Genomes and Genes
Summary: Molecules of DNA that possess enzymatic activity.
- Ferrari D, Peracchi A. A continuous kinetic assay for RNA-cleaving deoxyribozymes, exploiting ethidium bromide as an extrinsic fluorescent probe. Nucleic Acids Res. 2002;30:e112 pubmed..The method was developed for characterizing the so-called 8-17 catalytic DNA, but its general applicability in the deoxyribozyme field was verified using the 10-23 RNA-cleaving construct...
- Peracchi A. DNA catalysis: potential, limitations, open questions. Chembiochem. 2005;6:1316-22 pubmed
- Pan W, Devlin H, Kelley C, Isom H, Clawson G. A selection system for identifying accessible sites in target RNAs. RNA. 2001;7:610-21 pubmed..Identification of accessible sites should also be widely applicable to design of antisense oligonucleotides and DNAzymes. ..
- Brown A, Li J, Pavot C, Lu Y. A lead-dependent DNAzyme with a two-step mechanism. Biochemistry. 2003;42:7152-61 pubmed
- Zhang L, Gasper W, Stass S, Ioffe O, Davis M, Mixson A. Angiogenic inhibition mediated by a DNAzyme that targets vascular endothelial growth factor receptor 2. Cancer Res. 2002;62:5463-9 pubmed..This study indicates that DNAzymes, targeting angiogenic growth factors of tumors, show promise as antitumor agents. ..
- Sreedhara A, Li Y, Breaker R. Ligating DNA with DNA. J Am Chem Soc. 2004;126:3454-60 pubmed..However, the sequence requirements of the AppDNA and that of the 3' terminus of the deoxyribozyme ligase limit the range of sequences that can be ligated. ..
- Wang Y, Silverman S. Deoxyribozymes that synthesize branched and lariat RNA. J Am Chem Soc. 2003;125:6880-1 pubmed..Because nucleic acid enzymes apparently create branched RNA in nature (e.g., group II introns and the spliceosome), the new deoxyribozymes are of substantial mechanistic interest as well as practical importance. ..
- Ackermann J, Kanugula S, Pegg A. DNAzyme-mediated silencing of ornithine decarboxylase. Biochemistry. 2005;44:2143-52 pubmed..These results indicate that this DNAzyme may be a useful tool to study the function of ODC and may have potential therapeutic uses. ..
- Stojanovic M, de Prada P, Landry D. Homogeneous assays based on deoxyribozyme catalysis. Nucleic Acids Res. 2000;28:2915-8 pubmed..Deoxyribozymes with fluorescence-based reporting have the potential to serve as general analytical tools. ..
- Schubert S, Kurreck J. Ribozyme- and deoxyribozyme-strategies for medical applications. Curr Drug Targets. 2004;5:667-81 pubmed..Finally, the current significance of ribozymes will be discussed in the light of the emergence of new powerful anti-mRNA strategies, particularly RNA interference (RNAi). ..
- Chakraborti S, Banerjea A. Identification of cleavage sites in the HIV-1 TAR RNA by 10-23 and 8-17 catalytic motif containing DNA enzymes. Biomacromolecules. 2003;4:568-71 pubmed..These molecules, in principle, have the potential to down regulate expression of all HIV-1 transcripts from a wide range of isolates because this region is functionally very well conserved. ..
- Liu J, Lu Y. FRET study of a trifluorophore-labeled DNAzyme. J Am Chem Soc. 2002;124:15208-16 pubmed
- Vester B, Lundberg L, Sørensen M, Babu B, Douthwaite S, Wengel J. LNAzymes: incorporation of LNA-type monomers into DNAzymes markedly increases RNA cleavage. J Am Chem Soc. 2002;124:13682-3 pubmed..With the LNAzymes, efficient cleavage was accomplished also of a naturally occurring ribosomal RNA at a target site within a highly structured region. The reference DNAzyme was ineffective at cleaving the ribosomal RNA target. ..
- Mitchell A, Dass C, Sun L, Khachigian L. Inhibition of human breast carcinoma proliferation, migration, chemoinvasion and solid tumour growth by DNAzymes targeting the zinc finger transcription factor EGR-1. Nucleic Acids Res. 2004;32:3065-9 pubmedDNAzymes (synthetic catalytic DNA) have emerged as a new class of nucleic acid-based gene silencing agent...
