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Formation and Characterization of PNA-Containing Heteroquadruplexes

  • Bruce A. Armitage
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1050)

Abstract

The guanine quadruplex is a secondary structure formed by DNA and RNA that has been implicated in regulation of gene expression and maintenance of genome stability. Guanine-rich PNA oligomers can invade DNA or RNA quadruplex targets to form heteroquadruplex structures. Affinities in the low nanomolar range are routinely observed, making PNAs among the tightest binding of all quadruplex-targeted agents. Although inherently more promiscuous than heteroduplex formation based on Watson–Crick pairing, selectivity of heteroquadruplex formation can be improved through rational design of the sequence and backbone structure of the PNA. This chapter presents design rules and methods for characterizing PNA–DNA/RNA heteroquadruplexes.

Key words

Homologous hybridization Heteroquadruplex formation Backbone-modified PNA UV melting curves Surface plasmon resonance 

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Copyright information

© Springer Science+Business Media, New York 2014

Authors and Affiliations

  • Bruce A. Armitage
    • 1
  1. 1.Department of Chemistry, Center for Nucleic Acids Science and TechnologyCarnegie Mellon UniversityPittsburghUSA

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