Skip to main content
SpringerLink
Log in

Control of Helical Handedness in DNA and PNA Nanostructures

  • Protocol
  • First Online:
DNA Nanotechnology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 749))

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. (a) Hembury, G. A., Borovkov, V.V., and Inoue, Y. (2008) Chirality-Sensing Supramole­cular Systems Chem Rev 108, 1–73. (b) Green, M. M. (2000) A model for how polymers amplify chirality. In Circular Dichroism (2nd Edition) Berova, N., Nakanishi, K., Woody, R.W. Eds Wiley-VCH, New York, 491–520.

    Google Scholar 

  2. (a) Green, M.M., Peterson, N. C., Sato, T., Teramoto, A., Cook, R., and Lifson, S. (1995) A helical polymer with a cooperative response to chiral information Science 268, 1860–6. (b) Green, M.M., Park, J.-W., Sato, T., Teramoto, A., Lifson, S., Selinger, R.L.B., and Selinger J.V. (1999). The macromolecular route to chiral amplification Angew Chem, Int Ed 38, 3139–54.

    Google Scholar 

  3. Tomar S., Green M. M., and Day L. A. (2007) DNA-Protein Interactions as the Source of Large Length Scale Chirality Evident in the Liquid Crystal Behavior of Filamentous Bacteriophages J Amer Chem Soc 129, 3367–75.

    Article  CAS  Google Scholar 

  4. Hecht S.M. Ed. (1996) Bioorganic Chemistry-Nucleic Acids. Oxford University Press, Oxford-UK.

    Google Scholar 

  5. a) Seeman, N.C. (2007) An Overview of Structural DNA Nanotechnology Mol Biotechnol 37, 246–57. b) Brucale M., Zuccheri G., and Samorì B. (2006) Mastering the complexity of DNA nanostructures Trends in Biotech 24, 3427–34.

    Google Scholar 

  6. Mao, C.D., Sun, W.Q., Shen, Z.Y., and Seeman, N.C. (1999) A nanomechanical device based on the B-Z transition of DNA Nature 397, 144–6.

    Article  CAS  Google Scholar 

  7. Du S. M., Stollar B. D., and Seeman, N.C. (1995) A Synthetic DNA Molecule in Three Knotted Topologies J Am Chem Soc 117, 1194–1200.

    Article  CAS  Google Scholar 

  8. Michaud, M., Jourdan, E., Raavelet, C., Villet, A., Ravel, A., Grosset, C., and Peyrin, E. (2005) Immobilized DNA aptamers as target specific chiral stationary phases for resolution of nucleoside and amino acid derivative enantiomers Anal Chem 76, 1015–20.

    Article  Google Scholar 

  9. Roelfes, G., and Feringa, B.L. (2005) DNA-based asymmetric catalysis. Angew Chem Int Ed Engl 44, 3230–2.

    Article  CAS  Google Scholar 

  10. Li, X., and Liu, D. (2004) DNA-templated organic synthesis: nature’s strategy for controlling chemical reactivity applied to synthetic molecules Angew Chem Int Ed 43, 4848–70.

    Article  CAS  Google Scholar 

  11. Hannah, K.C., and Armitage, B.A. (2004) DNA-templated assembly of helical cyanine dye aggregates: a supramolecular chain polymerization Acc Chem. Res 37, 845–53.

    Article  CAS  Google Scholar 

  12. Shemer, G., Krichevski, O., Markovich, G., Molotsky, T., Lubitz, I., and Kotlyar, A.B. (2006) Chirality of Silver Nanoparticles Synthesized on DNA J Am Chem Soc 128, 11006–7.

    Article  CAS  Google Scholar 

  13. Dukovic, G., Balaz, M., Doak, P., Berova, N. D., Zheng, M., Mclean, R.S., and Brus, L.E. (2006) Racemic Single-Walled Carbon Nanotubes Exhibit Circular Dichroism When Wrapped with DNA J Am Chem Soc 128, 9004–5.

    Article  CAS  Google Scholar 

  14. Ha, S.C., Lowenhaupt, K., Rich A., Kim, Y.-G., and Kim, K.K. (2005) Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases Nature 437, 1183–6.

    Article  CAS  Google Scholar 

  15. Corradini, R., Sforza, S., Tedeschi, T., and Marchelli R. (2007) Chirality as a Tool in Nucleic Acid Recognition: Principles and Relevance in Biotechnology and in Medicinal Chemistry Chirality 19, 269–94.

