A Pyrene-Modified Serinol Nucleic Acid Nanostructure Converts the Chirality of Threoninol Nucleic Acids into Circularly Polarized Luminescence Signals

Kinetics of Strand Displacement Reaction with Acyclic Artificial Nucleic Acids

Toehold-mediated strand displacement (TMSD) reaction, one of the DNA nanotechnologies, has great potential as s biological programmable platform in the cellular environment. Various artificial nucleic acids have been developed to improve stability and affinity for biological applications. However, the lack of understanding of the kinetics of TMSD reaction among artificial nucleic acids has limited their applications. We herein systematically characterized the kinetics of TMSD reactions with acyclic xeno nucleic acids (XNAs): serinol nucleic acid (SNA), acyclic D-threoninol nucleic acid (D-aTNA), and acyclic L-threoninol nucleic acid (L-aTNA). We found that the strand displacement reactions by D-aTNA and by L-aTNA were highly dependent on temperature. D-aTNA and L-aTNA systems were orthogonal to each other, and chirality of the input can be switched by using SNA as an interface. We also applied TMSD reactions of XNAs to a seesaw gate amplification system which utilizes the orthogonality. This work will contribute to the developments of thermoresponsive and bioorthogonal nucleic acid circuits.

Template-Directed Incorporation of Functional Molecules into DNA

We report a versatile method for the incorporation of functional molecules into oligonucleotides carrying reactive groups by using a template-directed postsynthetic approach in the solution phase. For this purpose, we prepared oligonucleotides carrying an amino group on the backbone by using an acylic threoninol scaffold. The resulting oligonucleotides could be used to introduce almost any molecule carrying aldehyde, which can be, among other things, a metal-binding ligand or a fluorophore. In our study, we incorporated aldehyde-bearing phenanthroline, a metal-binding ligand, into oligonucleotides by template-directed reversible conjugation. We observed that the use of an abasic sugar site instead of a natural nucleobase in the template strand increased the yield of conjugation and induced selective incorporation of the phenanthroline. This method could lead progress in the development of probes for the recognition of abasic regions in duplex DNA. Moreover, template-directed formation of metal ligand-oligonucleotide conjugates might have potential applications in hybrid biocatalysis for enantioselective transformations.

Tunable Excimer Circularly Polarized Luminescence in Isohexide Derivatives from Renewable Resources

Organic compounds showing circularly polarized luminescence (CPL) are at the forefront of novel applications and technologies. Here we show the synthesis and chiroptical properties of pyrene and perylene derivatives of inexpensive chiral scaffolds: isomannide and isosorbide. Low‐intensity ECD spectra were obtained, suggesting the absence of chromophore interaction in the ground state, except in the case of isomannide bis‐perylenecarboxylate, whose ECD spectrum showed a positive exciton couplet. All isomannide derivatives, with the only exception of the one containing a pyrenecarboxylate and a perylenecarboxylate, exhibited excimer CPL spectra, whereas isosorbide derivatives did not show any CPL. Isomannide derivatives bearing two pyrenecarboxylate or two pyrenylacetate groups showed positive CPL emission with dissymmetry factors up to 10⁻², which depends on the conformational freedom of the appended units. The CPL sign, Stokes shift and order of magnitude of dissymmetry factor were reproduced by excited‐state calculations on a representative compound. Interestingly, the mixed derivative containing pyrenic units with different spacing from the isomannide scaffold showed an oppositely signed excimer band with respect to the homo‐substituted derivatives.

Xeno nucleic acids (XNAs) having non-ribose scaffolds with unique supramolecular properties

DNA and RNA have significance as a genetic materials, therapeutic potential, and supramolecular properties. Advances in nucleic acid chemistry have enabled large-scale synthesis of DNA and RNA oligonucleotides and oligomers...

Tuning exciton coupling of merocyanine nucleoside dimers by RNA, DNA and GNA double helix conformations

Exciton coupling between two or more chromophores in a specific environment is a key mechanism associated with color tuning and modulation of absorption energies. This concept is well exemplified by natural photosynthetic proteins, and can also be achieved in synthetic nucleic acid nanostructures. Here we report the coupling of barbituric acid merocyanine (BAM) nucleoside analogues and show that exciton coupling can be tuned by the double helix conformation. BAM is a nucleobase mimic that was incorporated in the phosphodiester backbone of RNA, DNA and GNA oligonucleotides. Duplexes with different backbone constitutions and geometries afforded different mutual dye arrangements, leading to distinct optical signatures due to competing modes of chromophore organization via electrostatic, dipolar, π–π‐stacking and hydrogen‐bonding interactions. The realized supramolecular motifs include hydrogen‐bonded BAM–adenine base pairs and antiparallel as well as rotationally stacked BAM dimer aggregates with distinct absorption, CD and fluorescence properties.