Abstract:
: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.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Moreno PM,Geny S,Pabon YV,Bergquist H,Zaghloul EM,Rocha CS,Oprea II,Bestas B,Andaloussi SE,Jørgensen PT,Pedersen EB,Lundin KE,Zain R,Wengel J,Smith CIdoi
10.1093/nar/gkt007subject
Has Abstractpub_date
2013-03-01 00:00:00pages
3257-73issue
5eissn
0305-1048issn
1362-4962pii
gkt007journal_volume
41pub_type
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