Divergent and Linear Solid‐Phase Synthesis of PNA Containing Thiazole Orange as Artificial Base

Abstract

Fluorescent nucleobase surrogates provide nucleic acids with interesting properties. We have recently introduced thiazole orange as base surrogate into PNA and found that the so-called FIT (Forced Intercalation of Thiazole orange) PNA probes signal hybridization by enhancements of fluorescence. Common approaches of modifying nucleobases or introducing nucleobase surrogates draw upon the usage of monomer building blocks that have been synthesized in solution phase. The need to prefabricate a base-modified building block can hold up progress if several base modifications or base surrogates are to be evaluated. Herein, a method for divergent solid-phase synthesis is presented that serves the

Postsynthetic modification of DNA via threoninol on a solid support by means of allylic protection

“…Here, we used thiazole orange (TO: see Scheme 2) as a target because TO, which is an effective fluorophore in detecting oligonucleotides sequence specifically, 8,9 is rather difficult to convert to a phosphoramidite monomer. Since TO hardly dissolved in DMF, pyridinium para-toluenesulfonate (PPTS) was added to the reaction mixture as an acidic additive.…”

“…Since TO hardly dissolved in DMF, pyridinium para-toluenesulfonate (PPTS) was added to the reaction mixture as an acidic additive. 8 After the coupling reaction, the DNA was cleaved from the support to evaluate the coupling efficiency by HPLC analysis. Among the coupling reagents we tried, PyBOP most efficiently accelerated the coupling compared with other reagents.…”

“…7 Recently, Seitz et al reported on the solid-phase modification of PNA with Alloc protection. 8 Here, we report a facile and versatile method to introduce functional molecules into oligonucleotides through amide bonds on a solid phase via an Alloc-protected phosphoramidite sub-monomer as illustrated in Schemes 1 and 2: the submonomer 3 is incorporated into DNA through the automated DNA synthesizer. The obtained controlled pore glass (CPG) support anchoring fully protected DNA is treated with palladium(0) to remove the Alloc group selectively, followed by the coupling with a functional molecule through an amide bond.…”

A Fmoc-based submonomeric strategy for the solid phase synthesis of optically pure chiral PNAs

“…Since the conjugation of PNAs with fluorophores and other labelling molecules, which are often labile at strong acidic conditions, is becoming of great interest, the use of a milder chemistry, such as in Fmocbased strategies, should be advisable. Recently, Seitz and co-workers 14 Hence, in this Letter we propose for the first time a new Fmocbased submonomeric strategy for the synthesis of optically pure chiral PNAs. We report the design and the synthesis of a new Fmoc-compatible submonomeric unit carrying a lysine side chain at the carbon 2.…”

Fluoreszenzbildgebung der mRNA von Influenza‐H1N1 in lebenden infizierten Zellen durch FIT‐PNA mit einem einzigen Chromophor

“…Die Zugänglichkeit des Zielsegments für Hybridisierungen, die durch die Sekundärstruktur der mRNA und Bindung von Proteinen erschwert werden kann, wurde bereits durch Zhang und Mitarbeiter demonstriert. [9] Die rasche Synthese [10] und Analyse von acht verschiedenen PNA-Oligomeren ergab die FIT-Sonde 1 a als das am besten geeignete System für unsere Untersuchung (siehe Hintergrundinformationen). 1 a lieferte Schema 1.…”