Deoxyribozymes: new activities and new applications

Emilsson, Gail Mitchell; Breaker, Ronald R.

doi:10.1007/s00018-002-8452-4

Cited by 142 publications

(95 citation statements)

References 75 publications

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“…(ii) The variety of tertiary structures is a fundamental property of the double (and of the single) strand, from the subtle variations of the 16 conformational local parameters used for its systematization (21) to the global dynamic properties characterizing topologically defined DNA domains (22). (iii) Although no deoxyribozyme has ever been isolated from extant organisms, DNA with catalytic activities were obtained, mostly by in vitro selection, that carry out a variety of chemical transformations (23)(24)(25)(26)(27)(28)(29). DNA catalytic potentialities and versatility are well established (recently reviewed in Ref.…”

Section: Comparison Of the Bond Stabilities In Ribo-and In 2ј-deoxyrimentioning

confidence: 99%

Origin of Informational Polymers

Saladino

Crestini

Ciciriello

et al. 2006

Journal of Biological Chemistry

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We have measured the stabilities of the bonds that are critical for determining the half-life of ribonucleotides and the ␤-glycosidic and 3-and 5-phosphoester bonds. Stabilities were measured under a wide range of temperatures and water/formamide ratios. The stability of phosphodiester bonds in oligoribonucleotides was determined in the same environments. The comparison of bond stabilities in the monomer versus the polymer forms of the ribo compounds revealed that physico-chemical conditions exist in which polymerization is thermodynamically favored. These conditions were compared with those determining a similar behavior for 2-deoxyribonucleosides, deoxyribonucleotides, and deoxyribooligonucleotides and were shown to profoundly differ. The implications of these facts on the origin of informational polymers are discussed.Minimal requirements for informational polymers to have originated under prebiotic conditions are a unitary chemical frame for the synthesis of nucleobases and a favorable thermodynamic energy balance for the polymerization of nucleotides to oligonucleotides.A Formamide-based Unitary Chemistry-To gather into a single reaction milieu all the precursors necessary for the assembly of the first informational polymers, a unitary chemical frame is needed. A series of observations suggest that formamide (NH 2 CHO) chemistry might have provided such a frame.To summarize the evidence: the one-carbon compound formamide is a highly versatile building block for the syntheses of all the necessary precursor nucleic bases. We have reported (Refs. 1-4 and references therein) the synthesis of purine, N 9 -formylpurine, adenine, N 9 , N6-diformyladenine, hypoxanthine, cytosine, hydroxypyrimidine, 4(3H)-pyrimidinone, uracil, 5,6-dihydrouracil, thymine, 5-hydroxymethyluracil, AICA (5-aminoimidazole-4-carboxamide), FAICA (5-formylaminoimidazole-4-carboxamide), and urea. These compounds are obtained from formamide heated in the presence of simple inorganic catalysts such as silica, alumina, zeolites, CaCO 3 , TiO 2 , common clays, kaolin, montmorillonites, olivines, and cosmic dust analogues of olivines. In all cases and for each catalyst several compounds were simultaneously formed, as summarized in Ref. 4.The richest yields were obtained in the presence of clays, TiO 2 , and cosmic dust analogues. Guanine is conspicuously absent, but a possible efficient substitute in base pairing might have been provided by hypoxanthine. Notably, formamide also yields purine acyclonucleosides through a formose-like condensation of N-formyl derivatives (2), providing a solution to the long-standing problem of the lack of reactivity between nucleobases and ribose or 2Ј-deoxyribose. In addition, formamide is an efficient activator of nucleoside transphosphorylation (Refs. 5-7), 2 further supporting its possible relevance in the prebiotic polymerization reactions that did lead to pregenetic informational macromolecules.Formamide is easily formed by hydrolysis of HCN and is stable in liquid form over a wide range of temperatures (2.5-2...

