201
|
Affiliation(s)
- Dana A Baum
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | | |
Collapse
|
202
|
Lu Y, Liu J. Smart nanomaterials inspired by biology: dynamic assembly of error-free nanomaterials in response to multiple chemical and biological stimuli. Acc Chem Res 2007; 40:315-23. [PMID: 17474707 DOI: 10.1021/ar600053g] [Citation(s) in RCA: 209] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three-dimensional functional nanoscale assembly requires not only self-assembly of individual nanomaterials responsive to external stimuli, such as temperature, light, and concentrations, but also directed assembly of many different nanomaterials in one-pot responsive to multiple internal stimuli signaling the needs for such materials at a specific location and a particular time. The use of functional DNA (DNAzymes, aptamers, and aptazymes) to meet these challenges is reviewed. In addition, a biology-inspired proof-reading and error correction method is introduced to cope with errors in nanomaterials assembly.
Collapse
Affiliation(s)
- Yi Lu
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana--Champaign, Urbana, Illinois 61801, USA.
| | | |
Collapse
|
203
|
Timofeev E, Mikhailov S, Zuev A, Efimtseva E, Herdewijn P, Somers R, Lemaitre M. Oligodeoxynucleotides Containing 2′-Deoxy-1-methyladenosine andDimroth Rearrangement. Helv Chim Acta 2007. [DOI: 10.1002/hlca.200790093] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
204
|
Synthesis of oligo-2′-O-methylribonucleotides containing α-amino acid residues in 2′-position. Russ Chem Bull 2007. [DOI: 10.1007/s11172-007-0120-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
205
|
Ting R, Thomas JM, Perrin DM. Kinetic characterization of a cis- and trans-acting M2+-independent DNAzyme that depends on synthetic RNaseA-like functionality — Burst-phase kinetics from the coalescence of two active DNAzyme folds. CAN J CHEM 2007. [DOI: 10.1139/v07-037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This work describes the kinetics of the DNAzyme 925-11, a combinatorially selected, M2+-independent ribophosphodiesterase that is covalently modified with both cationic amines and imidazoles. At 13 °C, cis- and trans-cleaving constructs of 925-11 demonstrate the highest rate constants reported to date for any M2+-independent nucleic acid catalyst, investigated at physiological ionic strength and pH 7.5 (0.3 min–1for self cleavage and 0.2 min–1for intermolecular cleavage). In contrast to the cis-cleaving species, single-turnover experiments with the trans-cleaving species exhibit biphasic cleavage data, suggesting the presence of two conformations of the catalyst–substrate complex. Pulse–chase experiments demonstrate that both complexes lead to substrate cleavage. Under multiple-turnover conditions, the higher rate constant appears in a burst phase that decays to a slower steady state exhibiting a rate constant of 0.0077 min–1, a value approximating that of the slow-cleaving phase seen in single-turnover experiments. Slow product release is excluded as the source of the burst phase. An integrated rate equation is derived to describe burst-phase kinetics based on the funneling of the initial population of fast-cleaving conformation into a steady-state population composed largely of the slow-cleaving conformation.Key words: RNase mimics, DNAzymes, ribozymes, kinetics, RNA cleavage.
