IRC-SET 2018 pp 335-347 | Cite as

Developing Modified Peptide Nucleic Acids to Regulate Dysregulated Splicing

  • Samuel Foo EnzeEmail author
  • Tristan Lim Yi Xuan
  • Jayden Kim Jun-Sheng
Conference paper


Peptide Nucleic Acid (PNA) can stabilise the Tau Exon 10-Intron 10 self-regulatory RNA hairpin, known to regulate the alternative splicing of exon 10 in Microtubule-Associated Protein Tau (MAPT) transcript [1], and thus rescue the aberrant ratio of protein isoforms (4R/3R), preventing tauopathy. We used antisense PNA (ASPNA) and triplex-forming PNA (TFPNA) methods, and compared the effectiveness of both. We synthesised PNA oligomers using solid phase peptide synthesis (SPPS) and tested binding affinity to the RNA hairpin using polyacrylamide gel electrophoresis (PAGE). TFPNA is less costly and more efficient to synthesise, but has low binding affinity, whereas ASPNA costs more to synthesise but has a higher binding affinity.

Hypothesis—Binding a PNA strand to the Tau Exon 10-Intron 10 self-regulatory hairpin can rescue the aberrant ratio of 3R:4R isoforms and thus cure tauopathy.


Antisense strands Alternative splicing Hairpins Hoogsteen base pair Missense mutation Peptide nucleic acid (PNA) Steric hindrance Isoform U1snRNP ASPNA TFPNA 



This project would not have been possible without the guidance and help of individuals who have extended their invaluable assistance in the completion of this project:

• Our external mentor, Mr. Alan Ong, for his immense help and advice throughout the course of our research

• Our internal teacher-mentor, Mrs. Elizabeth Foo, for guiding us through our internal school deadlines and keeping us up to date

• Assistant Professor Chen Gang, for regularly sending us informative emails related to our research topic as well as allowing us to use his lab for research

• NTU, RI and MOE-GEB for giving us this unique opportunity to participate in the programme

• Our friends and family who have morally supported us throughout our project.


  1. 1.
    Svoboda, S., & Di Cara, A. (2006, April). Hairpin RNA: A Secondary Structure of Primary Importance. Retrieved February 25, 2017 from
  2. 2.
    Koh, W. (n.d.). Peptide Nucleic Acid (PNA) and Its Applications. Yuseong-gu, Daejeon: Panagene Inc.Google Scholar
  3. 3.
    Nielsen, P. E., Egholm, M., Berg, R. H., & Buchardt, O. (1991). Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science, 254, 1497–1500.CrossRefGoogle Scholar
  4. 4.
    Wang, Y., & Mandelkow, E. (2016). Tau in physiology and pathology. Nature Reviews Neuroscience, 17, 5–21.CrossRefGoogle Scholar
  5. 5.
    Roca, X., Krainer, A. R., & Eperon, I. C. (2013). Pick one, but be quick: 5′ splice sites and the problems of too many choices. Genes and Development, 27, 129–144.CrossRefGoogle Scholar
  6. 6.
    Kar, A., Fushimi, K., Zhou, X., Ray, P., Shi, C., Chen, X., et al. (2011). RNA helicase p68 (DDX5) regulates tau exon 10 splicing by modulating a stem-loop structure at the 5’ splice site. Molecular and Cellular Biology, 31, 1812–1821.CrossRefGoogle Scholar
  7. 7.
    Ray, P., Kar, A., Fushimi, K., Havlioglu, N., Chen, X., & Wu, J. Y. (2011). PSF suppresses tau exon 10 inclusion by interacting with a stem-loop structure downstream of exon 10. Journal of Molecular Neuroscience, 45, 453–466.CrossRefGoogle Scholar
  8. 8.
    Chen, G. (n.d.). RNA Folding and Therapeutics. Retrieved February 25, 2017 from
  9. 9.
    Devi, G., Zhou, Y., Zhong, Z., Toh, D. K., & Chen, G. (2014). RNA triplexes: From structural principles to biological and biotech applications. John Wiley & Sons, Ltd.. Scholar
  10. 10.
    Fredericks, A. M., Cygan, K. J., Brown, B. A., & Fairbrother, W. G. (2015, June). RNA-Binding Proteins: Splicing Factors and Disease. Retrieved February 25, 2017 from
  11. 11.
    Nielsen, P. E., & Egholm, M. (1999). An introduction to peptide nucleic acid. Current Issues in Molecular Biology, 1, 89–104.PubMedGoogle Scholar
  12. 12.
    Cleveland, D. W., Hwo, S. Y., & Kirschner, M. W. (1977). Purification of tau, a microtubule-associated protein that induces assembly of microtubules from purified tubulin. Journal of Molecular Biology, 116(2), 207–225.CrossRefGoogle Scholar
  13. 13.
    Goedert, M. (2005). Tau gene mutations and their effects. Movement disorders: Official journal of the Movement Disorder Society, 20(Suppl 12), S45–52.CrossRefGoogle Scholar
  14. 14.
    Gaillard, F. (n.d.). Neurofibrillary tangles | Radiology Reference Article. Retrieved August 06, 2017 from
  15. 15.
    Hoogsteen Base Pairing (Molecular Biology). (n.d.). Retrieved February 25, 2017 from
  16. 16.
    Leontis, N. B., & Westhof, E. (2001). Geometric nomenclature and classification of RNA base pairs. RNA, 7(4), 499–512. (n.d.). Retrieved February 16, 2017 from
  17. 17.
    PNA: Peptide Nucleic Acid as a more stable alternative to DNA and RNA for many applications. (n.d.). Retrieved February 25, 2017 from
  18. 18.
    Poulos, M. G., Batra, R., Charizanis, K., & Swanson, M. S. (2011, January). Developments in RNA Splicing and Disease. Retrieved February 25, 2017 from
  19. 19.
    Sanders, R. (2015, April 6). New Target for Anticancer Drugs: RNA. Berkeley News. Retrieved February 25, 2017 from
  20. 20.
    Wang, G., & Xu, X. S. (n.d.). Peptide Nucleic Acid (PNA) Binding-Mediated Gene Regulation.
  21. 21.
    Warf, M. B., & Berglund, J. A. (2010, March). The Role of RNA Structure in Regulating pre-mRNA Splicing. Retrieved February 25, 2017 from
  22. 22.
    Jubilut, G. N., Cilli, E. M., Tominaga, M., Miranda, A., Okada, Y., & Nakaie, C. R. (2001, September). Evaluation of the Trifluoromethanosulfonic Acid/Trifluoroacetic Acid/Thioanisole Cleavage Procedure for Application in Solid-Phase Peptide Synthesis. Retrieved June 10, 2017 from

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Samuel Foo Enze
    • 1
    Email author
  • Tristan Lim Yi Xuan
    • 1
  • Jayden Kim Jun-Sheng
    • 1
  1. 1.Raffles InstitutionSingaporeSingapore

Personalised recommendations