Duplex‐forming Oligonucleotide of Triazole‐linked RNA

Abstract

An oligonucleotide of triazole‐linked RNA (TLRNA) was synthesized by performing consecutive copper‐catalyzed azide‐alkyne cycloaddition reactions for elongation. The reaction conditions that had been optimized for the synthesis of 3‐mer TLRNA were found to be inappropriate for longer oligonucleotides, and the conditions were reoptimized for the solid‐phase synthesis of an 11‐mer TLRNA oligonucleotide. Duplex formation of the 11‐mer TLRNA oligonucleotide was examined with the complementary oligonucleotide of natural RNA to reveal the effects of the 2′‐OH groups on the duplex stability.

A Hitchhiker’s Guide to Click-Chemistry with Nucleic Acids

“…In contrast, an 11-mer backbonemodified RNA analogue ( TL RNA) provided less stable RNA:RNA duplexes when compared to the natural RNA control. 174 A detailed thermodynamic analysis of modified and unmodified duplexes revealed that TL RNA:RNA structure had a much lower association enthalpy (ΔH = −52 kcal mol −1 ) compared to the control (ΔH = −87 kcal mol −1 ). Structural studies associated this reduction in association enthalpy with triazole/2′-OH interactions which inevitably constrain the triazole orientations, causing a mismatch in the internucleoside distance between the two strands.…”

“…Noticeably, this interaction is not present in the case of TL DNA duplexes (no 2′-OH present). 174 Although consecutive Trz C modifications in TL DNA apparently stabilize the duplex structure, isolated triazole modifications reduce the stability of the dsDNA helix (average ΔT M per modification ∼ −4 °C). Computational analysis of 12 structuresdiffering in the position of the triazole relative to the duplex axisidentified a longer helical pitch which may arise from a lesser twist of the triazole compared to the phosphodiester linkage.…”

“…Structural studies associated this reduction in association enthalpy with triazole/2′-OH interactions which inevitably constrain the triazole orientations, causing a mismatch in the internucleoside distance between the two strands. Noticeably, this interaction is not present in the case of TL DNA duplexes (no 2′-OH present) …”

“…In this case, the lack of repulsive interactions of the triazole backbone with the anionic phosphate backbone was essential to enhance the stability of dsDNA, but the spacer length was also thought to aid duplex stabilization. In contrast, an 11-mer backbone-modified RNA analogue ( TL RNA) provided less stable RNA:RNA duplexes when compared to the natural RNA control . A detailed thermodynamic analysis of modified and unmodified duplexes revealed that TL RNA:RNA structure had a much lower association enthalpy (Δ H = −52 kcal mol –1 ) compared to the control (Δ H = −87 kcal mol –1 ).…”

Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine—Specific Cancer Targeting with Undetectable Toxicity

“…The site-specific incorporation of labels and reactive groups can be introduced through synthetic chemistry. Solid-phase synthesis is the widely used method to incorporate the labels/functional tools by incorporating modified nucleotides/terminal modifiers having various functional groups such as alkyne, − thiol, − aldehyde, − amine, − carboxylic acid, − and biotin ,− into the extending RNA site specifically. These functional groups can be modified with drug molecules or imaging markers with orthogonal functional groups with appropriate chemistries, and they include N -hydroxysuccinimide (NHS) chemistry, copper-catalyzed click reaction, copper-free click chemistry, thiol chemistry, periodate chemistry, imine formation, and 5′-phosphate activation. ,− Among them, the NHS, thiol as well as copper-catalyzed and copper-free click chemistries are widely used for both internal and terminal modifications, whereas 5′-phosphate activation and periodate chemistry are mainly employed for terminal modifications.…”