Triazole linking for preparation of a next-generation sequencing library from single-stranded DNA.

Next-generation sequencing of single-stranded DNA (ssDNA) is attracting increased attention from a wide variety of research fields. Accordingly, various methods are actively being tested for the efficient adaptor-tagging of ssDNA. We conceived a novel chemo-enzymatic method termed terminal deoxynucleotidyl transferase (TdT)-assisted, copper-catalyzed azide-alkyne cycloaddition (CuAAC)-mediated ssDNA ligation (TCS ligation). In this method, TdT is used to incorporate a single 3'-azide-modified dideoxyribonucleotide onto the 3'-end of target ssDNA, followed by CuAAC-mediated click ligation of the azide-incorporated 3'-end to a 5'-ethynylated synthetic adaptor. This report presents the first proof-of-principle application of TCS ligation with its use in the preparation of a next-generation sequencing library.

Narrowing Segments of Helical Carbon Nanotubes with Curved Aromatic Panels.

Rigid molecular cylinders with a 1 nm diameter were synthesized by assembling arylene panels with Pt-mediated macrocylization. Chrysenylene panels that previously participated in tetrameric macrocyclization were contorted by the addition of two benzo groups on the sides to form dibenzochrysenylene, which allowed for a reduction in the numbers of participating panels to three. Consequently, narrowed cyclochrysenylene congeners were obtained. The narrowed chiral cylinders possessed width-dependent chiroptical properties. The magnetic transition dipole moment was dictated by the radius of a ring-current-like circle that was formed by local electric transition dipole moments on the cylinder.

Chimeric RNA Oligonucleotides Incorporating Triazole-Linked Trinucleotides: Synthesis and Function as mRNA in Cell-Free Translation Reactions.

A method for the synthesis of chimeric oligonucleotides was developed to incorporate purine nucleobases and multiple triazole linkers in natural, phosphate-linked structures of RNA. A solution-phase synthesis method for triazole-linked RNA oligomers via copper-catalyzed azide-alkyne cycloaddition reaction was optimized and tolerated purine nucleobases and protecting groups for further transformations. Three TLRNA trinucleotides with 5'-protected hydroxy and 3'-phosphoramidite groups were prepared, and one congener with a representative sequence was subjected to automated, solid-phase phosphoramidite synthesis. The synthesis allowed the efficient preparation of 13-mer chimeric RNA oligonucleotides with two triazole linkers, ten phosphate linkers and purine/pyrimidine nucleobases. The chimeric oligonucleotide was found applicable to a cell-free translation system as mRNA and provided the genetic code for dipeptide production.

A hybrid molecular peapod of sp2- and sp3-nanocarbons enabling ultrafast terahertz rotations.

The internal hollow space of carbon nanotubes provides a unique nanometre-sized space to capture various molecular entities. The inner space circumfused by sp2-carbon networks can also encapsulate diamondoid molecules to afford sp2/sp3-hybrid nanocarbon peapods that have recently emerged as unique nanostructures. In this study, the sp2/sp3-hybrid peapods have been mimicked by adopting a cylindrical molecule and the smallest diamondoid, i.e., adamantane, to demonstrate the existence of ultrafast rotational motion. The solid-state rotational frequency is measured by NMR spectroscopy to record 1.06 THz that is, to the best of our knowledge, the largest value recorded for solid-state rotations of molecules. Theoretical calculations reveal that multivalent CH-π hydrogen bonds anchored the diamondoid guest on the π-wall of the cylindrical host. The weak hydrogen bonds are prone not only to cleave but also to regenerate at the interfaces, which give freedom to the guest for ultrafast isotropic rotations in the inertial regime.

Enhanced yet Inverted Effects of π-Extension in Self-Assembly of Curved π-Systems with Helicity.

A sextuple helix molecule possessing four cove regions of helicene and two axes of biaryls was synthesized. The entropy-driven self-assembly in solution was determined by concentration- and temperature-dependent NMR spectra, which also revealed unique dynamics of isomerization involving structural changes at the cove regions. Unexpectedly, the assembly retarded the isomerization in solution, and the sextuple helix structure was rigidified.

Chimeric RNA Oligonucleotides with Triazole and Phosphate Linkages: Synthesis and RNA Interference.

Chimeric RNA oligonucleotides with an artificial triazole linker were synthesized using solution-phase click chemistry and solid-phase automated synthesis. Scalable synthesis methods for jointing units for the chimeric structure have been developed, and after click-coupling of the jointing units with triazole linkers, a series of chimeric oligonucleotides was prepared by utilizing the well-established phosphoramidite method for the elongation. The series of chimeric 21-mer oligonucleotides that possessed the triazole linker at different strands and positions allowed for a screening study of the RNA interference to clarify the preference of the triazole modifications in small-interfering RNA molecules.