201
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Fry I. The role of natural selection in the origin of life. ORIGINS LIFE EVOL B 2011; 41:3-16. [PMID: 20407927 DOI: 10.1007/s11084-010-9214-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 04/06/2010] [Indexed: 11/27/2022]
Abstract
It is commonly accepted among origin-of-life scientists that the emergence of life was an evolutionary process involving at one stage or other the working of natural selection. Researchers disagree, however, on the nature of the chemical infrastructure that could have formed prebiotically, enabling the evolutionary process. The division of the origin-of-life research community into 'geneticists' and 'metabolists' usually revolves around the issue whether the first to arise prebiotically was a genetic polymer or a primitive metabolic system. In this paper I offer an alternative classification based on the attitude to the onset of natural selection. From this perspective I add to the conventional division between gene-first and metabolism-first groups a position I call "preparatory metabolism". By this line of thought, an RNA or an RNA-like polymer could not have emerged prebiotically. Nevertheless, the onset of natural selection had to wait until such a polymer had arised. This paper examines the RNA-first, RNA-later, metabolism-first and preparatory-metabolism scenarios, assessing the weaknesses and strengths of each. I conclude that despite the recent theoretical advances in all these lines of research, and despite experimental breakthroughs, especially in overcoming several RNA-first hurdles, none of the examined paradigms has yet attained decisive experimental support. Demonstrating the evolvability of a potentially prebiotic infrastructure, whether genetic or metabolic, is a most serious challenge. So is the experimental demonstration of the emergence of such an infrastructure under prebiotic conditions. The current agenda before origin-of-life researchers of all stripes and colors is the search for the experimental means to tackle all these difficulties.
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Affiliation(s)
- Iris Fry
- Department of Humanities and Arts, Technion-Israel Institute of Technology, Technion City, Haifa, 32000, Israel.
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202
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Silverman SK. DNA as a versatile chemical component for catalysis, encoding, and stereocontrol. Angew Chem Int Ed Engl 2011; 49:7180-201. [PMID: 20669202 DOI: 10.1002/anie.200906345] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNA (deoxyribonucleic acid) is the genetic material common to all of Earth's organisms. Our biological understanding of DNA is extensive and well-exploited. In recent years, chemists have begun to develop DNA for nonbiological applications in catalysis, encoding, and stereochemical control. This Review summarizes key advances in these three exciting research areas, each of which takes advantage of a different subset of DNA's useful chemical properties.
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Affiliation(s)
- Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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203
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Shimron S, Magen N, Elbaz J, Willner I. pH-programmable DNAzyme nanostructures. Chem Commun (Camb) 2011; 47:8787-9. [DOI: 10.1039/c1cc12795k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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204
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Sugiyama R, Hayafune M, Habu Y, Yamamoto N, Takaku H. HIV-1 RT-dependent DNAzyme expression inhibits HIV-1 replication without the emergence of escape viruses. Nucleic Acids Res 2011; 39:589-98. [PMID: 20833635 PMCID: PMC3025543 DOI: 10.1093/nar/gkq794] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 08/18/2010] [Accepted: 08/23/2010] [Indexed: 12/12/2022] Open
Abstract
DNAzymes are easier to prepare and less sensitive to chemical and enzymatic degradation than ribozymes; however, a DNA enzyme expression system has not yet been developed. In this study, we exploited the mechanism of HIV-1 reverse transcription (RT) in a DNA enzyme expression system. We constructed HIV-1 RT-dependent lentiviral DNAzyme expression vectors including the HIV-1 primer binding site, the DNA enzyme, and either a native tRNA (Lys-3), tR(M)DtR(L), or one of two truncated tRNAs (Lys-3), tR(M)DΔARMtR(L) or tR(M)D3'-endtR(L). Lentiviral vector-mediated DNAzyme expression showed high levels of inhibition of HIV-1 replication in SupT1 cells. We also demonstrated the usefulness of this approach in a long-term assay, in which we found that the DNAzymes prevented escape from inhibition of HIV. These results suggest that HIV-1 RT-dependent lentiviral vector-derived DNAzymes prevent the emergence of escape mutations.
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Affiliation(s)
- Ryuichi Sugiyama
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Masaaki Hayafune
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Yuichiro Habu
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Norio Yamamoto
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hiroshi Takaku
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
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205
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Abstract
Nucleic acids have been demonstrated to be versatile nanoscale engineering materials with the construction of dynamic DNA structures, motors, and circuits. These constructions generally rely on the clever use and integration of relatively few reaction mechanisms and design primitives. Here, cooperative hybridization is introduced as a mechanism in which two oligonucleotides of independent sequence can stoichiometrically, simultaneously, and cooperatively hybridize to a DNA complex. Cooperative hybridization is rigorously characterized and modeled and is shown to implement digital concentration comparison with amplification, as well as digital Boolean logic. These designs, based on cooperative hybridization, excel in being robust to impurities and not requiring oligonucleotide purification.
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Affiliation(s)
- David Yu Zhang
- California Institute of Technology, Pasadena, California 91125, United States
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206
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207
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Xiao Y, Allen EC, Silverman SK. Merely two mutations switch a DNA-hydrolyzing deoxyribozyme from heterobimetallic (Zn2+/Mn2+) to monometallic (Zn2+-only) behavior. Chem Commun (Camb) 2010; 47:1749-51. [PMID: 21125108 DOI: 10.1039/c0cc04575f] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A deoxyribozyme that hydrolyzes DNA phosphodiester linkages with a requirement for both Zn(2+) and Mn(2+) is switched by only two nucleotide mutations to require Zn(2+) alone, demonstrating that DNA-catalyzed DNA hydrolysis can be achieved using only one metal ion cofactor.
