A Complex RNA-Cleaving DNAzyme That Can Efficiently Cleave a Pyrimidine–Pyrimidine Junction

Lam, Jeffrey C. F.; Withers, John; Li, Yingfu

doi:10.1016/j.jmb.2010.05.047

Cited by 18 publications

(18 citation statements)

References 53 publications

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“…These were 1–3 orders of magnitude faster than the best DNAzymes reported previously, although were still 10–100 fold slower than the DNAzymes that cleave purine‐purine junctions . A reselection was performed based on sequences from the rCT pool, and the obtained CT10‐3.29 DNAzyme with a more complex structure had a rate constant of 0.3–1.4 min −1 . Recently, Wang et al.…”

Section: Modifications Introduced In the Fixed Region Of The Selectiomentioning

confidence: 91%

In vitro Selection of Chemically Modified DNAzymes

Huang

Liu

2020

ChemistryOpen

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DNAzymes are in vitro selected DNA oligonucleotides with catalytic activities. RNA cleavage is one of the most extensively studied DNAzyme reactions. To expand the chemical functionality of DNA, various chemical modifications have been made during and after selection. In this review, we summarize examples of RNA‐cleaving DNAzymes and focus on those modifications introduced during in vitro selection. By incorporating various modified nucleotides via polymerase chain reaction (PCR) or primer extension, a few DNAzymes were obtained that can be specifically activated by metal ions such as Zn2+ and Hg2+. In addition, some modifications were introduced to mimic RNase A that can cleave RNA substrates in the absence of divalent metal ions. In addition, single modifications at the fixed regions of DNA libraries, especially at the cleavage junctions, have been tested, and examples of DNAzymes with phosphorothioate and histidine‐glycine modified tertiary amine were successfully obtained specific for Cu2+, Cd2+, Zn2+, and Ni2+. Labeling fluorophore/quencher pair right next to the cleavage junction was also used to obtain signaling DNAzymes for detecting various metal ions and cells. Furthermore, we reviewed work on the cleavage of 2′‐5′ linked RNA and L‐RNA substrates. Finally, applications of these modified DNAzymes as biosensors, RNases, and biochemical probes are briefly described with a few future research opportunities outlined at the end.

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Section: Modifications Introduced In the Fixed Region Of The Selectiomentioning

confidence: 91%

In vitro Selection of Chemically Modified DNAzymes

Huang

Liu

2020

ChemistryOpen

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“…Ideally, individual DNAzymes should selectively cleave only one out of the four targets. Since none of the previously reported 8-17 analogues is particularly good at cleaving N|C junctions in all-RNA substrates, 232,259 advanced in vitro evolution strategies need to be developed to overcome the tyranny of the 8-17 motif. 236 Deep sequencing analyses of enriched selection libraries with in situ analyses of cleavage activity and selectivity 26,260 may lead to the identification of new catalytic DNA motifs for the site-specific interrogation of difficult-to-cleave RNA substrates and isomers of posttranscriptional RNA modifications.…”

Section: Rna-cleaving Deoxyribozymesmentioning

confidence: 99%

Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes

2020

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“…Since then, a plethora of in vitro selection experiments have been performed to derive diverse RNase DNAzymes with widely different characteristics. The list includes DNAzymes utilizing Mg 2+ [12], Ca 2+ [13], Zn 2+ [14], Mn 2+ [15], and UO 2 2+ [16] as metal-ion cofactors, a cofactorless DNAzyme [17] and DNAzymes that use the amino acid histidine as the cofactor [18]. …”

Section: Deriving Rna-cleaving Dnazymes By In Vitro Selectionmentioning

confidence: 99%

Lighting Up RNA-Cleaving DNAzymes for Biosensing

Tram

Kanda

2012

Journal of Nucleic Acids

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The development of the in vitro selection technique has allowed the isolation of functional nucleic acids, including catalytic DNA molecules (DNAzymes), from random-sequence pools. The first-ever catalytic DNA obtained by this technique in 1994 is a DNAzyme that cleaves RNA. Since then, many other RNase-like DNAzymes have been reported from multiple in vitro selection studies. The discovery of various RNase DNAzymes has in turn stimulated the exploration of these enzymatic species for innovative applications in many different areas of research, including therapeutics, biosensing, and DNA nanotechnology. One particular research topic that has received considerable attention for the past decade is the development of RNase DNAzymes into fluorescent reporters for biosensing applications. This paper provides a concise survey of the most significant achievements within this research topic.

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A Complex RNA-Cleaving DNAzyme That Can Efficiently Cleave a Pyrimidine–Pyrimidine Junction

Cited by 18 publications

References 53 publications

In vitro Selection of Chemically Modified DNAzymes

In vitro Selection of Chemically Modified DNAzymes

Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes

Lighting Up RNA-Cleaving DNAzymes for Biosensing

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