Synthesis of 5-[3,6-di(pyridin-2-yl)pyridazine-4-yl]-2′-deoxyuridine-5′-O-triphosphate—a potential probe for fluorescence detection and imaging DNA

[4+2] and [2+4] cycloaddition reactions on single- and double-stranded DNA: a dual-reactive nucleoside

Here we report dual reactivity of diene-modified duplex DNA containing 5-(1,3-butadienyl)-2'-deoxyuridine “BDdU”. Regular-electron demand [4+2] cycloaddition proceeded upon addition of a maleimide, whereas inversed-electron demand [2+4] cycloaddition occurred upon addition...

Crystal structure, Hirshfeld surface analysis and inter-action energy and DFT studies of methyl 4-[3,6-bis-(pyridin-2-yl)pyridazin-4-yl]benzoate

The title com-pound, C22H16N4O2, contains two pyridine rings and one meth-oxy-carbonyl-phenyl group attached to a pyridazine ring which deviates very slightly from planarity. In the crystal, ribbons consisting of inversion-related chains of mol-ecules extending along the a-axis direction are formed by C-HMthy⋯OCarbx (Mthy = methyl and Carbx = carboxyl-ate) hydrogen bonds. The ribbons are connected into layers parallel to the bc plane by C-HBnz⋯π(ring) (Bnz = benzene) inter-actions. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (39.7%), H⋯C/C⋯H (27.5%), H⋯N/N⋯H (15.5%) and O⋯H/H⋯O (11.1%) inter-actions. Hydrogen-bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. Computational chemistry indicates that in the crystal, C-HMthy⋯OCarbx hydrogen-bond energies are 62.0 and 34.3 kJ mol-1, respectively. Density functional theory (DFT) optimized structures at the B3LYP/6-311G(d,p) level are com-pared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap.

Crystal structure, Hirshfeld surface analysis and inter-action energy and DFT studies of 4-[(prop-2-en-1-yl-oxy)meth-yl]-3,6-bis-(pyridin-2-yl)pyridazine

The title compound, C18H16N4O, consists of a 3,6-bis-(pyridin-2-yl)pyridazine moiety linked to a 4-[(prop-2-en-1-yl-oxy)meth-yl] group. The pyridine-2-yl rings are oriented at a dihedral angle of 17.34 (4)° and are rotated slightly out of the plane of the pyridazine ring. In the crystal, C-HPyrd⋯NPyrdz (Pyrd = pyridine and Pyrdz = pyridazine) hydrogen bonds and C-HPrp-oxy⋯π (Prp-oxy = prop-2-en-1-yl-oxy) inter-actions link the mol-ecules, forming deeply corrugated layers approximately parallel to the bc plane and stacked along the a-axis direction. Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H⋯H (48.5%), H⋯C/C⋯H (26.0%) and H⋯N/N⋯H (17.1%) contacts, hydrogen bonding and van der Waals inter-actions being the dominant inter-actions in the crystal packing. Computational chemistry indicates that in the crystal, the C-HPyrd⋯NPyrdz hydrogen-bond energy is 64.3 kJ mol-1. Density functional theory (DFT) optimized structures at the B3LYP/6-311 G(d,p) level are compared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap.

Crystal structure, Hirshfeld surface analysis and corrosion inhibition study of 3,6-bis-(pyridin-2-yl)-4-{[(3aS,5S,5aR,8aR,8bS)-2,2,7,7-tetra-methyl-tetra-hydro-5H-bis-[1,3]dioxolo[4,5-b:4',5'-d]pyran-5-yl)meth-oxy]meth-yl}pyridazine monohydrate

In the title compound, C27H30N4O6·H2O, the two dioxolo rings are in envelope conformations, while the pyran ring is in a twisted-boat conformation. The pyradizine ring is oriented at dihedral angles of 9.23 (6) and 12.98 (9)° with respect to the pyridine rings, while the dihedral angle between the two pyridine rings is 13.45 (10)°. In the crystal, O-Hwater⋯Opyran, O-Hwater⋯Ometh-oxy-meth-yl and O-Hwater⋯Npyridazine hydrogen bonds link the mol-ecules into chains along [010]. In addition, weak C-Hdioxolo⋯Odioxolo hydrogen bonds and a weak C-Hmeth-oxy-meth-yl⋯π inter-action complete the three-dimensional structure. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (55.7%), H⋯C/C⋯H (14.6%), H⋯O/O⋯H (14.5%) and H⋯N/N⋯H (9.6%) inter-actions. Hydrogen-bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. Electrochemical measurements are also reported.

