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 ( F orced I ntercalation of T hiazole 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 purpose to facilitate the screening for base surrogates that fluoresce upon hybridization. An Fmoc/Aloc‐protected submonomer allowed the application of commonly used Fmoc‐based solid‐phase synthesis protocols while removal of the fully orthogonal Aloc group enabled the on‐resin introduction of base surrogates after the linear chain assembly had been completed. The divergent solid‐phase synthesis strategy is automatable, gives overall yields matching those of linear solid‐phase synthesis and, most importantly, provides rapid access to any kind of base‐modified PNA. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)