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Affiliation(s)
- Ying Xiao
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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208
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209
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Ruff KM, Snyder TM, Liu DR. Enhanced functional potential of nucleic acid aptamer libraries patterned to increase secondary structure. J Am Chem Soc 2010; 132:9453-64. [PMID: 20565094 PMCID: PMC2898215 DOI: 10.1021/ja103023m] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The in vitro selection of nucleic acid libraries has driven the discovery of RNA and DNA receptors (aptamers) and catalysts with tailor-made functional properties. Functional nucleic acids emerging from selections have been observed to possess an unusually high degree of secondary structure. In this study, we experimentally examined the relationship between the degree of secondary structure in a nucleic acid library and its ability to yield aptamers that bind protein targets. We designed a patterned nucleic acid library (denoted R*Y*) to enhance the formation of stem-loop structures without imposing any specific sequence or secondary structural requirement. This patterned library was predicted computationally to contain a significantly higher average folding energy compared to a standard, unpatterned N(60) library of the same length. We performed three different iterated selections for protein binding using patterned and unpatterned libraries competing in the same solution. In all three cases, the patterned R*Y* library was enriched relative to the unpatterned library over the course of the 9- to 10-round selection. Characterization of individual aptamer clones emerging from the three selections revealed that the highest affinity aptamer assayed arose from the patterned library for two protein targets, while in the third case, the highest affinity aptamers from the patterned and random libraries exhibited comparable affinity. We identified the binding motif requirements for the most active aptamers generated against two of the targets. The two binding motifs are 3.4- and 27-fold more likely to occur in the R*Y* library than in the N(60) library. Collectively, our findings suggest that researchers performing selections for nucleic acid aptamers and catalysts should consider patterned libraries rather than commonly used N(m) libraries to increase both the likelihood of isolating functional molecules and the potential activities of the resulting molecules.
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Affiliation(s)
- Karen M Ruff
- Howard Hughes Medical Institute and the Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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210
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Mazumdar D, Nagraj N, Kim HK, Meng X, Brown AK, Sun Q, Li W, Lu Y. Activity, folding and Z-DNA formation of the 8-17 DNAzyme in the presence of monovalent ions. J Am Chem Soc 2010; 131:5506-15. [PMID: 19326878 DOI: 10.1021/ja8082939] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The effect of monovalent ions on both the reactivity and global folding of the 8-17 DNAzyme is investigated, and the results are compared with those of the hammerhead ribozyme, which has similar size and secondary structure. In contrast to the hammerhead ribozyme, the 8-17 DNAzyme activity is not detectable in the presence of 4 M K(+), Rb(+), or Cs(+) or in the presence of 80 mM, [Co(NH(3))(6)](3+). Only 4 M Li(+), NH(4)(+) and, to a lesser extent, Na(+) conferred detectable activity. The observed rate constants (k(obs) approximately 10(-3) min(-1) for Li(+) and NH(4)(+)) are approximately 1000-fold lower than that in the presence of 10 mM Mg(2+), and approximately 200,000-fold slower than that in the presence of 100 microM Pb(2+). Since the hammerhead ribozyme displays monovalent ion-dependent activity that is often within approximately 10-fold of divalent metal ion-dependent activity, these results suggest that the 8-17 DNAzyme, obtained by in vitro selections, has evolved to have a more stringent divalent metal ion requirement for high activity as compared to the naturally occurring ribozymes, making the 8-17 DNAzyme an excellent choice as a Pb(2+) sensor with high selectivity. In contrast to the activity data, folding was observed in the presence of all the monovalent ions investigated, although those monovalent ions that do not support DNAzyme activity have weaker binding affinity (K(d) approximately 0.35 M for Rb(+) and Cs(+)), while those that confer DNAzyme activity possess stronger affinity (K(d) approximately 0.22 M for Li(+), Na(+) and NH(4)(+)). In addition, a correlation between metal ion charge density, binding affinity and enzyme activity was found among mono- and divalent metal ions except Pb(2+); higher charge density resulted in stronger affinity and higher activity, suggesting that the observed folding and activity is at least partially due to electrostatic interactions between ions and the DNAzyme. Finally, circular dichroism (CD) study has revealed Z-DNA formation with the monovalent metal ions, Zn(2+) and Mg(2+); the K(d) values obtained using CD were in the same range as those obtained from folding studies using FRET. However, Z-DNA formation was not observed with Pb(2+). These results indicate that Pb(2+)-dependent function follows a different mechanism from the monovalent metal ions and other divalent metal ions; in the presence of latter metal ions, metal-ion dependent folding and structural changes, including formation of Z-DNA, play an important role in the catalytic function of the 8-17 DNAzyme.