Collapse
|
206
|
Ali MM, Kandadai SA, Li Y. Characterization of pH3DZ1 — An RNA-cleaving deoxyribozyme with optimal activity at pH 3. CAN J CHEM 2007. [DOI: 10.1139/v07-017] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We previously described a cis-acting RNA-cleaving deoxyribozyme known as pH3DZ1 that exhibits optimal catalytic activity at pH 3.0 (Zhongjie Liu, Shirley H. Mei, John D. Brennan, and Yingfu Li. J. Am. Chem. Soc. 125, 7539 (2003)). This DNA catalyst was made of a 99-nucleotide (nt) catalytic domain covalently linked to a 23-nt DNA–RNA chimeric substrate containing a single ribonucleotide as the cleavage site. In the present work, we conducted an extensive sequence examination of this deoxyribozyme via nucleotide truncation and reselection experiments, with a goal to minimize its size and identify the nucleotides that are crucial to its catalytic function. A trans-acting deoxyribozyme that can process an external substrate was also successfully designed. Stretches of 30 and 17 nucleotides from the 5′ and 3′ ends of the trans catalyst, respectively, were found to be completely dispensable; in contrast, few nucleotides could be deleted internally without producing a detrimental effect. The reselection experiment led to the discovery of 7 and 5 absolutely conserved nucleotides located at the 5′ and 3′ ends of the minimized catalyst, respectively, separated by a 31-nt element in which 14 highly conserved nucleotides were scattered among 17 variable nucleotides. The shortened deoxyribozyme and the original catalyst showed a similar pH profile with the optimal activity at pH 3; however, the minimized deoxyribozyme still exhibited strong catalytic activity at pH 2.5, while the full-length catalyst was barely active at this pH. Finally, it was found that this deoxyribozyme generated two cleavage fragments, one with 2′,3′-cyclic phosphate and the other with 5′-OH.Key words: DNA, deoxyribozyme, RNA cleavage, in vitro selection, catalysis.
Collapse
|
207
|
Buchhaupt M, Peifer C, Entian KD. Analysis of 2′-O-methylated nucleosides and pseudouridines in ribosomal RNAs using DNAzymes. Anal Biochem 2007; 361:102-8. [PMID: 17181990 DOI: 10.1016/j.ab.2006.11.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Revised: 10/21/2006] [Accepted: 11/01/2006] [Indexed: 11/21/2022]
Abstract
Ribosomal RNAs (rRNAs) contain a large number of posttranscriptionally modified nucleosides, the physiological function of which is still unclear. The great majority of modifications in eukaryotes and archaea are 2'-O-ribose methylated nucleosides and pseudouridines. The current methods to identify rRNA modifications are difficult to perform and need expensive reagents. Here we report an easy method to detect 2'-O-ribose methylations using RNA-cleaving deoxyribozymes (DNAzymes) and demonstrate its application using rRNA of the yeast Saccharomyces cerevisiae. Using DNAzymes of the 10-23 type, we could show that cleavage at A(973) in the 18S rRNA or at G(1450) in the 25S rRNA from S. cerevisiae occurs only if the 2'-O-ribose methylations at these positions were missing. We also designed 8-17-DNAzymes for the detection of 2'-O-ribose methylations. This makes all 2'-O-ribose methylations accessible to the DNAzyme technique as variants of the 8-17-DNAzyme that together have the ability to cleave nearly any dinucleotide junction are known. Furthermore, we found that pseudouridine also decreases the DNAzyme cleavage efficiency at the adjacent phosphodiester bond and thus can also be identified with DNAzymes. The analysis using DNAzymes provides a new tool to easily identify ribose methylations in rRNAs and will help to unravel the physiological function of nucleotide modifications.
