Universal Base Analogues and their Applications to Biotechnology

C2′-Pyrene-Functionalized Triazole-Linked DNA: Universal DNA/RNA Hybridization Probes

“…Development of universal hybridization probes has been a longstanding goal due to their potential as degenerate PCR primers and microarray probes when the identity of one or more nucleotides in a target sequence is unknown. 28–31 The classic approach toward this end has been the use of ONs containing ‘universal bases’, 32 which fall into two categories: a) aromatic base analogs without hydrogen-bonding capabilities such as 3-nitropyrrole, 29 5-nitroindole, 33 isocarbostyril 34 or pyrene, 13,35–38 and b) hydrogen-bonding universal bases based on inosine 39–41 or other purine moieties. 42,43 However, development of truly ‘universal’ hybridization probes that do not compromise duplex thermostability has generally proven challenging.…”

“…Here we demonstrate that ONs modified with C2′-pyrene-functionalized triazole-linked monomers are robust universal DNA/RNA hybridization probes; that is, they display virtually identical DNA/RNA target affinity regardless of the nucleotide opposite of the modification site. Development of universal hybridization probes has been a longstanding goal due to their potential as degenerate PCR primers and microarray probes when the identity of one or more nucleotides in a target sequence is unknown. − The classic approach toward this end has been the use of ONs containing “universal bases”, which fall into two categories: (a) aromatic base analogues without hydrogen-bonding capabilities such as 3-nitropyrrole, 5-nitroindole, isocarbostyril, or pyrene; ,− and (b) hydrogen-bonding universal bases based on inosine − or other purine moieties. , However, development of truly “universal” hybridization probes that do not compromise duplex thermostability has proven challenging …”

Computational Aspects of DNA Sequencing by Hybridization – a Survey

“…The degenerate bases are complementary to more than one type of nucleotide but not to all of them. Such artificial nucleotides have already been developed, but using them in the SBH methodology is uncommon [43,44]. Such an approach has been proposed and analyzed in a different scientific papers, for example in [45] where different chip idea has been proposed and its properties analyzed.…”

Multicomponent reactions in nucleoside chemistry

“…Moreover, several novel nucleoside analogs (including those embedded in versatile conjugate or pronucleotide scaffolds) are under clinical or preclinical trials [ 1 ]. Recent studies have also revealed a potential of nucleoside analogs as radiopharmaceuticals [ 2 – 6 ], antibiotics [ 7 – 9 ], anti-infective agents [ 10 – 12 ], or molecular probes [ 13 – 14 ]. Taking into account the importance of nucleoside analogs in medicine and biotechnology, there is a considerable interest in the development of simple and efficient synthesis of these compounds.…”