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Development of bis-locked nucleic acid (bisLNA) oligonucleotides for efficient invasion of supercoiled duplex DNA

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Authors:
  • Moreno, Pedro M D ;
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    unknown
  • Geny, Sylvain ;
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    unknown
  • Pabon, Y Vladimir ;
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    unknown
  • Bergquist, Helen ;
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    unknown
  • Zaghloul, Eman M ;
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    unknown
  • Rocha, Cristina S J ;
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    unknown
  • Oprea, Iulian I ;
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    unknown
  • Bestas, Burcu ;
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    unknown
  • Andaloussi, Samir El ;
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    unknown
  • Jørgensen, Per T ;
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    Orcid logo0000-0003-3932-5921
    Department of Physics, Chemistry and Pharmacy, Faculty of Science, SDU
  • Pedersen, Erik B ;
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    Orcid logo0000-0002-7917-2379
    Department of Physics, Chemistry and Pharmacy, Faculty of Science, SDU
  • Lundin, Karin E ;
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    unknown
  • Zain, Rula ;
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    unknown
  • Wengel, Jesper ;
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    Orcid logo0000-0001-9835-1009
    Department of Physics, Chemistry and Pharmacy, Faculty of Science, SDU
  • Smith, C I Edvard
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    unknown
DOI:
10.1093/nar/gkt007
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.
Type:
Journal article
Language:
English
Published in:
Nucleic Acids Research, 2013, Vol 41, Issue 5, p. 3257-3273
Main Research Area:
Science/technology
Publication Status:
Published
Review type:
Peer Review
Submission year:
2013
Scientific Level:
Scientific
ID:
239778956

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