- Pavlov V, Xiao Y, Gill R, Dishon A, Kotler M, Willner I. Amplified chemiluminescence surface detection of DNA and telomerase activity using catalytic nucleic acid labels. Anal Chem. 2004;76:2152-6 pubmed..The detection limit of the system corresponds to 1000 HeLa cells in the analyzed sample. ..
- Peracchi A. Preferential activation of the 8-17 deoxyribozyme by Ca(2+) ions. Evidence for the identity of 8-17 with the catalytic domain of the Mg5 deoxyribozyme. J Biol Chem. 2000;275:11693-7 pubmed..An 8-17 deoxyribozyme modeled after the Mg5 conserved region displayed catalytic features comparable with those reported for the full-length Mg5 deoxyribozyme. ..
- Liu J, Lu Y. A DNAzyme catalytic beacon sensor for paramagnetic Cu2+ ions in aqueous solution with high sensitivity and selectivity. J Am Chem Soc. 2007;129:9838-9 pubmed
- Hoadley K, Purtha W, Wolf A, Flynn Charlebois A, Silverman S. Zn2+-dependent deoxyribozymes that form natural and unnatural RNA linkages. Biochemistry. 2005;44:9217-31 pubmed
- Carrigan M, Ricardo A, Ang D, Benner S. Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selection. Biochemistry. 2004;43:11446-59 pubmed..This study of a specific catalytically active DNAzyme is an example of studies that will be necessary generally to permit in vitro selection to help us understand the distribution of function in sequence space. ..
- Steele D, Kertsburg A, Soukup G. Engineered catalytic RNA and DNA : new biochemical tools for drug discovery and design. Am J Pharmacogenomics. 2003;3:131-44 pubmed..The remarkable versatility of nucleic acid catalysis is thus the fountainhead for wide-ranging applications of ribozymes and deoxyribozymes in biomedical and biotechnological research. ..
- Cheong H, Hwang E, Lee C, Choi B, Cheong C. Rapid preparation of RNA samples for NMR spectroscopy and X-ray crystallography. Nucleic Acids Res. 2004;32:e84 pubmed..The 3' end tag is then removed by sequence-specific cleavage using trans-acting DNAzyme, the arm lengths of which are optimized for turnover number. This purification method is simpler and faster than the conventional method. ..
- Sioud M. Ribozyme- and siRNA-mediated mRNA degradation: a general introduction. Methods Mol Biol. 2004;252:1-8 pubmed
- Kubo T, Takamori K, Kanno K, Bakalova R, Rumiana B, Ohba H, et al. Efficient cleavage of RNA, enhanced cellular uptake, and controlled intracellular localization of conjugate DNAzymes. Bioorg Med Chem Lett. 2005;15:167-70 pubmed..To be pointed out, intracellular localization of DNAzymes could be controlled by conjugated with naturally occurring signal peptides responsible for nuclear cytoplasmic transport of proteins. ..
- Sando S, Sasaki T, Kanatani K, Aoyama Y. Amplified nucleic acid sensing using programmed self-cleaving DNAzyme. J Am Chem Soc. 2003;125:15720-1 pubmed..e., isothermal and enzyme/reagent-free, conditions. A fluorescence-reporting TASC probe having a fluorescein/dabsyl FRET pair across the cleavage site allows a mix-and-read discrimination of single-nucleotide differences in the target. ..
- Trülzsch B, Wood M. Applications of nucleic acid technology in the CNS. J Neurochem. 2004;88:257-65 pubmed..Recent advances in chemical modifications and delivery techniques are summarized. Applications in the CNS, including their use in primary neuronal cells, organotypic slice culture and the brain in vivo are further discussed. ..
- Yim T, Liu J, Lu Y, Kane R, Dordick J. Highly active and stable DNAzyme-carbon nanotube hybrids. J Am Chem Soc. 2005;127:12200-1 pubmed..Such high activity may allow myriad applications ranging from the directed assembly of nanomaterials to nanoscale cellular therapeutics that rely on the RNA cleaving ability of DNAzymes. ..
