Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Cationic comb-type copolymers for DNA analysis

Nature Materials volume 2, pages 815–820 (2003)Cite this article

Abstract

Genetic diagnoses, such as single nucleotide polymorphism (SNP) typing, allow elucidation of gene-based physiological differences, such as susceptibility to diseases and response to drugs, among individuals. Many detection technologies, including allele-specific hybridization, allele-specific primer extension and oligonucleotide ligation, are being used to discriminate SNP alleles1,2. These methods still have many unsolved practical issues1,2,3. In general they require adequate and specific hybridizations of primer or probe DNAs with target DNAs. This frequently needs optimization of the probe/primer structures and operating conditions. In nature, highly homology-sensitive hybridization is assisted by a nucleic acid chaperone that reduces the energy barrier associated with breakage and reassociation of nucleic base pairs4,5. Here we report a simple, quick, precise but enzyme-free method for SNP analysis. The method uses cationic comb-type copolymers (CCCs) producing high nucleic acid chaperone activities. A single-base mismatch in 20-mer DNA can be detected within a few minutes at ambient temperatures (25–37 °C). Even without careful optimization processes, the method has the sensitivity to detect the mismatches causing subtle changes (ΔTm ≈ 1 °C) in duplex thermal stability. CCCs may have various bioanalytical applications where precise hybridization of nucleic acids is needed.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Strand exchange assay accelerated by cationic comb-type copolymer (CCC).
Figure 2: Ultraviolet absorption/melting analyses and PASE assays of diverse mismatches in various sequences.
Figure 3: Ultraviolet absorption/melting analyses and PASE assays of ss targets with mismatches at varying locations.
Figure 4: Simultaneous PASE assays in 96-well microplates.

Similar content being viewed by others

References

  1. Brennan, M.D. High throughput genotyping technologies for pharmacogenomics. Am. J. Pharmacogenomics 1, 295–302 (2001).

    Article  CAS  Google Scholar 

  2. Kwok, P.Y. Methods for genotyping single nucleotide polymorphisms. Annu. Rev. Genom. Hum. Genet. 2, 235–258 (2001).

    Article  CAS  Google Scholar 

  3. Chicurel, M. Faster, better, cheaper genotyping. Nature 412, 580–582 (2001).

    Article  CAS  Google Scholar 

  4. Tsuchihashi, Z. & Brown, P.O. DNA strand exchange and selective DNA annealing promoted by the human immunodeficiency virus type 1 nucleocapsid protein. J. Virol. 68, 5863–5870 (1994).

    CAS  Google Scholar 

  5. Rein, A., Henderson, L.E. & Levin, J.G. Nucleic-acid-chaperone activity of retroviral nucleocapsid proteins: significance for viral replication. Trends Biochem. Sci. 23, 297–301 (1998).

    Article  CAS  Google Scholar 

  6. Reynaldo, L.P., Vologodskii, A.V., Neri, B.P. & Lyamichev, V.I. The kinetic of oligonucleotide replacements. J. Mol. Biol. 297, 511–520 (2000).

    Article  CAS  Google Scholar 

  7. Panyutin, I.G. & Hsieh, P. Formation of a single base mismatch impedes spontaneous DNA branch migration. J. Mol. Biol. 230, 413–424 (1993).

    Article  CAS  Google Scholar 

  8. Li, Q., Luan, G., Guo, Q. & Liang, J. A new class of homogeneous nucleic acid probes based on specific displacement hybridisation. Nucleic Acids Res. 30, e5 (2002).

    Article  Google Scholar 

  9. Kim, W.J., Ishihara, T., Akaike, T. & Maruyama, A. Comb-type cationic copolymer expedites DNA strand exchange while stabilizing DNA duplex. Chem. Eur. J. 7, 176–180 (2001).

    Article  CAS  Google Scholar 

  10. Kim, W.J., Akaike, T. & Maruyama, A. DNA strand exchange stimulated by spontaneous complex formation with cationic comb-type copolymer. J. Am. Chem. Soc. 124, 12676–12677 (2002).

    Article  CAS  Google Scholar 

  11. Maruyama, A., Katoh, M., Ishihara, T. & Akaike, T. Comb-type polycations effectively stabilize DNA triplex. Bioconjugate Chem. 8, 3–6 (1997).

    Article  CAS  Google Scholar 

  12. Torigoe, H., Ferdous, A., Watanabe, H., Akaike, T. & Maruyama, A. Poly(L-lysine)-graft-dextran copolymer promotes pyrimidine motif triplex DNA formation at physiological pH. J. Biol. Chem. 274, 6161–6167 (1999).

    Article  CAS  Google Scholar 

  13. Ferdous, A., Watanabe, H., Akaike, T. & Maruyama, A. Poly(L-lysine)-graft-dextran copolymer: amazing effects on triplex stabilization under physiological pH and ionic conditions (in vitro). Nucleic Acids Res. 26, 3949–3954 (1998).