Collapse
Affiliation(s)
- Markus Buchhaupt
- Center of Excellence, Macromolecular Complexes, Johann Wolfgang Goethe-University, Institute of Molecular Biosciences, 60438 Frankfurt/Main, Germany
| | | | | |
Collapse
|
208
|
Nawrot B, Widera K, Wojcik M, Rebowska B, Nowak G, Stec WJ. Mapping of the functional phosphate groups in the catalytic core of deoxyribozyme 10-23. FEBS J 2007; 274:1062-72. [PMID: 17250742 DOI: 10.1111/j.1742-4658.2007.05655.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The RNA phosphodiester bond cleavage activity of a series of 16 thio-deoxyribozymes 10-23, containing a P-stereorandom single phosphorothioate linkage in predetermined positions of the catalytic core from P1 to P16, was evaluated under single-turnover conditions in the presence of either 3 mM Mg(2+) or 3 mM Mn(2+). A metal-specificity switch approach permitted the identification of nonbridging phosphate oxygens (proR(P) or proS(P)) located at seven positions of the core (P2, P4 and P9-13) involved in direct coordination with a divalent metal ion(s). By contrast, phosphorothioates at positions P3, P6, P7 and P14-16 displayed no functional relevance in the deoxyribozyme-mediated catalysis. Interestingly, phosphorothioate modifications at positions P1 or P8 enhanced the catalytic efficiency of the enzyme. Among the tested deoxyribozymes, thio-substitution at position P5 had the largest deleterious effect on the catalytic rate in the presence of Mg(2+), and this was reversed in the presence of Mn(2+). Further experiments with thio-deoxyribozymes of stereodefined P-chirality suggested direct involvement of both oxygens of the P5 phosphate and the proR(P) oxygen at P9 in the metal ion coordination. In addition, it was found that the oxygen atom at C6 of G(6) contributes to metal ion binding and that this interaction is essential for 10-23 deoxyribozyme catalytic activity.
Collapse
Affiliation(s)
- Barbara Nawrot
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies of the Polish Academy of Sciences, Lodz, Poland.
| | | | | | | | | | | |
Collapse
|
209
|
Abstract
One of the hallmarks of DNA and RNA structures is their elegant chirality. Using these chiral structures to induce enantioselectivity in chemical synthesis is as enticing as it is challenging. In recent years, three general approaches have been developed to achieve this, including chirality transfer by nucleotide templated synthesis, enantioselective catalysis by RNA/DNAzymes and DNA-based asymmetric catalysis. In this article the concepts behind these strategies as well as the important achievements in this field will be discussed.
Collapse
Affiliation(s)
- Gerard Roelfes
- Department of Organic Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| |
Collapse
|
210
|
Leung EKY, Sen D. Electron Hole Flow Patterns through the RNA-Cleaving 8-17 Deoxyribozyme Yield Unusual Information about Its Structure and Folding. ACTA ACUST UNITED AC 2007; 14:41-51. [PMID: 17254951 DOI: 10.1016/j.chembiol.2006.11.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Revised: 10/31/2006] [Accepted: 11/06/2006] [Indexed: 11/21/2022]
Abstract
DNA double helices have been shown to conduct electron holes over significant distances. Here, we report on the hole flow patterns within a more intricately folded DNA complex, the 8-17 deoxyribozyme bound to a DNA pseudosubstrate, incorporating three helical elements and two catalytically relevant loops. The observed hole flow patterns within the complex permitted a quantitative assessment of the stacking preferences of the three constituent helices and provided evidence for significant transitions within the complex's global geometry. The patterns further suggested varying levels of solvent exposure of the complex's constituent parts, and revealed that a catalytically relevant cytosine within the folded complex exists in an unusual structural/electronic environment. Our data suggest that the study of charge flow may provide novel perspectives on the structure and folding of intricately folded DNAs and RNAs.
Collapse
Affiliation(s)
- Edward K Y Leung
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | | |
Collapse
|
211
|
Chiuman W, Li Y. Efficient signaling platforms built from a small catalytic DNA and doubly labeled fluorogenic substrates. Nucleic Acids Res 2006; 35:401-5. [PMID: 17169997 PMCID: PMC1802601 DOI: 10.1093/nar/gkl1056] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RNA-cleaving deoxyribozyme 8-17 has been increasingly used in nanotechnology and biosensing applications. Conventional methods to equip 8-17 with fluorescent signaling property usually involve covalent attachment of two dyes at nucleotide positions that are far away from the catalytic core, such that the bulky dye structures would not affect the deoxyribozyme activity. However, the maximum fluorescent enhancement associated with these 8-17 constructs is typically ≤10-fold, due to a high fluorescent background. To find an optimal balance between signal enhancement and signaling speed, we have conducted a comprehensive study on the effects of the nature of dyes (Alexa Fluor 488, 546 and 647; QSY 9 and 21) as well as their attaching positions along the substrate strand on the catalytic and signaling performance of 8-17. Our results have indicated that 8-17 is able to cleave almost every modified substrate, including those that have chromophores only 1 nt away from the cleavage site. Most importantly, almost all of these substrates are able to generate 15- to 85-fold signal enhancement within 10 min. We have also provided guidelines for selecting substrates that could offer the best signal enhancement, the fastest signaling speed, or the best balance between signal enhancement and signaling speed.