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Affiliation(s)
- Debapriya Mazumdar
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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211
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Attwater J, Wochner A, Pinheiro VB, Coulson A, Holliger P. Ice as a protocellular medium for RNA replication. Nat Commun 2010; 1:76. [PMID: 20865803 DOI: 10.1038/ncomms1076] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 08/23/2010] [Indexed: 11/09/2022] Open
Abstract
A crucial transition in the origin of life was the emergence of an informational polymer capable of self-replication and its compartmentalization within protocellular structures. We show that the physicochemical properties of ice, a simple medium widespread on a temperate early Earth, could have mediated this transition prior to the advent of membraneous protocells. Ice not only promotes the activity of an RNA polymerase ribozyme but also protects it from hydrolytic degradation, enabling the synthesis of exceptionally long replication products. Ice furthermore relieves the dependence of RNA replication on prebiotically implausible substrate concentrations, while providing quasicellular compartmentalization within the intricate microstructure of the eutectic phase. Eutectic ice phases had previously been shown to promote the de novo synthesis of nucleotide precursors, as well as the condensation of activated nucleotides into random RNA oligomers. Our results support a wider role for ice as a predisposed environment, promoting all the steps from prebiotic synthesis to the emergence of RNA self-replication and precellular Darwinian evolution.
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Affiliation(s)
- James Attwater
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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212
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Huang PJJ, Liu J. Flow cytometry-assisted detection of adenosine in serum with an immobilized aptamer sensor. Anal Chem 2010; 82:4020-6. [PMID: 20405823 DOI: 10.1021/ac9028505] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aptamers are single-stranded nucleic acids that can selectively bind to essentially any molecule of choice. Because of their high stability, low cost, ease of modification, and availability through selection, aptamers hold great promise in addressing key challenges in bioanalytical chemistry. In the past 15 years, many highly sensitive fluorescent aptamer sensors have been reported. However, few such sensors showed high performance in serum samples. Further challenges related to practical applications include detection in a very small sample volume and a low dependence of sensor performance on ionic strength. We report the immobilization of an aptamer sensor on a magnetic microparticle and the use of flow cytometry for detection. Flow cytometry allows the detection of individual particles in a capillary and can effectively reduce the light scattering effect of serum. Since DNA immobilization generated a highly negatively charged surface and caused an enrichment of counterions, the sensor performance showed a lower salt dependence. The detection limits for adenosine are determined to be 178 microM in buffer and 167 microM in 30% serum. Finally, we demonstrated that the detection can be carried out in 10 microL of 90% human blood serum.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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213
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Kumar A, Sharma S, Maurya RA. Single Nucleotide-Catalyzed Biomimetic Reductive Amination. Adv Synth Catal 2010. [DOI: 10.1002/adsc.201000178] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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214
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Rowe W, Platt M, Wedge DC, Day PJR, Kell DB, Knowles JD. Convergent evolution to an aptamer observed in small populations on DNA microarrays. Phys Biol 2010; 7:036007. [PMID: 20811084 DOI: 10.1088/1478-3975/7/3/036007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The development of aptamers on custom synthesized DNA microarrays, which has been demonstrated in recent publications, can facilitate detailed analyses of sequence and fitness relationships. Here we use the technique to observe the paths taken through sequence-fitness space by three different evolutionary regimes: asexual reproduction, recombination and model-based evolution. The different evolutionary runs are made on the same array chip in triplicate, each one starting from a small population initialized independently at random. When evolving to a common target protein, glucose-6-phosphate dehydrogenase (G6PD), these nine distinct evolutionary runs are observed to develop aptamers with high affinity and to converge on the same motif not present in any of the starting populations. Regime specific differences in the evolutions, such as speed of convergence, could also be observed.
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Affiliation(s)
- W Rowe
- Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, UK.
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215
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Afonin KA, Bindewald E, Yaghoubian AJ, Voss N, Jacovetty E, Shapiro BA, Jaeger L. In vitro assembly of cubic RNA-based scaffolds designed in silico. NATURE NANOTECHNOLOGY 2010; 5:676-82. [PMID: 20802494 PMCID: PMC2934861 DOI: 10.1038/nnano.2010.160] [Citation(s) in RCA: 256] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 07/09/2010] [Indexed: 05/19/2023]
Abstract
The organization of biological materials into versatile three-dimensional assemblies could be used to build multifunctional therapeutic scaffolds for use in nanomedicine. Here, we report a strategy to design three-dimensional nanoscale scaffolds that can be self-assembled from RNA with precise control over their shape, size and composition. These cubic nanoscaffolds are only approximately 13 nm in diameter and are composed of short oligonucleotides, making them amenable to chemical synthesis, point modifications and further functionalization. Nanocube assembly is verified by gel assays, dynamic light scattering and cryogenic electron microscopy. Formation of functional RNA nanocubes is also demonstrated by incorporation of a light-up fluorescent RNA aptamer that is optimally active only upon full RNA assembly. Moreover, we show that the RNA nanoscaffolds can self-assemble in isothermal conditions (37 degrees C) during in vitro transcription, which opens a route towards the construction of sensors, programmable packaging and cargo delivery systems for biomedical applications.
