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

Fingerprint

Catalytic DNA
Catalysis
DNA
Nucleotide Aptamers
RNA
Catalyst activity
Catalytic RNA
DNA sequences
Nucleic Acids
Metal ions
Tyrosine
Hydrolysis
Catalysts

Keywords

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

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Systematic evaluation of the dependence of deoxyribozyme catalysis on random region length. / Velez, Tania E.; Singh, Jaydeep; Xiao, Ying; Allen, Emily C.; Wong, On Yi; Chandra, Madhavaiah; Kwon, Sarah C.; Silverman, Scott K.

In: ACS Combinatorial Science, Vol. 14, No. 12, 10.12.2012, p. 680-687.

Research output: Contribution to journalArticle

Velez, TE, Singh, J, Xiao, Y, Allen, EC, Wong, OY, Chandra, M, Kwon, SC & Silverman, SK 2012, 'Systematic evaluation of the dependence of deoxyribozyme catalysis on random region length', ACS Combinatorial Science, vol. 14, no. 12, pp. 680-687. https://doi.org/10.1021/co300111f
Velez, Tania E. ; Singh, Jaydeep ; Xiao, Ying ; Allen, Emily C. ; Wong, On Yi ; Chandra, Madhavaiah ; Kwon, Sarah C. ; Silverman, Scott K. / Systematic evaluation of the dependence of deoxyribozyme catalysis on random region length. In: ACS Combinatorial Science. 2012 ; Vol. 14, No. 12. pp. 680-687.
@article{b598cebb8a1646908288a1309c5a9099,
title = "Systematic evaluation of the dependence of deoxyribozyme catalysis on random region length",
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.",
keywords = "DNA and RNA aptamers, DNA catalysts, RNA catalysts, deoxyribozyme catalysis, nucleic acids, random region length",
author = "Velez, {Tania E.} and Jaydeep Singh and Ying Xiao and Allen, {Emily C.} and Wong, {On Yi} and Madhavaiah Chandra and Kwon, {Sarah C.} and Silverman, {Scott K.}",
year = "2012",
month = "12",
day = "10",
doi = "10.1021/co300111f",
language = "English (US)",
volume = "14",
pages = "680--687",
journal = "ACS Combinatorial Science",
issn = "2156-8952",
publisher = "American Chemical Society",
number = "12",

}

TY - JOUR

T1 - Systematic evaluation of the dependence of deoxyribozyme catalysis on random region length

AU - Velez, Tania E.

AU - Singh, Jaydeep

AU - Xiao, Ying

AU - Allen, Emily C.

AU - Wong, On Yi

AU - Chandra, Madhavaiah

AU - Kwon, Sarah C.

AU - Silverman, Scott K.

PY - 2012/12/10

Y1 - 2012/12/10

N2 - 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.

AB - 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.

KW - DNA and RNA aptamers

KW - DNA catalysts

KW - RNA catalysts

KW - deoxyribozyme catalysis

KW - nucleic acids

KW - random region length

UR - http://www.scopus.com/inward/record.url?scp=84870937297&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84870937297&partnerID=8YFLogxK

U2 - 10.1021/co300111f

DO - 10.1021/co300111f

M3 - Article

C2 - 23088677

AN - SCOPUS:84870937297

VL - 14

SP - 680

EP - 687

JO - ACS Combinatorial Science

JF - ACS Combinatorial Science

SN - 2156-8952

IS - 12

ER -