Collapse
Affiliation(s)
- William Chiuman
- Department of Biochemistry and Biomedical Sciences, McMaster University1280 Main Street W. Hamilton, ON, Canada L8N 3Z5
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University1280 Main Street W. Hamilton, ON, Canada L8N 3Z5
- Department of Chemistry, McMaster University1280 Main Street W. Hamilton, ON, Canada L8N 3Z5
- To whom correspondence should be addressed. Tel: +1 905 525 9140 ext. 22462; Fax: +1 905 522 9033;
| |
Collapse
|
212
|
Shen Y, Chiuman W, Brennan JD, Li Y. Catalysis and rational engineering of trans-acting pH6DZ1, an RNA-cleaving and fluorescence-signaling deoxyribozyme with a four-way junction structure. Chembiochem 2006; 7:1343-8. [PMID: 16888734 DOI: 10.1002/cbic.200600195] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yutu Shen
- Department of Chemistry, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
| | | | | | | |
Collapse
|
213
|
Chiuman W, Li Y. Evolution of High-Branching Deoxyribozymes from a Catalytic DNA with a Three-Way Junction. ACTA ACUST UNITED AC 2006; 13:1061-9. [PMID: 17052610 DOI: 10.1016/j.chembiol.2006.08.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 08/11/2006] [Accepted: 08/25/2006] [Indexed: 11/25/2022]
Abstract
Here, we report the evolution of two star-shaped (five-way junction) deoxyribozymes from a catalytic DNA containing a three-way junction scaffold. The transition was shown to be a switch rather than a gradual progression. The star-shaped motifs, surprisingly, only took five selection cycles to be detected, and another four to dominate the evolving population. Chemical probing experiments indicated that the two deoxyribozymes belong to the same family despite noticeable variations in both the primary sequence and the secondary structure. Our findings not only describe the evolution of high-branching nucleic acid structures from a low-branching catalytic module, but they also illustrate the idea of deriving a rare structural motif by sampling the sequence variants of a given functional nucleic acid.
Collapse
Affiliation(s)
- William Chiuman
- Department of Biochemistry and Biomedical Sciences and Department of Chemistry, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
| | | |
Collapse
|
214
|
Abstract
RNA molecules play important and diverse regulatory roles in the cell by virtue of their interaction with other nucleic acids, proteins and small molecules. Inspired by this natural versatility, researchers have engineered RNA molecules with new biological functions. In the last two years efforts in synthetic biology have produced novel, synthetic RNA components capable of regulating gene expression in vivo largely in bacteria and yeast, setting the stage for scalable and programmable cellular behavior. Immediate challenges for this emerging field include determining how computational and directed-evolution techniques can be implemented to increase the complexity of engineered RNA systems, as well as determining how such systems can be broadly extended to mammalian systems. Further challenges include designing RNA molecules to be sensors of intracellular and environmental stimuli, probes to explore the behavior of biological networks and components of engineered cellular control systems.
