DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides

Schlosser, Kenny; Li, Yingfu

doi:10.1093/nar/gkn930

Cited by 29 publications

(26 citation statements)

References 33 publications

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“…Our discovery that the most active split enzymes are those divided after the 7 th or 8 th nucleotide is consistent with earlier observations that the full-length DNAzyme best tolerates mutations and deletions closest to the center of the catalytic core [16]. This flexibility of the catalytic loop is not unique to the 10-23 DNAzyme: studies of the 8-17 DNAzyme have demonstrated that its catalytic domain can be modified to contain only guanosine and cytidine residues while still preserving detectable enzymatic activity [43], and an extensive mutational analysis of its catalytic core has shown the ability to retain activity [44]. We also demonstrated that the ability of DNAzymes to function as split enzymes imparts greater selectivity towards the RNA target.…”

Section: Discussionsupporting

confidence: 86%

Mismatch discrimination and efficient photomodulation with split 10–23 DNAzymes

Ruble¹,

Richards²,

Cheung-Lau³

et al. 2012

Inorganica Chimica Acta

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DNA enzymes (DNAzymes) that catalyze the degradation of complementary RNA molecules have been investigated for many biochemical and sensing applications. Here, we investigated a 10-23 DNAzyme that has been shown previously to possess cellular activity. We determined that it has very low Mg2+ ion dependence, with DNAzyme activity observed at [Mg2+] = 0.01 mM. This metal ion dependence is much lower than is typical for DNAzymes studied to date, and suggests that DNAzymes may be engineered for many additional biological applications. Recently, we demonstrated that this 10-23 DNAzyme can be divided into two parts, which assemble into an active oligonucleotide complex. We investigated in more detail the functionality of the split 10-23 DNAzyme and found that dividing the 15-nucleotide catalytic loop after the 7th or 8th base maximized its activity. The split DNAzymes required higher metal ion concentrations ([Mg2+] = 5 mM), and as we anticipated due to their lower hybridization activity, the split enzymes had the advantage of being more sensitive to single base mismatches in the DNAzyme-RNA duplex. Finally, we demonstrated facile photomodulation of split DNAzyme activity by incorporating a photocleavable biotin moiety bound to streptavidin.

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Section: Discussionsupporting

confidence: 86%

Mismatch discrimination and efficient photomodulation with split 10–23 DNAzymes

Ruble¹,

Richards²,

Cheung-Lau³

et al. 2012

Inorganica Chimica Acta

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“…24,44,45 The four examples in Figure 1 represent the main independent and well characterized metal-specific DNAzymes reported so far. 46,47 Note that many other DNAzymes contain required fluorophore/quencher or base modifications for activity; they are not studied here. 19,48 For the GR5 DNAzyme, indeed only Pb 2+ cleaved the normal PO substrate ( Figure 2B).…”

Section: Ps-modified Enzymesmentioning

confidence: 99%

Sensing Parts-per-Trillion Cd²⁺, Hg²⁺, and Pb²⁺ Collectively and Individually Using Phosphorothioate DNAzymes

2014

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Cadmium, mercury and lead are collectively banned by many countries and regions in electronic devices due to their extremely high toxicity. To date, no sensing method can detect them as a group and also individually with sufficient sensitivity and selectivity. An RNA-cleaving DNAzyme (Ce13d) was recently reported to be active with trivalent lanthanides, which are hard Lewis acids. In this work, phosphorothioate (PS) modifications were systematically made on Ce13d. A single PS at the substrate cleavage site shifts the activity from being dependent on lanthanide to soft thiophilic metals.By incorporating the PS modification to a few other DNAzymes, a sensor array was prepared to detect each metal. Individual sensors have excellent sensitivity (limit of detection = 4.8 nM Cd 2+ , 2.0 nM Hg 2+ , and 0.1 nM Pb 2+ ). This study provides a new route to obtain metal-specific DNAzymes by atomic replacement and also offers important mechanistic insights into metal binding and DNAzyme catalysis.3

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“…Within living cells, mRNA transcripts exist in secondary structures and interact with cytoplasmic proteins, therefore, some of the mRNA sequences are hidden and only partial sequences are accessible [39]. mRNAs exist in several cellular compartments, including the cytoplasm, nucleus and nucleolus.…”

Section: Discussionmentioning

confidence: 99%

Efficient Silencing of Gene Expression by an ASON–Bulge–DNAzyme Complex

Jiang

Liu

2011

PLoS ONE

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BackgroundDNAzymes are DNA molecules that can directly cleave cognate mRNA, and have been developed to silence gene expression for research and clinical purposes. The advantage of DNAzymes over ribozymes is that they are inexpensive to produce and exhibit good stability. The “10-23 DNA enzyme” is composed of a catalytic domain of 15 deoxynucleotides, flanked by two substrate-recognition domains of approximately eight nucleotides in each direction, which provides the complementary sequence required for specific binding to RNA substrates. However, these eight nucleotides might not afford sufficient binding energy to hold the RNA substrate along with the DNAzyme, which would interfere with the efficiency of the DNAzyme or cause side effects, such as the cleavage of non-cognate mRNAs.MethodologyIn this study, we inserted a nonpairing bulge at the 5′ end of the “10–23 DNA enzyme” to enhance its efficiency and specificity. Different sizes of bulges were inserted at different positions in the 5′ end of the DNAzyme. The non-matching bulge will avoid strong binding between the DNAzyme and target mRNA, which may interfere with the efficiency of the DNAzyme.ConclusionsOur novel DNAzyme constructs could efficiently silence the expression of target genes, proving a powerful tool for gene silencing. The results showed that the six oligo bulge was the most effective when the six oligo bulge was 12–15 bp away from the core catalytic domain.

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DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides

Cited by 29 publications

References 33 publications

Mismatch discrimination and efficient photomodulation with split 10–23 DNAzymes

Mismatch discrimination and efficient photomodulation with split 10–23 DNAzymes

Sensing Parts-per-Trillion Cd²⁺, Hg²⁺, and Pb²⁺ Collectively and Individually Using Phosphorothioate DNAzymes

Efficient Silencing of Gene Expression by an ASON–Bulge–DNAzyme Complex

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DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides

Cited by 29 publications

References 33 publications

Mismatch discrimination and efficient photomodulation with split 10–23 DNAzymes

Mismatch discrimination and efficient photomodulation with split 10–23 DNAzymes

Sensing Parts-per-Trillion Cd2+, Hg2+, and Pb2+ Collectively and Individually Using Phosphorothioate DNAzymes

Efficient Silencing of Gene Expression by an ASON–Bulge–DNAzyme Complex

Contact Info

Product

Resources

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Sensing Parts-per-Trillion Cd²⁺, Hg²⁺, and Pb²⁺ Collectively and Individually Using Phosphorothioate DNAzymes