Systematic evaluation of the dependence of deoxyribozyme catalysis on random region length

Tania E. Velez, Jaydeep Singh, Ying Xiao, Emily C. Allen, On Yi Wong, Madhavaiah Chandra, Sarah C. Kwon, Scott K. Silverman

Research output: Contribution to journalArticle

Abstract

Functional nucleic acids are DNA and RNA aptamers that bind targets, or they are deoxyribozymes and ribozymes that have catalytic activity. These functional DNA and RNA sequences can be identified from random-sequence pools by in vitro selection, which requires choosing the length of the random region. Shorter random regions allow more complete coverage of sequence space but may not permit the structural complexity necessary for binding or catalysis. In contrast, longer random regions are sampled incompletely but may allow adoption of more complicated structures that enable function. In this study, we systematically examined random region length (N20 through N 60) for two particular deoxyribozyme catalytic activities, DNA cleavage and tyrosine-RNA nucleopeptide linkage formation. For both activities, we previously identified deoxyribozymes using only N40 regions. In the case of DNA cleavage, here we found that shorter N20 and N 30 regions allowed robust catalytic function, either by DNA hydrolysis or by DNA deglycosylation and strand scission via Β-elimination, whereas longer N50 and N60 regions did not lead to catalytically active DNA sequences. Follow-up selections with N20, N30, and N40 regions revealed an interesting interplay of metal ion cofactors and random region length. Separately, for Tyr-RNA linkage formation, N30 and N60 regions provided catalytically active sequences, whereas N20 was unsuccessful, and the N 40 deoxyribozymes were functionally superior (in terms of rate and yield) to N30 and N60. Collectively, the results indicate that with future in vitro selection experiments for DNA and RNA catalysts, and by extension for aptamers, random region length should be an important experimental variable.

Original languageEnglish (US)
Pages (from-to)680-687
Number of pages8
JournalACS Combinatorial Science
Volume14
Issue number12
DOIs
StatePublished - Dec 10 2012

Keywords

  • DNA and RNA aptamers
  • DNA catalysts
  • RNA catalysts
  • deoxyribozyme catalysis
  • nucleic acids
  • random region length

ASJC Scopus subject areas

  • Chemistry(all)

Fingerprint Dive into the research topics of 'Systematic evaluation of the dependence of deoxyribozyme catalysis on random region length'. Together they form a unique fingerprint.

  • Cite this

    Velez, T. E., Singh, J., Xiao, Y., Allen, E. C., Wong, O. Y., Chandra, M., Kwon, S. C., & Silverman, S. K. (2012). Systematic evaluation of the dependence of deoxyribozyme catalysis on random region length. ACS Combinatorial Science, 14(12), 680-687. https://doi.org/10.1021/co300111f