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Affiliation(s)
- Kirill A Afonin
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Eckart Bindewald
- Basic Science Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Alan J. Yaghoubian
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Neil Voss
- Automated Molecular Imaging Group, Dept. of Cell Biology, The Scripps Research Institute, MC CB129, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Erica Jacovetty
- Automated Molecular Imaging Group, Dept. of Cell Biology, The Scripps Research Institute, MC CB129, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | | | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
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216
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Kleiner RE, Dumelin CE, Tiu GC, Sakurai K, Liu DR. In vitro selection of a DNA-templated small-molecule library reveals a class of macrocyclic kinase inhibitors. J Am Chem Soc 2010; 132:11779-91. [PMID: 20681606 PMCID: PMC2924185 DOI: 10.1021/ja104903x] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Indexed: 12/12/2022]
Abstract
DNA-templated organic synthesis enables the translation of DNA sequences into synthetic small-molecule libraries suitable for in vitro selection. Previously, we described the DNA-templated multistep synthesis of a 13,824-membered small-molecule macrocycle library. Here, we report the discovery of small molecules that modulate the activity of kinase enzymes through the in vitro selection of this DNA-templated small-molecule macrocycle library against 36 biomedically relevant protein targets. DNA encoding selection survivors was amplified by PCR and identified by ultra-high-throughput DNA sequencing. Macrocycles corresponding to DNA sequences enriched upon selection against several protein kinases were synthesized on a multimilligram scale. In vitro assays revealed that these macrocycles inhibit (or activate) the kinases against which they were selected with IC(50) values as low as 680 nM. We characterized in depth a family of macrocycles enriched upon selection against Src kinase, and showed that inhibition was highly dependent on the identity of macrocycle building blocks as well as on backbone conformation. Two macrocycles in this family exhibited unusually strong Src inhibition selectivity even among kinases closely related to Src. One macrocycle was found to activate, rather than inhibit, its target kinase, VEGFR2. Taken together, these results establish the use of DNA-templated synthesis and in vitro selection to discover small molecules that modulate enzyme activities, and also reveal a new scaffold for selective ATP-competitive kinase inhibition.
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Affiliation(s)
- Ralph E. Kleiner
- Department of Chemistry and Chemical Biology and the Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Christoph E. Dumelin
- Department of Chemistry and Chemical Biology and the Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Gerald C. Tiu
- Department of Chemistry and Chemical Biology and the Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Kaori Sakurai
- Department of Chemistry and Chemical Biology and the Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - David R. Liu
- Department of Chemistry and Chemical Biology and the Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
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217
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Lee CS, Mui TP, Silverman SK. Improved deoxyribozymes for synthesis of covalently branched DNA and RNA. Nucleic Acids Res 2010; 39:269-79. [PMID: 20739352 PMCID: PMC3017605 DOI: 10.1093/nar/gkq753] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A covalently branched nucleic acid can be synthesized by joining the 2′-hydroxyl of the branch-site ribonucleotide of a DNA or RNA strand to the activated 5′-phosphorus of a separate DNA or RNA strand. We have previously used deoxyribozymes to synthesize several types of branched nucleic acids for experiments in biotechnology and biochemistry. Here, we report in vitro selection experiments to identify improved deoxyribozymes for synthesis of branched DNA and RNA. Each of the new deoxyribozymes requires Mn2+ as a cofactor, rather than Mg2+ as used by our previous branch-forming deoxyribozymes, and each has an initially random region of 40 rather than 22 or fewer combined nucleotides. The deoxyribozymes all function by forming a three-helix-junction (3HJ) complex with their two oligonucleotide substrates. For synthesis of branched DNA, the best new deoxyribozyme, 8LV13, has kobs on the order of 0.1 min−1, which is about two orders of magnitude faster than our previously identified 15HA9 deoxyribozyme. 8LV13 also functions at closer-to-neutral pH than does 15HA9 (pH 7.5 versus 9.0) and has useful tolerance for many DNA substrate sequences. For synthesis of branched RNA, two new deoxyribozymes, 8LX1 and 8LX6, were identified with broad sequence tolerances and substantial activity at pH 7.5, versus pH 9.0 for many of our previous deoxyribozymes that form branched RNA. These experiments provide new, and in key aspects improved, practical catalysts for preparation of synthetic branched DNA and RNA.
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Affiliation(s)
- Christine S Lee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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218
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Nickens DG, Bardiya N, Patterson JT, Burke DH. Template-directed ligation of tethered mononucleotides by t4 DNA ligase for kinase ribozyme selection. PLoS One 2010; 5:e12368. [PMID: 20811490 PMCID: PMC2927549 DOI: 10.1371/journal.pone.0012368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 07/27/2010] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND In vitro selection of kinase ribozymes for small molecule metabolites, such as free nucleosides, will require partition systems that discriminate active from inactive RNA species. While nucleic acid catalysis of phosphoryl transfer is well established for phosphorylation of 5' or 2' OH of oligonucleotide substrates, phosphorylation of diffusible small molecules has not been demonstrated. METHODOLOGY/PRINCIPAL FINDINGS This study demonstrates the ability of T4 DNA ligase to capture RNA strands in which a tethered monodeoxynucleoside has acquired a 5' phosphate. The ligation reaction therefore mimics the partition step of a selection for nucleoside kinase (deoxy)ribozymes. Ligation with tethered substrates was considerably slower than with nicked, fully duplex DNA, even though the deoxynucleotides at the ligation junction were Watson-Crick base paired in the tethered substrate. Ligation increased markedly when the bridging template strand contained unpaired spacer nucleotides across from the flexible tether, according to the trends: A(2)>A(1)>A(3)>A(4)>A(0)>A(6)>A(8)>A(10) and T(2)>T(3)>T(4)>T(6) approximately T(1)>T(8)>T(10). Bridging T's generally gave higher yield of ligated product than bridging A's. ATP concentrations above 33 microM accumulated adenylated intermediate and decreased yields of the gap-sealed product, likely due to re-adenylation of dissociated enzyme. Under optimized conditions, T4 DNA ligase efficiently (>90%) joined a correctly paired, or TratioG wobble-paired, substrate on the 3' side of the ligation junction while discriminating approximately 100-fold against most mispaired substrates. Tethered dC and dG gave the highest ligation rates and yields, followed by tethered deoxyinosine (dI) and dT, with the slowest reactions for tethered dA. The same kinetic trends were observed in ligase-mediated capture in complex reaction mixtures with multiple substrates. The "universal" analog 5-nitroindole (dNI) did not support ligation when used as the tethered nucleotide. CONCLUSIONS/SIGNIFICANCE Our results reveal a novel activity for T4 DNA ligase (template-directed ligation of a tethered mononucleotide) and establish this partition scheme as being suitable for the selection of ribozymes that phosphorylate mononucleoside substrates.
