| Abstract
| - Oligonucleotides (ONs) modified with a 2′-N-(pyren-1-yl)acetyl-2′-amino-α-L-LNA thymine monomer Y flanked on the 3′-side by an abasic site Φ (i.e., YΦ-unit) exhibit unprecedented increases in thermal affinity (ΔTm values) toward target strands containing abasic sites (ΔTm per YΦ unit >+33.0 °C in 9-mer duplexes relative to unmodified ONs). Biophysical studies along with force field calculations suggest that the conformationally locked 2-oxo-5-azabicyclo[2.2.1]heptane skeleton of monomer Y, in concert with the short rigid acetyl linker, efficiently forces the thymine and pyrene moieties to adopt an interplanar distance of ∼3.4 Å. This precisely positions the pyrene moiety in the duplex core void formed by abasic sites (Φ:Φ pair) for optimal π−π overlap. Duplexes with multiple YΦ:AΦ units separated by one base pair are tolerated extraordinarily well, as exemplified by a 13-mer duplex containing four separated YΦ:AΦ units (8 abasic sites distributed over 13 “base pairs”), which exhibit a thermal denaturation temperature of 60.5 °C. The YΦ probes display up to 16-fold increases in fluorescence intensity at 380 nm upon hybridization with abasic target strands, whereby self-assembly of these complex architectures can be easily monitored. This study underlines the potential of N2′-functionalized 2′-amino-α-L-LNA as building blocks in nucleic acid based diagnostics and nanomaterial engineering.
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