A Quencher‐Free Linear Probe from Serinol Nucleic Acid with a Fluorescent Uracil Analogue

Abstract

With the goal of developing a quencher‐free probe composed of an artificial nucleic acid, the fluorescent nucleobase analogue 5‐(perylenylethynyl)uracil (PeU), which was incorporated into totally artificial serinol nucleic acid (SNA) as a substitute for thymine, has been synthesized. In the context of a 12‐mer duplex with RNA, these fluorophores reduce duplex stability slightly compared with that of an SNA without PeU modification; thus suggesting that structural distortion is not induced by the modification. If two PeUs were incorporated at separate positions in an SNA, the fluorescent emission at λ≈490 nm was clearly enhanced upon hybridization with complementary RNA. A quencher‐free SNA linear probe containing three PeUs, each separated by six nucleobases, has been designed. Detection of target RNA with high sensitivity and discrimination of a single‐base mismatch has also been demonstrated.

Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS)

“…12,13 The need to achieve more costeffective, faster analysis and higher single nucleotide resolution continues to drive technological developments. 14 Recent examples include amendments to existing technologies such as molecular beacons, 15,16 melting analysis, 17,18 environmentally sensitive uorescent nucleobases, [19][20][21][22][23][24] and strand displacement probes 25,26 or new technologies such as polymerase-amplied release of ATP (POLARA) 27 or graphene-based biosensors for real-time kinetic monitoring of hybridization. 28 The analysis of SNVs requires technologies with the highest nucleotide resolution to ascertain the polymorphism or variation.…”

Intrastrand backbone-nucleobase interactions stabilize unwound right-handed helical structures of heteroduplexes of L-aTNA/RNA and SNA/RNA

“…We recently discovered acyclic nucleic acids serinol nucleic acid (SNA) and L-threoninol nucleic acid (L-aTNA) can form stable duplexes with RNA in a sequence-specific manner [33][34][35] . Since they are structurally simple, readily synthesized, excellent water solubility, and high nucleases resistance, various applications have been realized based on hybridization with RNA such as a high-sensitive molecular beacon and nucleic acid-based drug candidates, including siRNAs, anti-miRNA oligonucleotides, and exon-skipping type antisense oligonucleotides [36][37][38][39][40][41][42][43] . However, how SNA and L-aTNA hybridize with natural nucleic acid have remained unknown.…”

Acyclic Nucleic Acids with Phosphodiester Linkages—Synthesis, Properties and Potential Applications

“…SNA constructs are also used as analytical tools in biology and biochemistry. In a similar approach to the DNA probe using aTNA-perylene units [66], a fluorescent 5-(perylenylethynyl)uracil unit ( Pe U) was incorporated into SNA molecules as a substitute for thymine [74]. In the single-stranded state, interactions between the perylenes resulted in self-quenching of the fluorophores.…”