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Affiliation(s)
- David G. Nickens
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Nirmala Bardiya
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - James T. Patterson
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Donald H. Burke
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
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219
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Silverman SK. DNA - eine vielseitige chemische Verbindung für die Katalyse, zur Kodierung und zur Stereokontrolle. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906345] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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220
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Abstract
RNA has played a variety of roles in the evolutionary history of life on the Earth. While this molecule was once considered a poor cousin of the more influential polymers in the cell, namely DNA and proteins, a string of important discoveries over the last 50 years has revealed that RNA may in fact be the cornerstone of biological function. In particular, the finding that RNA can be catalytic, and thus possess both a genotype and a phenotype, has forced us to consider the possibility that life's origins began with RNA, and that the subsequent diversification of life is aptly described as a string of innovations by RNA to adapt to a changing environment. Some of these adaptations include riboswitches, ribonucleoproteins (RNPs), RNA editing, and RNA interference (RNAi). Although many of these functions may seem at first glance to be recent evolutionary developments, it may be the case that all of their catalytic activities trace their roots back to a primordial 'RNA World' some four billion years ago, and that RNA's diversity has a continuous thread that pervades life from its very origins.
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Affiliation(s)
- Niles Lehman
- Department of Chemistry, Portland State University, Portland, OR 97207, USA.
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221
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Zhou M, Liang X, Mochizuki T, Asanuma H. A light-driven DNA nanomachine for the efficient photoswitching of RNA digestion. Angew Chem Int Ed Engl 2010; 49:2167-70. [PMID: 20175178 DOI: 10.1002/anie.200907082] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Mengguang Zhou
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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222
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Li D, Song S, Fan C. Target-responsive structural switching for nucleic acid-based sensors. Acc Chem Res 2010; 43:631-41. [PMID: 20222738 DOI: 10.1021/ar900245u] [Citation(s) in RCA: 580] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Interest in the development of sensitive, selective, rapid, and cost-effective biosensors for biomedical analysis, environmental monitoring, and the detection of bioterrorism agents is rapidly increasing. A classic biosensor directly transduces ligand-target binding events into a measurable physical readout. More recently, researchers have proposed novel biosensing strategies that couple ligand-induced structural switching of biomolecules with advanced optical and electronic transducers. This approach has proven to be a highly general platform for the development of new biosensors. In this Account, we describe a series of electrochemical and optical nucleic acid sensors that use target-responsive DNA structures. By employing surface-confined DNA structures with appropriate redox labels, we can monitor target-induced structural switching of DNA or aptamer-specific small molecule probes by measuring electrochemical currents that are directly associated with the distance between the redox label and the electrode surface. We have also demonstrated significant improvements in sensing performance through optimization of the DNA self-assembly process at electrode surfaces or the introduction of nanomaterial-based signal amplification. Alternatively, gold nanoparticles interact differently with folded and unfolded DNA structures, which provides a visual method for detecting target-induced structural switching based on the plasmonic change of gold nanoparticles. This novel method using gold nanoparticles has proven particularly suitable for the detection of a range of small-molecule targets (e.g., cocaine) and environmentally toxic metal ions (e.g., Hg(2+)). Rational sequence design of DNA aptamers improves the sensitivity and increases the reaction kinetics. Recently, we have also designed microfluidic devices that allow rapid and portable mercury detection with the naked eye. This Account focuses on the use of bulk and nanoscale gold and DNA/aptamer molecules. We expect that researchers will further expand the analyte spectrum and improve the sensitivity and selectivity of nucleic acid sensors using functional biomolecules, such as DNAzymes, peptide aptamers and engineered proteins, and nanomaterials of different sizes, dimensions and compositions, such as carbon nanotubes, graphene, silicon nanowires, and metal nanoparticles or nanorods.
