Protocol

DNA Nanotechnology

Volume 749 of the series Methods in Molecular Biology pp 79-92

Date:

Control of Helical Handedness in DNA and PNA Nanostructures

  • Roberto Corradini
  • , Tullia Tedeschi
  • , Stefano Sforza
  • , Mark M. Green
  • , Rosangela MarchelliAffiliated withDipartimento di Chimica Organica e Industriale, Univeristà di Parma Email author 

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Abstract

Helical handedness and the twist and tilt parameters of the base pairs in duplex DNA can be affected by base sequence variation and change in environmental conditions as occurs in the transformation between right-handed B-DNA and left-handed Z-DNA. For duplexes of DNA with oligonucleotide analogs such as peptide nucleic acids (PNAs), less is known about the effects on structure such as the base pair twist and tilt parameters and handedness. However, in PNA:PNA duplexes, the absence of chiral information determining helical handedness allows the relationship between preferred helical handedness and structural design to be manipulated and, therefore, better understood. In this chapter, we report a protocol for switching between B- and Z-DNA:DNA duplexes, and the experimental procedures for obtaining right- or left-handed PNA:PNA duplexes.

Key words

Helical handedness Z-DNA B-DNA Chiral PNAs PNA:PNA duplex