    Article  CAS  Google Scholar 

  16. a) Nielsen, P.E., Egholm, M., Berg, R.H., and Buchardt, O. (1991) Sequence-Selective Recognition of DNA by Strand Displacement with A Thymine-Substituted Polyamide Science 254, 1497–1500. b) Nielsen P.E. (Ed.) (2004) Peptide Nucleic Acids: Protocols and Applications (Second Edition) Horizon Bioscience, Norfolk (UK).

    Google Scholar 

  17. Corradini, R., Sforza, S., Tedeschi, T., Totsingan, F., and Marchelli, R. (2007) Peptide nucleic acids with a structurally biased backbone: effect of conformational constraints and stereochemistry Curr Top Med Chem 7, 681–94.

    Article  CAS  Google Scholar 

  18. Menchise, V., De Simone, G., Tedeschi, T., Corradini, R., Sforza, S., Marchelli, R., Capasso, D., Saviano, and M., Pedone, C. (2003) Insights into peptide nucleic acid (PNA) structural features: the crystal structure of a D-lysine-based chiral PNA–DNA duplex Proc Natl Acad Sci USA 100, 12021–6.

    Article  CAS  Google Scholar 

  19. Lukeman, P.S., Mittal, A.C., and Seeman, N.C. (2004) Two dimensional PNA/DNA arrays: estimating the helicity of unusual nucleic acid polymers Chem Commun 1694–5.

    Google Scholar 

  20. Wittung, P., Eriksson, M., Lyng, R., Nielsen, and P. E., Norden, B. (1995) Induced Chirality in PNA-PNA Duplexes J Am Chem Soc 117, 10167–73.

    Article  CAS  Google Scholar 

  21. Totsingan, F., Jain, V., Bracken, W. C., Faccini, A., Tedeschi, T., Marchelli, R., Corradini, R., Kallenbach, N.R., and Green, M.M. (2010) Conformational Heterogeneity in PNA:PNA Duplexes Macromolecules 43, 2692–2703.

    Article  CAS  Google Scholar 

  22. Rasmussen, H., Liljefors, T., Petersson, B., Nielsen, P. E., and Kastrup, J. S. (2004) The influence of a chiral amino acid on the helical handedness of PNA in solution and in crystals J Biomol Struct Dyn 21, 495–502.

    CAS  Google Scholar 

  23. Pino, P., and Luisi, P.L. (1968) Optical activity and conformation in stereoregular vinyl polymers J Chimie Physique Physico-Chimie Bio. 65, 130–9.

    CAS  Google Scholar 

  24. Puschl, A., Sforza S., Haaima, G., Dahl, O., and Nielsen, P.E. (1998) Peptide nucleic acids (PNAs) with a functional backbone Tetrahedron Lett 39, 4707–10.

    Article  CAS  Google Scholar 

  25. Sforza, S., Haaima, G., Marchelli, R., and Nielsen, P.E. (1999) Chiral peptide nucleic acids (PNAs). Helical handedness and DNA recognition Eur J Org Chem 197–204.

    Google Scholar 

  26. Sforza, S., Corradini, R., Ghirardi, S., Dossena, A., and Marchelli, R. (2000) DNA Binding of a D-Lysine-Based Chiral PNA: Direction Control and Mismatch Recognition Eur J Org Chem 2905–13.

    Google Scholar 

  27. Smith, J.O., Olson, D.A., and Armitage B.A. (1999) Molecular Recognition of PNA-Containing Hybrids: Spontaneous Assembly of Helical Cyanine Dye Aggregates on PNA Templates J Am Chem Soc 121, 2686–95.

    Article  CAS  Google Scholar 

  28. Behe, M., and Felsenfeld, G. (1981) Effects of methylation on a synthetic polynucleotide: The B-Z transition in poly(dG-m5dC)poly(dG-m5dC) Proc Natl Acad Sci USA 78, 1619–23.

    Article  CAS  Google Scholar 

  29. Uhlmann, E., Peyman, A., Breipohl, G., and Will D.W. (1998) PNA: Synthetic Polyamide Nucleic Acids with Unusual Binding Properties Angew Chem Int Ed 37, 2796–2823.

    Article  CAS  Google Scholar 

  30. Sforza, S., Tedeschi, T., Corradini, R., Ciavardelli, D., Dossena, A., and Marchelli, R. (2003) Fast, Solid-Phase Synthesis of Chiral Peptide Nucleic Acids with a High Optical Purity by a Submonomeric Strategy Eur J Org Chem 1056–63.