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Affiliation(s)
- Di Li
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Shiping Song
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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223
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Kumar P, Sood V, Vyas R, Gupta N, Banerjea AC, Khanna M. Potent inhibition of influenza virus replication with novel siRNA-chimeric-ribozyme constructs. Antiviral Res 2010; 87:204-12. [PMID: 20471429 DOI: 10.1016/j.antiviral.2010.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2010] [Revised: 04/27/2010] [Accepted: 05/04/2010] [Indexed: 10/19/2022]
Abstract
A multitarget approach is needed for effective gene silencing for RNA viruses that combines, more than one antiviral approach. Towards this end, we designed a wild-type (wt) chimeric construct, that consisted of small hairpin siRNA joined by a short intracellular cleavable linker to a known, hammerhead ribozyme (Rz), both targeted against M1 genome segment of influenza A virus. When this, wt chimeric RNA construct was introduced into a mammalian cell line, along with the M1 substrate, encoding DNA, very significant (67%) intracellular down regulation in the levels of target RNA was, observed. When the siRNA portion of this chimeric construct was mutated keeping the Rz region, unchanged, it caused only 33% intracellular reduction. On the contrary, when only the Rz was made, catalytically inactive, keeping the siRNA component unchanged, about 20% reduction in the target M1, specific RNA was observed. This wt chimeric construct showed impressive (>80%) protection against, virus challenge, on the other hand, the selectively disabled mutant constructs were less effective. Thus, in this proof of concept study we show that varying levels of protection against virus challenge was, observed with novel mutant versions of the chimeric constructs.
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Affiliation(s)
- Prashant Kumar
- Department of Respiratory Virology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India
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224
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Kim N, Izzo JA, Elmetwaly S, Gan HH, Schlick T. Computational generation and screening of RNA motifs in large nucleotide sequence pools. Nucleic Acids Res 2010; 38:e139. [PMID: 20448026 PMCID: PMC2910066 DOI: 10.1093/nar/gkq282] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although identification of active motifs in large random sequence pools is central to RNA in vitro selection, no systematic computational equivalent of this process has yet been developed. We develop a computational approach that combines target pool generation, motif scanning and motif screening using secondary structure analysis for applications to 10(12)-10(14)-sequence pools; large pool sizes are made possible using program redesign and supercomputing resources. We use the new protocol to search for aptamer and ribozyme motifs in pools up to experimental pool size (10(14) sequences). We show that motif scanning, structure matching and flanking sequence analysis, respectively, reduce the initial sequence pool by 6-8, 1-2 and 1 orders of magnitude, consistent with the rare occurrence of active motifs in random pools. The final yields match the theoretical yields from probability theory for simple motifs and overestimate experimental yields, which constitute lower bounds, for aptamers because screening analyses beyond secondary structure information are not considered systematically. We also show that designed pools using our nucleotide transition probability matrices can produce higher yields for RNA ligase motifs than random pools. Our methods for generating, analyzing and designing large pools can help improve RNA design via simulation of aspects of in vitro selection.
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Affiliation(s)
- Namhee Kim
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
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225
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Gerasimova YV, Cornett E, Kolpashchikov DM. RNA-cleaving deoxyribozyme sensor for nucleic acid analysis: the limit of detection. Chembiochem 2010; 11:811-7, 729. [PMID: 20301161 PMCID: PMC2949061 DOI: 10.1002/cbic.201000006] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Indexed: 12/31/2022]
Abstract
Along with biocompatibility, chemical stability, and simplicity of structural prediction and modification, deoxyribozyme-based molecular sensors have the potential of an improved detection limit due to their ability to catalytically amplify signal. This study contributes to the understanding of the factors responsible for the limit of detection (LOD) of RNA-cleaving deoxyribozyme sensors. A new sensor that detects specific DNA/RNA sequences was designed from deoxyribozyme OA-II [Chiuman, W.; Li, Y. (2006) J. Mol. Biol. 357, 748-754]. The sensor architecture allows for a unique combination of high selectivity, low LOD and the convenience of fluorescent signal monitoring in homogeneous solution. The LOD of the sensor was found to be approximately 1.6 x 10(-10) M after 3 h of incubation. An equation that allows estimation of the lowest theoretical LOD using characteristics of parent deoxyribozymes and their fluorogenic substrates was derived and experimentally verified. According to the equation, "catalytically perfect" enzymes can serve as scaffolds for the design of sensors with the LOD not lower than approximately 2 x 10(-15) M after 3 h of incubation. A new value termed the detection efficiency (DE) is suggested as a time-independent characteristic of a sensor's sensitivity. The expressions for the theoretical LOD and DE can be used to evaluate nucleic acid and protein enzymes for their application as biosensing platforms.
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Affiliation(s)
| | | | - Dmitry M. Kolpashchikov
- Dr. Y. V. Gerasimova, E. Cornett, Dr. D. M. Kolpashchikov Chemistry Department, University of Central Florida 4000 Central Florida Blvd, Orlando, FL 32816-2366 (USA)
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226
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Díaz Arenas C, Lehman N. Quasispecies-like behavior observed in catalytic RNA populations evolving in a test tube. BMC Evol Biol 2010; 10:80. [PMID: 20331885 PMCID: PMC2850355 DOI: 10.1186/1471-2148-10-80] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 03/23/2010] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND During the RNA World, molecular populations were probably very small and highly susceptible to the force of strong random drift. In conjunction with Muller's Ratchet, this would have imposed difficulties for the preservation of the genetic information and the survival of the populations. Mechanisms that allowed these nascent populations to overcome this problem must have been advantageous. RESULTS Using continuous in vitro evolution experimentation with an increased mutation rate imposed by MnCl2, it was found that clonal 100-molecule populations of ribozymes clearly exhibit certain characteristics of a quasispecies. This is the first time this has been seen with a catalytic RNA. Extensive genotypic sampling from two replicate lineages was gathered and phylogenetic networks were constructed to elucidate the structure of the evolving RNA populations. A common distribution was found in which a mutant sequence was present at high frequency, surrounded by a cloud of mutant with lower frequencies. This is a typical distribution of quasispecies. Most of the mutants in these clouds were connected by short Hamming distance values, indicating their close relatedness. CONCLUSIONS The quasispecies nature of mutant RNA clouds facilitates the recovery of genotypes under pressure of being removed from the population by random drift. The empirical populations therefore evolved a genotypic resiliency despite a high mutation rate by adopting the characteristics of quasispecies, implying that primordial RNA pools could have used this strategy to avoid extinction.
