Emissive RNA Alphabet

Abstract

A fluorescent ribonucleoside alphabet, comprised of highly emissive purine (thA, thG) and pyrimidine (thU, thC) analogs, all derived from thieno[3,4-d]pyrimidine as the heterocyclic nucleus, is described. Structural and biophysical analyses demonstrate that the emissive analogs are faithful isomorphic nucleoside surrogates. Photophysical analysis establishes that the nucleosides offer highly desirable qualities, including visible emission, high quantum yield and responsiveness to environmental perturbations, traits entirely lacking in their native counterparts.

Density Functional Theoretical Study on the Acid Dissociation Constant of an Emissive Analogue of Guanine

“…[1][2][3] Recently, a fluorescent guanine analogue, 2-aminothieno [3,4-d]pyrimidine ( th G), was developed. 4 One of the essential criteria of a successful analogue is to minimize the structural and functional disturbances when replacing any native residue. Along with many structural, photochemical, and biophysical characteristics, the acid dissociation constant, pK a , would be an important parameter to be monitored, particularly when an aqueous solution is used in the assay because pKa value is related to the stability of nucleic base, Watson-Crick base pairing, proton migration, and the mispair formation during the DNA replication.…”

La première étape de la transmission d’un caractère épigénétique suivie par fluorescence

“…Pour atteindre cet objectif, nous avons utilisé deux analogues fluorescents de nucléosides très innovants, la 2-thiényl-3-hydroxychromone (3HCnt) capable de substituer toutes les nucléobases de l'ADN [7] et la thiénoguanosine (thG) qui remplace parfaitement la guanine [8,9]. En incorporant la 3HCnt ou la thG à des positions choisies d'un ADN double brin hémi-méthylé ou non méthylé, nous avons montré par spectroscopie de fluorescence qu'il était possible de suivre de manière sensible et fidèle le basculement des cytosines méthylées, induit par le domaine SRA de la protéine UHRF1 (Figure 2).…”

Synthesis, Photophysical Properties, and Enzymatic Incorporation of an Emissive Thymidine Analogue

“…Recently, Tor and coworkers developed isomorphic fluorescent RNA nucleosides derived from thieno [3,4-d]-pyrimidine and reported that the nucleosides have important photophysical properties including visible light emission and a high quantum yield. 22 In addition, they have showed the usefulness of the nucleoside analogues in various applications. 2329 We have taken note of the potential of isomorphic nucleoside analogues based on a thieno [3,4-d]pyrimidine core and exploited the emissive DNA nucleoside analogues.…”

“…22,37,38 The fluorescent base This glycosylation reaction yielded a mixture of β-and α-anomer at a β:α ratio of 3:2. After the benzoyl protecting groups of the deoxyribonucleoside 4 were removed in aqueous ammonia, the 5¤-hydroxy group of the nucleoside analogue 5 was protected with dimethoxytrityl ether (DMTr), and the desired β-anomer was isolated in 27% yield by column chromatography.…”

“…In solvents with lower polarity, the emission intensity of th dT decreases and the emission maxima are shifted toward a shorter wavelength (see SI). 22 To evaluate oligonucleotides containing the isomorphic dT analogue, the phosphoramidite of th dT was incorporated into the center of 18-mer DNA oligonucleotides of 5¤-(CGTCCGTCXTACGCACGC)-3¤ by automated solidphase synthesis, where X = th dT. The complementary strands of ODN1 containing matched or mismatched bases with th dT, ODN37, and corresponding natural DNA duplexes with thymine, ODN2, were also prepared.…”