Moreno, Pedro M D3; Geny, Sylvain3; Pabon, Y Vladimir3; Bergquist, Helen3; Zaghloul, Eman M3; Rocha, Cristina S J3; Oprea, Iulian I3; Bestas, Burcu3; Andaloussi, Samir El3; Jørgensen, Per T4; Pedersen, Erik B4; Lundin, Karin E3; Zain, Rula3; Wengel, Jesper4; Smith, C I Edvard3
1 Department of Physics, Chemistry and Pharmacy, Faculty of Science, SDU2 NAC, Institut for Fysik og Kemi, Department of Physics, Chemistry and Pharmacy, Faculty of Science, SDU3 unknown4 Department of Physics, Chemistry and Pharmacy, Faculty of Science, SDU
In spite of the many developments in synthetic oligonucleotide (ON) chemistry and design, invasion into double-stranded DNA (DSI) under physiological salt and pH conditions remains a challenge. In this work, we provide a new ON tool based on locked nucleic acids (LNAs), designed for strand invasion into duplex DNA (DSI). We thus report on the development of a clamp type of LNA ON-bisLNA-with capacity to bind and invade into supercoiled double-stranded DNA. The bisLNA links a triplex-forming, Hoogsteen-binding, targeting arm with a strand-invading Watson-Crick binding arm. Optimization was carried out by varying the number and location of LNA nucleotides and the length of the triplex-forming versus strand-invading arms. Single-strand regions in target duplex DNA were mapped using chemical probing. By combining design and increase in LNA content, it was possible to achieve a 100-fold increase in potency with 30% DSI at 450 nM using a bisLNA to plasmid ratio of only 21:1. Although this first conceptual report does not address the utility of bisLNA for the targeting of DNA in a chromosomal context, it shows bisLNA as a promising candidate for interfering also with cellular genes.
Nucleic Acids Research, 2013, Vol 41, Issue 5, p. 3257-3273