- Kolpashchikov D. A binary deoxyribozyme for nucleic acid analysis. Chembiochem. 2007;8:2039-42 pubmed
- Schlosser K, Li Y. DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides. Nucleic Acids Res. 2009;37:413-20 pubmed publisher..The demonstration of a catalytic DNA molecule made from a binary nucleotide alphabet broadens our understanding of the fundamental limits of ..
- Nunamaker E, Zhang H, Shirasawa Y, Benoit J, Dean D. Electroporation-mediated delivery of catalytic oligodeoxynucleotides for manipulation of vascular gene expression. Am J Physiol Heart Circ Physiol. 2003;285:H2240-7 pubmed..These results suggest that electroporation can be used to deliver DNAzymes and other DNA oligonucleotides to the vasculature in vivo and can decrease gene expression for a window of time that can be used for experimental studies. ..
- Sun L, Cairns M, Gerlach W, Witherington C, Wang L, King A. Suppression of smooth muscle cell proliferation by a c-myc RNA-cleaving deoxyribozyme. J Biol Chem. 1999;274:17236-41 pubmedA small catalytic DNA molecule targeting c-myc RNA was found to be a potent inhibitor of smooth muscle cell (SMC) proliferation. The catalytic domain of this molecule was based on that previously derived by in vitro selection (Santoro, S...
- Ricca B, Wolf A, Silverman S. Optimization and generality of a small deoxyribozyme that ligates RNA. J Mol Biol. 2003;330:1015-25 pubmed..The compact 7Q10 deoxyribozyme has both practical utility and the potential for increasing our structural and mechanistic understanding of how nucleic acids can mediate chemical reactions. ..
- Wang D, Lai B, Feldman A, Sen D. A general approach for the use of oligonucleotide effectors to regulate the catalysis of RNA-cleaving ribozymes and DNAzymes. Nucleic Acids Res. 2002;30:1735-42 pubmed..Expansive regulation therefore represents a new and potentially useful technology for both the regulation of nucleic acid enzymes and the detection of specific RNA transcripts. ..
- Tan X, Rose K, Margolin W, Chen Y. DNA enzyme generated by a novel single-stranded DNA expression vector inhibits expression of the essential bacterial cell division gene ftsZ. Biochemistry. 2004;43:1111-7 pubmed
- Stojanovic M, Stefanovic D. Deoxyribozyme-based half-adder. J Am Chem Soc. 2003;125:6673-6 pubmed..Together, this system represents the first example of a decision-making enzymatic network with two inputs and two outputs. Similar systems could be applied to control autonomous therapeutic and diagnostic devices. ..
- Schlosser K, Li Y. Diverse evolutionary trajectories characterize a community of RNA-cleaving deoxyribozymes: a case study into the population dynamics of in vitro selection. J Mol Evol. 2005;61:192-206 pubmed..This is the first study which thoroughly documents the topography of a deoxyribozyme fitness landscape over many generations of in vitro selection. ..
- Kim H, Rasnik I, Liu J, Ha T, Lu Y. Dissecting metal ion-dependent folding and catalysis of a single DNAzyme. Nat Chem Biol. 2007;3:763-8 pubmed..These features may contribute to the unusually fast Pb2+-dependent reaction of the DNAzyme. These results suggest that DNAzymes can use all modes of activation that metalloproteins use. ..
- Swearingen C, Wernette D, Cropek D, Lu Y, Sweedler J, Bohn P. Immobilization of a catalytic DNA molecular beacon on Au for Pb(II) detection. Anal Chem. 2005;77:442-8 pubmed
- Okumoto Y, Ohmichi T, Sugimoto N. Immobilized small deoxyribozyme to distinguish RNA secondary structures. Biochemistry. 2002;41:2769-73 pubmed..These results show that the immobilized deoxyribozymes on a column and on an SPR sensor chip become a novel and useful tool to distinguish the RNA foldings. ..
- Wang W, Billen L, Li Y. Sequence diversity, metal specificity, and catalytic proficiency of metal-dependent phosphorylating DNA enzymes. Chem Biol. 2002;9:507-17 pubmed..8 min(-1). Our findings suggest that DNA has sufficient structural diversity to facilitate efficient catalysis using a broad scope of metal cofactor utilizing mechanisms. ..
