs as conventional medicine. One strategy that has been employed to optimize the delivery profile of ASOs, is the functionalization of ASOs with cationic amine groups, either by direct conjugation onto the sugar, nucleobase or internucleotide linkage. The introduction of these positively charged groups has improved properties like nuclease resistance, increased binding to the nucleic acid target and improved cell uptake for oligonucleotides (ONs) and ASOs. The modifications highlighted in this review are some of the most prevalent cationic amine groups which have been attached as single modifications onto ONs/ASOs. The review has been separated into three sections, nucleobase, sugar and backbone modifications, highlighting what impact the cationic amine groups have on the ONs/ASOs physiochemical and biological properties. Finally, a concluding section has been added, summarizing the important knowledge from the three chapters, and examining the future design for ASOs.

We analyzed the effect of modified nucleotides within gapmer antisense oligonucleotides on RNase H mediated gene silencing. Additionally, short hairpins were introduced into antisense oligonucleotides as structural motifs, and their influence on biological and physicochemical properties of pre-structured gapmers was investigated for the first time. The results indicate that two LNA residues in specified positions of the gap flanking regions are sufficient and favorable for efficient knock-down of the β-actin gene. Furthermore, the introduction of other modified nucleotides, i. e. glycyl-amino-LNAÀ T, 2'-O-propagyluridine, polyamine functionalized uridine, and UNA, in specified positions, also increases the inhibition of β-actin expression. Importantly, the presence of hairpins within the gapmers improves their silencing properties.