Bioorthogonal Metabolic DNA Labelling using Vinyl Thioether-Modified Thymidine and o-Quinolinone Quinone Methide

Bioorthogonal metabolic DNA labeling with fluorochromes is a powerful strategy to visualize DNA molecules and their functions. Here, we report the development of a new DNA metabolic labeling strategy enabled by the catalyst-free bioorthogonal ligation using vinyl thioether modified thymidine and o-quinolinone quinone methide. With the newly designed vinyl thioether-modified thymidine (VTdT), we added labeling tags on cellular DNA, which could further be linked to fluorochromes in cells. Therefore, we successfully visualized the DNA localization within cells as well as single DNA molecules without other staining reagents. In addition, we further characterized this bioorthogonal DNA metabolic labeling using DNase I digestion, MS characterization of VTdT as well as VTdT-oQQF conjugate in cell nuclei or mitochondria. This technique provides a powerful strategy to study DNA in cells, which paves the way to achieve future spatiotemporal deciphering of DNA synthesis and functions.

Chemoselective Modification of Vinyl DNA by Triazolinediones

A new method for the post-synthetic modification of nucleic acids was developed that involves mixing a phenyl triazolinedione (PTAD) derivative with DNA containing a vinyl nucleobase. The resulting reactions proceeded through step-wise mechanisms, giving either a formal [4+2] cycloaddition product, or, depending on the context of nucleobase, PTAD addition along with solvent trapping to give a secondary alcohol in water. Catalyst-free addition between PTAD and the terminal alkene of 5-vinyl-2'-deoxyuridine (VdU) was exceptionally fast, with a second-order rate constant of 2×10³  m^-1  s^-1 . PTAD derivatives selectively reacted with VdU-containing oligonucleotides in a conformation-selective manner, with higher yields observed for G-quadruplex versus duplex DNA. These results demonstrate a new strategy for copper-free bioconjugation of DNA that can potentially be used to probe nucleic acid conformations in cells.

Vinyluridine as a Versatile Chemoselective Handle for the Post-transcriptional Chemical Functionalization of RNA

The development of modular and efficient methods to functionalize RNA with biophysical probes is very important in advancing the understanding of the structural and functional relevance of RNA in various cellular events. Herein, we demonstrate a two-step bioorthogonal chemical functionalization approach for the conjugation of multiple probes onto RNA transcripts using a 5-vinyl-modified uridine nucleotide analog (VUTP). VUTP, containing a structurally noninvasive and versatile chemoselective handle, was efficiently incorporated into RNA transcripts by in vitro transcription reactions. Furthermore, we show for the first time the use of a palladium-mediated oxidative Heck reaction in functionalizing RNA with fluorogenic probes by reacting vinyl-labeled RNA transcripts with appropriate boronic acid substrates. The vinyl label also permitted the post-transcriptional functionalization of RNA by a reagent-free inverse electron demand Diels-Alder (IEDDA) reaction in the presence of tetrazine substrates. Collectively, our results demonstrate that the incorporation of VUTP provides newer possibilities for the modular functionalization of RNA with variety of reporters.

Synthesis of 1-(β-D-Galactopyranosyl)Thymine-6'-O-Triphosphate - A Potential Probe to Generate Reactive Dialdehyde for DNA-Enzyme Cross-Linking

Concise, facile, and efficient synthesis of 1-(β-D-galactopyranosyl)thymine-6'-O-triphosphate, a potential probe that can generate reactive dialdehyde for DNA-enzyme cross-linking applications, was described starting from O,O'-bis(trimethylsilyl)thymine. Stannic chloride promoted glycosylation of 1,2,3,4,6-penta-O-acetyl-α-D-galactopyranose with O,O'-bis(trimethylsilyl)thymine, resulting in the formation of 1-(2,3,4,6-O-tetraacetyl-β-D-galactopyranosyl)thymine in 91% yield. Acetyl deprotection using methanolic ammonia afforded 1-(β-D-galactopyranosyl)thymine in 98% yield. The modified one-pot methodology was used to convert 1-(β-D-galactopyranosyl)thymine into 1-(β-D-galactopyranosyl)thymine-6'-O-triphosphate in 72% yield, which involves the formation of 1-(β-D-galactopyranosyl)thymine dichlorophosphoridate using POCl3 as the reagent at the monophosphorylation step followed by reaction with tributylammonium pyrophosphate and hydrolysis of resulting cyclic intermediate.