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Affiliation(s)
- Carolina Díaz Arenas
- Department of Chemistry, Portland State University, PO Box 751, Portland, Oregon, 97207, USA
| | - Niles Lehman
- Department of Chemistry, Portland State University, PO Box 751, Portland, Oregon, 97207, USA
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227
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Zhou M, Liang X, Mochizuki T, Asanuma H. A Light-Driven DNA Nanomachine for the Efficient Photoswitching of RNA Digestion. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200907082] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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228
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Arenas CD, Lehman N. The continuous evolution in vitro technique. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2010; Chapter 9:Unit 9.7.1-17. [PMID: 20201030 DOI: 10.1002/0471142700.nc0907s40] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In vitro experimentation techniques were developed in response to the necessity of exploring new molecular structures and functions and to better understand evolutionary phenomena that shape organismal and molecular populations. The advancement of these techniques has allowed further exploration of more complicated evolutionary dynamics. One such technique is the continuous evolution in vitro (CE) method, to which this unit is devoted. The CE method is characterized by continuous cycles of amplification of RNA molecules that occur without much participation of the researcher. This feature allows us to evolve lineages in which the evolutionary phenomena occurring at the molecular level more closely mimic what happens in organismal populations in the present, or what may have happened in RNA populations during the RNA world stage of life.
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229
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Sachdeva A, Silverman SK. DNA-catalyzed serine side chain reactivity and selectivity. Chem Commun (Camb) 2010; 46:2215-7. [PMID: 20234910 DOI: 10.1039/b927317d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New deoxyribozymes are shown to catalyze reactions of serine side chains, forming nucleopeptide linkages and discriminating between serine and tyrosine or between two competing serines.
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Affiliation(s)
- Amit Sachdeva
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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230
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Zhu C, Wen Y, Li D, Wang L, Song S, Fan C, Willner I. Inhibition of the in vitro replication of DNA by an aptamer-protein complex in an autonomous DNA machine. Chemistry 2010; 15:11898-903. [PMID: 19777511 DOI: 10.1002/chem.200901275] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
DNA replication plays a central role in living organisms. Unregulated or uncontrollable DNA replication is well known to result in many pathological states, such as cancer, autoimmune diseases, and viral/bacterial infections. We report that an aptamer-protein complex could indirectly inhibit in vitro replication of DNA. An isothermal DNA machine based on the strand-displacement amplification is employed to support our assumption. An antithrombin aptamer sequence is rationally encoded into the DNA replication template. Once thrombin binds to the template, the as-formed aptamer-protein complexes can, in turn, become a barrier to the polymerase and inhibit the DNA replication activities in both static and dynamic modes. The inhibition is successfully confirmed by both fluorescence and gel-electrophoresis experiments. Considering the availability of a broad library of aptamers and the existence of various DNA/protein interactions, our results imply the possibility for the rational regulation of DNA replication in vivo.
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Affiliation(s)
- Changfeng Zhu
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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231
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Zhang J, Wang L, Zhang H, Boey F, Song S, Fan C. Aptamer-based multicolor fluorescent gold nanoprobes for multiplex detection in homogeneous solution. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:201-204. [PMID: 19957283 DOI: 10.1002/smll.200901012] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The design of a novel multicolor fluorescent gold nanoprobe for homogeneous detection of small-molecule targets is reported, which combines the specific binding abilities of aptamers with the ultrahigh quenching ability of gold nanoparticles (AuNPs). Dye-tagged aptamers and their complementary sequence with thiol labels are co-assembled at the surface of AuNPs. As a proof of concept, it is demonstrated that such a multicolor fluorescent gold nanoprobe can simultaneously detect adenosine, potassium ion, and cocaine with high selectivity. This potentially generic strategy is shown to be promising for rapid screening of small molecular targets.
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Affiliation(s)
- Juan Zhang
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, P. R. China
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232
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Shechner DM, Grant RA, Bagby SC, Koldobskaya Y, Piccirilli JA, Bartel DP. Crystal structure of the catalytic core of an RNA-polymerase ribozyme. Science 2009; 326:1271-5. [PMID: 19965478 DOI: 10.1126/science.1174676] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Primordial organisms of the putative RNA world would have required polymerase ribozymes able to replicate RNA. Known ribozymes with polymerase activity best approximating that needed for RNA replication contain at their catalytic core the class I RNA ligase, an artificial ribozyme with a catalytic rate among the fastest of known ribozymes. Here we present the 3.0 angstrom crystal structure of this ligase. The architecture resembles a tripod, its three legs converging near the ligation junction. Interacting with this tripod scaffold through a series of 10 minor-groove interactions (including two A-minor triads) is the unpaired segment that contributes to and organizes the active site. A cytosine nucleobase and two backbone phosphates abut the ligation junction; their location suggests a model for catalysis resembling that of proteinaceous polymerases.