    Article  CAS  Google Scholar 

  14. Urbaneja, M.A., Wu, M., Casas-Finet, J.R. & Karpel, R.L. HIV-1 Nucleocapsid protein as a nucleic acid chaperone: spectroscopic study of its helix-destabilizing properties, structural binding specificity, and annealing activity. J. Mol. Biol. 318, 749–764 (2002).

    Article  CAS  Google Scholar 

  15. Bazemore, L.R., Takahashi, M. & Radding, C.M. Kinetic analysis of pairing and strand exchange catalyzed by RecA. J. Biol. Chem. 272, 14672–14682 (1997).

    Article  CAS  Google Scholar 

  16. Wilson, J.F. et al. Population genetic structure of variable drug response. Nature Genet. 29, 265–269 (2001).

    Article  CAS  Google Scholar 

  17. Morais, S.M.F. et al. The major genetic defect responsible for polymorphism of S-mephenytoin metabolism in humans. J. Biol. Chem. 269, 15419–15422 (1994).

    Google Scholar 

  18. Goldstein, J.A. & Morais, S.M.F. Biochemistry and molecular biology of the human CYP2C subfamily. Pharmacogenetics 4, 285–299 (2002).

    Article  Google Scholar 

  19. Elghanian, R., Storhoff, J.J., Mucic, R.C., Letsinger, R.L. & Mirkin, C.A. Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science 277, 1078–1081 (1997).

    Article  CAS  Google Scholar 

  20. Kajiyama, T. et al. Genotyping on a thermal gradient DNA chip. Genome Res. 13, 467–475 (2003).

    Article  CAS  Google Scholar 

  21. Santalucia, J. Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA 95, 1460–1465 (1998).

    Article  CAS  Google Scholar 

  22. Chee, M. et al. Accessing genetic information with high-density DNA arrays. Science 274, 610–614 (1996).

    Article  CAS  Google Scholar 

  23. Han, M., Gao, X., Su, J.Z. & Nie, S. Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules. Nature Biotechnol. 19, 631–635 (2001).

    Article  CAS  Google Scholar 

  24. Yang, L., Tran, D.K. & Wang, X. BADGE, Beads array for the detection of gene expression, a high-throughput diagnostic bioassay. Genome Res. 11, 1888–1898 (2001).

    Article  CAS  Google Scholar 

  25. Boon, E.M., Ceres, D.M., Drummond, T.G., Hill, M.G. & Barton, J.K. Mutation detection by electrocatalysis at DNA-modified electrodes. Nature Biotechnol. 18, 1096–1100 (2000).

    Article  CAS  Google Scholar 

  26. Mazumder, A., Majlessi, M. & Becker, M.M. A high throughput method to investigate oligodeoxyribonucleotide hybridisation kinetics and thermodynamics. Nucleic Acids Res. 26, 1996–2000 (1998).

    Article  CAS  Google Scholar 

  27. Jenison, R., Yang, S., Haeberli, A. & Polisky, B. Interference-based detection of nucleic acid targets on optically coated silicon. Nature Biotechnol. 19, 62–65 (2001).

    Article  CAS  Google Scholar 

  28. Cao, Y.C., Jin, R. & Mirkin, C.A. Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection. Science 297, 1536–1540 (2002).

    Article  CAS  Google Scholar 

  29. Takahashi, T., Ueno, A. & Mihara, H. Nucleobase amino acids incorporated into the HIV-1 nucleocapsid protein increased the binding affinity and specificity for a hairpin RNA. ChemBioChem 3, 543–549 (2002).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank H. Mihara for discussion and the gift of NCp7, and D. W. Grainger and K. Yamana for critical reading of the manuscript. We acknowledge FASMAC, for oligonucleotide syntheses and K. Tajima for experimental assistance. This work was supported in part by grant-in-aids (11167225 and 12480260) for scientific research from Ministry of Education, Culture, Sports, Science, and Technology of Japan. W.J.K. was supported by the Japanese Government Scholarship.

Author information

Authors and Affiliations

  1. Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori, Yokohama, 226-8501, Japan

    Won Jong Kim, Toshihiro Akaike & Atsushi Maruyama

  2. PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan

    Yuichi Sato & Atsushi Maruyama

Authors
  1. Won Jong Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yuichi Sato
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Toshihiro Akaike
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Atsushi Maruyama
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Atsushi Maruyama.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information, Fig. S1

Supplementary Information, Fig. S2 (PDF 4171 kb)

Supplementary Information, Fig. S3

Supplementary Information, Fig. S4

Supplementary Information, Fig. S5

Supplementary Information, Fig. S6

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kim, W., Sato, Y., Akaike, T. et al. Cationic comb-type copolymers for DNA analysis. Nature Mater 2, 815–820 (2003). https://doi.org/10.1038/nmat1021

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmat1021

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing