The effect of local structural disruption on the yield of photochemical ligation between anthracene-oligonucleotide conjugates

Reactions templated by nucleic acids: more ways to translate oligonucleotide-based instructions into emerging function

The programmability of oligonucleotide recognition offers an attractive platform to direct the assembly of reactive partners that can engage in chemical reactions. Recently, significant progress has been made in both the breadth of chemical transformations and in the functional output of the reaction. Herein we summarize these recent progresses and illustrate their applications to translate oligonucleotide instructions into functional materials and novel architectures (conductive polymers, nanopatterns, novel oligonucleotide junctions); into fluorescent or bioactive molecule using cellular RNA; to interrogate secondary structures or oligonucelic acids; or a synthetic oligomer.

(E)-4-(2-Hy-droxy-3-meth-oxy-benzyl-idene-amino)-6-methyl-3-sulfanyl-idene-3,4-dihydro-1,2,4-triazin-5(2H)-one

In the title mol-ecule, C(12)H(12)N(4)O(3)S, there is an intra-molecular O-H⋯N hydrogen bond. The dihedral angle between the benzene and triazine rings is 65.9 (3)°. In the crystal, N-H⋯S and O-H⋯N hydrogen bonds link the mol-ecules into chains along [010]. In addition, there are weak π-π stacking inter-actions between symmetry-related triazine rings with a centroid-centroid distance of 3.560 (3)°.

Oligonucleotide-templated reactions for sensing nucleic acids

Oligonucleotide-templated reactions are useful for applying nucleic acid sensing. Various chemistries for oligonucleotide-templated reaction have been reported so far. Major scientific interests are focused on the development of signal amplification systems and signal generation systems. We introduce the recent advances of oligonucleotide-templated reaction in consideration of the above two points.

DNA analysis based on the local structural disruption to the duplexes carrying a luminous lanthanide complex

The two DNA conjugates (split probes) carrying a metal chelator form an integrated luminous lanthanide (Ln(3+): Tb(3+) or Eu(3+)) complex on the complementary template DNA (target). The luminous property of this Ln(3+) complex has been used for DNA assay. The intensity of the luminescence was affected by the local structural disruption caused by one-base mispairing around the complex. Among the mispairings systematically introduced around the Ln(3+) center, vicinal mispairings to the center decreased the emission intensity more. This would be a novel nucleobase-discriminating principle, in which the split probes bind the target tightly, yet still retain sequence selectivity.

Eth-oxy-carbonyl-methyl 3-(4-chloro-benzyl-idene)dithio-carbazate

Mol-ecules of the title compound, C(12)H(13)ClN(2)O(2)S(2), are linked into centrosymmetric dimers by pairs of inter-molecular N-H⋯S hydrogen bonds. In the crystal structure, there are π-π stacking inter-actions between symmetry-related benzene rings with a centroid-centroid distance of 3.7305 (13) Å, a perpendicular distance between the planes of 3.2851 (9) Å and a slippage of 1.768 Å. The structure is further stabilized by weak inter-molecular C-H⋯O hydrogen bonds.

Reversible circularization of an anthracene-modified DNA conjugate through bimolecular triplex formation and its analytical application

We prepared an oligodeoxyribonucleotide conjugate (5-3ant(2)18) carrying two anthracenes, each of which was tethered to both ends of the conjugate through hexamethylene linker chains. The conjugate has a mirror repeat of two heptamer sequences, such that it forms a bimolecular triplex with the single stranded target, forming a two-fold U-shaped conformation. The conformation of the conjugate in its triplex structure could be frozen instantaneously by circularization through photodimerization of the anthracenes. Compared with the duplex formation of linear probes with relevant sequences, bimolecular triplex formation of 5-3ant(2)18 shows a unique feature in its target recognition; it binds the target tightly, yet still retains high sequence selectivity. Circularization of 5-3ant(2)18 by UV photoirradiation was verified as the probe reaction for a DNA assay. The probe reaction could be performed in a few seconds over a wide range of temperatures, at least between 0 and 25 °C. In addition, the reaction could be regarded as a reversible method for the preparation of circular DNA that shows higher affinity for the target.

4-Methyl-N-[(E)-4-methyl-1-(4-methyl-phenyl-sulfon-yl)-1,2-dihydropyridin-2-yl-idene]benzene-sulfonamide

The reaction of 2-(amino­meth­yl)pyridine and 4-toluene­sulfonyl chloride in CH₂Cl₂ at pH 8 led to the title compound, C₂₀H₂₀N₂O₄S₂. The aromatic rings are almost perpendicular to each other and the dihedral angles between the aromatic ring planes are 74.33 (9) (central pyridine versus benzene ring of the tosyl group bonded to the imine functionality), 73.77 (6) (pyridine versus benzene ring of the tosyl group bonded to pyridinic N atom) and 79.83 (9)° (benzene rings of tosyl groups). In the crystal structure, inter­molecular aromatic π–π stacking inter­actions [centroid–centroid separation = 3.6274 (14) Å] help to consolidate the packing.

1-(2-Pyrid-yl)-N,N'-dipyrimidin-2-ylmethane-diamine

In the title compound, C₁₄H₁₃N₇, inter­molecular N—H⋯N and C—H⋯N hydrogen bonds link the mol­ecules into infinite one-dimensional chains along (100). A C—H⋯π inter­action also occurs in the crystal.