    Google Scholar 

  31. Tedeschi, T., Sforza, S., Maffei, F., Corradini, R., and Marchelli R. (2008) A Fmoc-based submonomeric strategy for the solid phase synthesis of optically pure chiral PNAs Tetrahedron Lett 49, 4958–61.

    Article  CAS  Google Scholar 

  32. Sforza, S., Tedeschi, T., Corradini, R., and Marchelli, R. (2007) Induction of Helical Handedness and DNA Binding Properties of Peptide Nucleic Acids (PNAs) with Two Stereogenic Centres Eur J Org Chem 5879–85.

    Google Scholar 

  33. Corradini, R., Di Silvestro, G., Sforza, S., Palla, G., Dossena, A., Nielsen, P.E., and Marchelli, R. (1999) Direct Enantiomeric Separation of N-aminoethyl amino acids: Determination of the Optical Purity of Chiral Peptide Nucleic Acids (PNAs) by GC Tetrahedron Asymm 10, 2063–6.

    Article  CAS  Google Scholar 

  34. Fuertes, M.A., Cepeda, V., Alonso, C., and Pérez, J.M. (2006) Molecular Mechanisms for the B  −  Z Transition in the Example of Poly[d(G  −  C)·d(G  −  C)] Polymers. A Critical Review Chem Rev 106, 2045–64.

    Article  CAS  Google Scholar 

  35. Pohl, F.M., and Jovin, T.M. (1972) Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly (dG-dC) J Mol Biol 67, 375–96.

    Article  CAS  Google Scholar 

  36. Wang, A.H., Quigley, G.J., Kolpak, F.J., Crawford, J.L., van Boom, J.H., van der Marel, G., and Rich, A. (1979) The molecular Structure of the Left-Handed Z-DNA Double Helix at 1.0 Angstrom Atomic Resolution. Nature 282, 680–6.

    Article  CAS  Google Scholar 

  37. Herbert, A., and Rich, A. (1999) Left-handed Z-DNA: structure and function Genetica 106, 37–47.

    Article  CAS  Google Scholar 

  38. Spingler B. (2005) Anions or Cations: Who Is in Charge of Inhibiting the Nickel(II) Promoted B- to Z-DNA Transition? Inorg Chem 44, 831–3.

    Article  CAS  Google Scholar 

  39. Jares-Erijman, E.A., and Jovin, T.M. (1996) Determination of DNA Helical Handedness by Fluorescence Resonance Energy Transfer J Mol Biol 257, 597–617.

    Article  CAS  Google Scholar 

  40. a) Balaz, M., De Napoli, M., Holmes, A.E., Mammana, A., Nakanishi, K., Berova, and N., Purrello, R. (2005) A Cationic Zinc Porphyrin as a Chiroptical Probe for Z-DNA Angew Chem Int Ed 44, 4006-9. b) Balaz, M., Li, B.C., Steinkruger, J.D., Ellestad, G.A., Nakanishi, K., and Berova, N. (2006) Porphyrins conjugated to DNA as CD reporters of the salt-induced B to Z-DNA transition Org Biomol Chem 4, 1865–7.

    Google Scholar 

  41. Dai, Z.Y., Thomas, G.A., Evertsz, E., and Peticolas, W.L. (1989) The length of a junction between the B and Z conformations in DNA is three base pairs or less Biochemistry 28, 6991–6.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Dipartimento di Chimica Organica e Industriale, Univeristà di Parma, Parma, Italy

    Rosangela Marchelli

Authors
  1. Roberto Corradini
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tullia Tedeschi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Stefano Sforza
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mark M. Green
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Rosangela Marchelli
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rosangela Marchelli .

Editor information

Editors and Affiliations

  1. Dipto. Biochimica, Università Bologna, Via Irnerio 48, Bologna, 40126, Italy

    Giampaolo Zuccheri

  2. Dipto. Biochimica, Università Bologna, Via Irnerio 48, Bologna, 40126, Italy

    Bruno Samorì

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Corradini, R., Tedeschi, T., Sforza, S., Green, M.M., Marchelli, R. (2011). Control of Helical Handedness in DNA and PNA Nanostructures. In: Zuccheri, G., Samorì, B. (eds) DNA Nanotechnology. Methods in Molecular Biology, vol 749. Humana Press. https://doi.org/10.1007/978-1-61779-142-0_6

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-142-0_6

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-141-3

  • Online ISBN: 978-1-61779-142-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation