Assessing Oligonucleotide Binding to Double-Stranded DNA

  • Negin MozafariEmail author
  • Tea UmekEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2036)


Sequence-specific targeting of double-stranded DNA (dsDNA) using synthetic oligonucleotides (ONs) has been under investigation in different therapeutic approaches. Several methods can be used to evaluate ONs effect and binding capacity to their target sequence. Here we describe some of the methods, which have been frequently used for assessing ONs binding to dsDNA.

Key words

Antigene oligonucleotides EMSA S1 nuclease assay Restriction inhibition assay BQQ-OP cleavage CAA chemical probing 



This work was supported by the European Union’s Horizon 2020 under the Marie Skłodowska-Curie grant agreement No 721613, the Swedish Research Council, the Stockholm County Council, Hjärnfonden, and Vinnova/SweLife.


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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Laboratory Medicine, Center for Advanced Therapies, Karolinska InstitutetKarolinska University Hospital HuddingeStockholmSweden

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