- Coppins R, Silverman S. A DNA enzyme that mimics the first step of RNA splicing. Nat Struct Mol Biol. 2004;11:270-4 pubmed..First, branch-site adenosine reactivity seems to be mechanistically favored by nucleic acid enzymes. Second, hydroxyl groups are not obligatory components of nucleic acid enzymes that carry out biologically related catalysis. ..
- Todd A, Fuery C, Impey H, Applegate T, Haughton M. DzyNA-PCR: use of DNAzymes to detect and quantify nucleic acid sequences in a real-time fluorescent format. Clin Chem. 2000;46:625-30 pubmed..DzyNA-PCR is a simple, rapid, and sensitive technique for homogeneous amplification and quantification of nucleic acids in clinical specimens. ..
- Hengesbach M, Meusburger M, Lyko F, Helm M. Use of DNAzymes for site-specific analysis of ribonucleotide modifications. RNA. 2008;14:180-7 pubmed..The excised fragment is isolated by electrophoresis and submitted to further conventional analysis. These results establish DNAzymes as valuable tools for the site-specific and highly sensitive detection of ribonucleotide modifications. ..
- Vester B, Hansen L, Lundberg L, Babu B, Sørensen M, Wengel J, et al. Locked nucleoside analogues expand the potential of DNAzymes to cleave structured RNA targets. BMC Mol Biol. 2006;7:19 pubmed..014 min-1 to 0.78 min-1). The data demonstrate how hydrolytic performance can be enhanced by design of LNAzymes, and indicate that there are optimal lengths for the binding arms and for the number of modified LNA monomers. ..
- Peracchi A. Prospects for antiviral ribozymes and deoxyribozymes. Rev Med Virol. 2004;14:47-64 pubmed
- Lederman H, Macdonald J, Stefanovic D, Stojanovic M. Deoxyribozyme-based three-input logic gates and construction of a molecular full adder. Biochemistry. 2006;45:1194-9 pubmed..Similar systems could be applied to control autonomous therapeutic and diagnostic devices. ..
- Liu J, Lu Y. A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles. J Am Chem Soc. 2003;125:6642-3 pubmed
- Liu J, Lu Y. Improving fluorescent DNAzyme biosensors by combining inter- and intramolecular quenchers. Anal Chem. 2003;75:6666-72 pubmed..The design principle presented here should be applicable to other nucleic acid-based biosensors to decrease background fluorescence. ..
- Schlosser K, Li Y. Tracing sequence diversity change of RNA-cleaving deoxyribozymes under increasing selection pressure during in vitro selection. Biochemistry. 2004;43:9695-707 pubmed..Thus, sufficient sequence diversity in the DNA pool (and hence more catalytic DNA sequences) is a prerequisite for the successful isolation of efficient deoxyribozymes...
- Fiammengo R, Jäschke A. Nucleic acid enzymes. Curr Opin Biotechnol. 2005;16:614-21 pubmed..The versatility of these catalysts supports the idea of an ancestral world based on RNA predating the emergence of proteins, and also drives many studies towards practical applications for nucleic acid enzymes. ..
- Emilsson G, Breaker R. Deoxyribozymes: new activities and new applications. Cell Mol Life Sci. 2002;59:596-607 pubmed..These results indicate that the true catalytic power of DNA is limited by discovery and not by chemistry. ..
- Achenbach J, Jeffries G, McManus S, Billen L, Li Y. Secondary-structure characterization of two proficient kinase deoxyribozymes. Biochemistry. 2005;44:3765-74 pubmed
- Cieslak M, Niewiarowska J, Nawrot M, Koziolkiewicz M, Stec W, Cierniewski C. DNAzymes to beta 1 and beta 3 mRNA down-regulate expression of the targeted integrins and inhibit endothelial cell capillary tube formation in fibrin and matrigel. J Biol Chem. 2002;277:6779-87 pubmed..In conclusion, DNAzymes to beta(1) and beta(3) mRNAs with 2'-O-methyl modifications are potentially useful as gene-inactivating agents and may ultimately provide a therapeutic means to inhibit angiogenesis in vivo. ..
- Fahmy R, Khachigian L. Locked nucleic acid modified DNA enzymes targeting early growth response-1 inhibit human vascular smooth muscle cell growth. Nucleic Acids Res. 2004;32:2281-5 pubmed..These studies also demonstrate that LNA modification increases DNAzyme potency without necessarily compromising specificity. ..