Collapse
Affiliation(s)
- Farren J Isaacs
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
| | | | | |
Collapse
|
215
|
Hou W, Ni Q, Wo J, Li M, Liu K, Chen L, Hu Z, Liu R, Hu M. Inhibition of hepatitis B virus X gene expression by 10-23 DNAzymes. Antiviral Res 2006; 72:190-6. [PMID: 16930733 DOI: 10.1016/j.antiviral.2006.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2005] [Revised: 06/03/2006] [Accepted: 07/04/2006] [Indexed: 01/08/2023]
Abstract
The X protein (HBx) of human hepatitis B virus (HBV) is a transcriptional activator protein. The HBx protein plays an important role in viral replication in HBV infected cells and the liver diseases including hepatitis, cirrhosis and hepatocellular carcinoma (HCC). Therefore, the repression of HBx gene expression by 10-23 DNAzymes might be a good way to inhibit HBV replication and counteract HBV-related liver diseases. We designed three 10-23 DNAzymes with different substrate-recognition domains. When each of the 10-23 DNAzymes were cotransfected into human AD293 cells with HBx-EGFP expression plasmid, they could all reduce the level of HBx mRNA as well as the HBx-EGFP protein. These results suggest that the 10-23 DNAzymes might be used for gene therapy of liver diseases caused by HBV.
Collapse
Affiliation(s)
- Wei Hou
- Key Laboratory of Infectious Diseases, Ministry of Public Health of China, Institute of Infectious Diseases, First Affiliated Hospital, College of Medical Sciences, Zhejiang University, Qingchun Road 79, Hangzhou, Zhejiang 310003, China
| | | | | | | | | | | | | | | | | |
Collapse
|
216
|
Keiper S, Vyle JS. Reversible Photocontrol of Deoxyribozyme-Catalyzed RNA Cleavage under Multiple-Turnover Conditions. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600164] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
217
|
Liu J, Lu Y. Design of asymmetric DNAzymes for dynamic control of nanoparticle aggregation states in response to chemical stimuli. Org Biomol Chem 2006; 4:3435-41. [PMID: 17036137 DOI: 10.1039/b605799c] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynamic control of nanomaterial assembly states in response to chemical stimuli is critical in making multi-component materials with interesting properties. Previous work has shown that a Pb2+-specific DNAzyme allowed dynamic control of gold nanoparticle aggregation states in response to Pb2+, and the resulting color change from blue aggregates to red dispersed particles can be used as a convenient way of sensing Pb2+. However, a small piece of DNA (called invasive DNA) and low ionic strength (approximately 30 mM) were required for the process, limiting the scope of application in assembly and sensing. To overcome this limitation, a series of asymmetric DNAzymes, in which one of the two substrate binding regions is longer than the other, has been developed. With such a system, we demonstrated Pb2+-induced disassembly of gold nanoparticle aggregates and corresponding color change at room temperature without the need for invasive DNA, while also making the system more tolerant to ionic strength (33-100 mM). The optimal lengths of the long and short arms were determined to be 14 and 5 base pairs, respectively. In nanoparticle aggregates, the activity of the DNAzyme increased with decreasing ionic strength of the reaction buffer. This simpler and more versatile system allows even better dynamic control of nanoparticle aggregation states in response to chemical stimuli such as Pb2+, and can be used in a wider range of applications for colorimetric sensing of metal ions.
Collapse
Affiliation(s)
- Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | |
Collapse
|
218
|
Kandadai SA, Chiuman W, Li Y. Phosphoester-transfer mechanism of an RNA-cleaving acidic deoxyribozyme revealed by radioactivity tracking and enzymatic digestion. Chem Commun (Camb) 2006:2359-61. [PMID: 16733579 DOI: 10.1039/b604682g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A convenient method involving 32P-labeling of an RNA substrate at the cleavage site and subsequent enzymatic digestion of cleavage products via phosphatases reveals that pH4DZ1--an RNA-cleaving deoxyribozyme with optimal activity at pH 4--forms a 5'-cleavage fragment with 2',3'-cyclic phosphate group and a 3'-cleavage fragment with 5'-OH group.
Collapse
Affiliation(s)
- Srinivas A Kandadai
- Department of Biochemistry and Biomedical Sciences, Department of Chemistry, McMaster University, 1280 Main St. W. Hamilton, ON L8N 3Z5, Canada
| | | | | |
Collapse
|