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Enzymatic Synthesis of Nucleobase-Modified Single-Stranded DNA Offers Tunable Resistance to Nuclease Degradation.

Publication ,  Journal Article
Gu, R; Oweida, T; Yingling, YG; Chilkoti, A; Zauscher, S
Published in: Biomacromolecules
August 2018

We synthesized long, nucleobase-modified, single-stranded DNA (ssDNA) using terminal deoxynucleotidyl transferase (TdT) enzymatic polymerization. Specifically, we investigated the effect of unnatural nucleobase size and incorporation density on ssDNA resistance to exo- and endonuclease degradation. We discovered that increasing the size and density of unnatural nucleobases enhances ssDNA resistance to degradation in the presence of exonuclease I, DNase I, and human serum. We also studied the mechanism of this resistance enhancement using molecular dynamics simulations. Our results show that the presence of unnatural nucleobases in ssDNA decreases local chain flexibility and hampers nuclease access to the ssDNA backbone, which hinders nuclease binding to ssDNA and slows its degradation. Our discoveries suggest that incorporating nucleobase-modified nucleotides into ssDNA, using enzymatic polymerization, is an easy and efficient strategy to prolong and tune the half-life of DNA-based materials in nucleases-containing environments.

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Published In

Biomacromolecules

DOI

EISSN

1526-4602

ISSN

1525-7797

Publication Date

August 2018

Volume

19

Issue

8

Start / End Page

3525 / 3535

Related Subject Headings

  • Purine Nucleosides
  • Protein Binding
  • Polymers
  • Hydrolysis
  • Deoxyribonucleases
  • DNA, Single-Stranded
  • DNA Nucleotidylexotransferase
  • Biocatalysis
  • 40 Engineering
  • 34 Chemical sciences
 

Citation

APA
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ICMJE
MLA
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Gu, R., Oweida, T., Yingling, Y. G., Chilkoti, A., & Zauscher, S. (2018). Enzymatic Synthesis of Nucleobase-Modified Single-Stranded DNA Offers Tunable Resistance to Nuclease Degradation. Biomacromolecules, 19(8), 3525–3535. https://doi.org/10.1021/acs.biomac.8b00816
Gu, Renpeng, Thomas Oweida, Yaroslava G. Yingling, Ashutosh Chilkoti, and Stefan Zauscher. “Enzymatic Synthesis of Nucleobase-Modified Single-Stranded DNA Offers Tunable Resistance to Nuclease Degradation.Biomacromolecules 19, no. 8 (August 2018): 3525–35. https://doi.org/10.1021/acs.biomac.8b00816.
Gu R, Oweida T, Yingling YG, Chilkoti A, Zauscher S. Enzymatic Synthesis of Nucleobase-Modified Single-Stranded DNA Offers Tunable Resistance to Nuclease Degradation. Biomacromolecules. 2018 Aug;19(8):3525–35.
Gu, Renpeng, et al. “Enzymatic Synthesis of Nucleobase-Modified Single-Stranded DNA Offers Tunable Resistance to Nuclease Degradation.Biomacromolecules, vol. 19, no. 8, Aug. 2018, pp. 3525–35. Epmc, doi:10.1021/acs.biomac.8b00816.
Gu R, Oweida T, Yingling YG, Chilkoti A, Zauscher S. Enzymatic Synthesis of Nucleobase-Modified Single-Stranded DNA Offers Tunable Resistance to Nuclease Degradation. Biomacromolecules. 2018 Aug;19(8):3525–3535.

Published In

Biomacromolecules

DOI

EISSN

1526-4602

ISSN

1525-7797

Publication Date

August 2018

Volume

19

Issue

8

Start / End Page

3525 / 3535

Related Subject Headings

  • Purine Nucleosides
  • Protein Binding
  • Polymers
  • Hydrolysis
  • Deoxyribonucleases
  • DNA, Single-Stranded
  • DNA Nucleotidylexotransferase
  • Biocatalysis
  • 40 Engineering
  • 34 Chemical sciences