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Section: Comparison Of the Bond Stabilities In Ribo-and In 2ј-deoxyrimentioning

confidence: 99%

Origin of Informational Polymers

Saladino

Crestini

Ciciriello

et al. 2006

Journal of Biological Chemistry

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“…DNAzymes are catalytic single-stranded DNAs that can be obtained through in-vitro selection [21][22][23][24][25] . Two kinds of catalytic DNA sequences, RNA-cleaving DNAzyme (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23) 26,27 and G-quadruplex horseradish peroxidase-mimicking DNAzyme (PW17) [28][29][30] were applied in our research.…”

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confidence: 99%

“…Two kinds of catalytic DNA sequences, RNA-cleaving DNAzyme (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23) 26,27 and G-quadruplex horseradish peroxidase-mimicking DNAzyme (PW17) [28][29][30] were applied in our research. The 10-23 RNAcleaving DNAzyme has been reported to cleave any purinepyrimidine (RY) junction under simulated physiological conditions 26 ; hence, it was applied in our strategy for the cleaving of target RNA molecule to initiate the following exponential amplification.…”

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Cleavage-based signal amplification of RNA

2013

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RNA detection has become an integral part of current biomedical research. Up to now, the reverse transcription-PCR has been the most practical method to detect mRNA targets. However, RNA detection by reverse transcription-PCR requires sophisticated equipment and it is highly sensitive to contamination with genomic DNA. Here we report a new isothermal reaction to simultaneously amplify and detect RNA, based on cleavage by DNAzyme and signal amplification. Cleavage-based signal amplification of RNA cannot be contaminated by genomic DNA and is suitable for the detection of both mRNA and microRNA targets, with high specificity and sensitivity. Moreover, the detection results can be reported in a colorimetric or real-time fluorometric way for different detection purposes.

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“…21 Some of these involve changes in the phosphorylation status of an RNA or DNA strand, specifically DNA phosphorylation 23 and DNA adenylation (capping). 24 Other reactions include DNA deglycosylation, 25 porphyrin metalation, 26 thymine dimer photoreversion 27 and DNA cleavage.…”

Section: Deoxyribozymes That Covalently Modify Nucleic Acidsmentioning

confidence: 99%

“…32,33 Rate enhancements for other deoxyribozymes are as high as 10 10 . 21 Little is known about the structures and mechanisms of any deoxyribozymes. Only one crystal structure of a deoxyribozyme (the 10-23) has been obtained, and the structure revealed a catalytically inactive 2 : 2 DNA:RNA stoichiometry.…”

Section: Deoxyribozyme Catalytic Parameters Mechanisms and Structuresmentioning

confidence: 99%

Deoxyribozymes: DNA catalysts for bioorganic chemistry

Silverman

2004

Org. Biomol. Chem.

125

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T h i s j o u r n a l i s © T h e R o y a l S o c i e t y o f C h e m i s t r y 2 0 0 4 2 7 0 1 O r g . B i o m o l . C h e m . , 2 0 0 4 , 2 , 2 7 0 1 -2 7 0 6 OBC www.rsc.org/obc Deoxyribozymes are DNA molecules with catalytic activity. For historical and practical reasons, essentially all reported deoxyribozymes catalyze reactions of nucleic acid substrates, although this is probably not a fundamental limitation. In vitro selection strategies have been used to identify many deoxyribozymes that catalyze RNA cleavage, RNA and DNA ligation, and a variety of covalent modification reactions of nucleic acid substrates. Many deoxyribozymes are capable of catalysis with substantial rate enhancements reaching up to 10 10 -fold over background, and their very high selectivities would often be difficult or impossible to achieve using traditional organic synthesis approaches. This report summarizes the current utility and potential future applications of deoxyribozymes from the bioorganic chemistry perspective.

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Deoxyribozymes: new activities and new applications

Cited by 142 publications

References 75 publications

Origin of Informational Polymers

Origin of Informational Polymers

Cleavage-based signal amplification of RNA

Deoxyribozymes: DNA catalysts for bioorganic chemistry

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