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Affiliation(s)
- David M Shechner
- Whitehead Institute for Biomedical Research and Howard Hughes Medical Institute, 9 Cambridge Center, Cambridge, MA 02142, USA
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233
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An in vitro translation, selection and amplification system for peptide nucleic acids. Nat Chem Biol 2009; 6:148-55. [PMID: 20081830 PMCID: PMC2808706 DOI: 10.1038/nchembio.280] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 11/09/2009] [Indexed: 01/05/2023]
Abstract
Methods to evolve synthetic, rather than biological, polymers could significantly expand the functional potential of polymers that emerge from in vitro evolution. Requirements for synthetic polymer evolution include (i) sequence-specific polymerization of synthetic building blocks on an amplifiable template, (ii) display of the newly translated polymer strand in a manner that allows it to adopt folded structures, (iii) selection of synthetic polymer libraries for desired binding or catalytic properties and (iv) amplification of template sequences that survive selection in a manner that allows subsequent translation. Here we report the development of such a system for peptide nucleic acids (PNAs) using a set of 12 PNA pentamer building blocks. We validated the system by performing six iterated cycles of translation, selection and amplification on a library of 4.3 x 10(8) PNA-encoding DNA templates and observed >1,000,000-fold overall enrichment of a template encoding a biotinylated (streptavidin-binding) PNA. These results collectively provide an experimental foundation for PNA evolution in the laboratory.
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234
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Ma W, Yu C, Zhang W, Zhou P, Hu J. The emergence of ribozymes synthesizing membrane components in RNA-based protocells. Biosystems 2009; 99:201-9. [PMID: 19961895 DOI: 10.1016/j.biosystems.2009.11.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2009] [Revised: 11/12/2009] [Accepted: 11/26/2009] [Indexed: 11/24/2022]
Abstract
A significant problem of the origin of life is the emergence of cellular self-replication. In the context of the "RNA world", a crucial concern is how the RNA-based protocells could achieve the ability to produce their own membrane. Here we show, with the aid of a computer simulation, that for these protocells, there would be "immediately" a selection pressure for the emergence of a ribozyme synthesizing membrane components. The ribozyme would promote the enlargement of cellular space and favor the incoming (by permeation) of RNA's precursors, thus benefit the replication of inner RNA, including itself. Via growth and division, protocells containing the ribozyme would achieve superiority and spread in the system, and meanwhile the ribozyme would spread in the system. The present work is inspiring because it suggests that the transition from molecular self-replication to cellular self-replication might have occurred naturally (and necessarily) in the origin of life, leading to the emergence of Darwinian evolution at the cellular level.
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235
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Chen X, Xing D, Zhang L, Cukier RI, Bu Y. Effect of metal ions on radical type and proton-coupled electron transfer channel: σ-Radical vs π-radical and σ-channel vs π-channel in the imide units. J Comput Chem 2009; 30:2694-705. [DOI: 10.1002/jcc.21284] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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236
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Costanzo G, Pino S, Ciciriello F, Di Mauro E. Generation of long RNA chains in water. J Biol Chem 2009; 284:33206-16. [PMID: 19801553 PMCID: PMC2785163 DOI: 10.1074/jbc.m109.041905] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 10/02/2009] [Indexed: 11/06/2022] Open
Abstract
The synthesis of RNA chains from 3',5'-cAMP and 3',5'-cGMP was observed. The RNA chains formed in water, at moderate temperatures (40-90 degrees C), in the absence of enzymes or inorganic catalysts. As determined by RNase analyses, the bonds formed were canonical 3',5'-phosphodiester bonds. The polymerizations are based on two reactions not previously described: 1) oligomerization of 3', 5'-cGMP to approximately 25-nucleotide-long RNA molecules, and of 3',5'-cAMP to 4- to 8-nucleotide-long molecules. Oligonucleotide A molecules were further extended by reciprocal terminal ligation to yield RNA molecules up to >120 nucleotides long and 2) chain extension by terminal ligation of newly polymerized products of 3',5'-cGMP on preformed oligonucleotides. The enzyme- and template-independent synthesis of long oligomers in water from prebiotically affordable precursors approaches the concept of spontaneous generation of (pre)genetic information.
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Affiliation(s)
| | - Samanta Pino
- the Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza di Roma, and
| | - Fabiana Ciciriello
- the Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza di Roma, and
| | - Ernesto Di Mauro
- the Fondazione Istituto Pasteur-Fondazione Cenci-Bolognetti, c/o Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza di Roma, P. le Aldo Moro, 5, Rome 00185, Italy
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237
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Abstract
As the focus of synthesis increasingly shifts from its historical emphasis on molecular structure to function, improved strategies are clearly required for the generation of molecules with defined physical, chemical, and biological properties. In contrast, living organisms are remarkably adept at producing molecules and molecular assemblies with an impressive array of functions - from enzymes and antibodies to the photosynthetic center. Thus, the marriage of Nature's synthetic strategies, molecules, and biosynthetic machinery with more traditional synthetic approaches might enable the generation of molecules with properties difficult to achieve by chemical strategies alone. Here we illustrate the potential of this approach and overview some opportunities and challenges in the coming years.
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Affiliation(s)
- Xu Wu
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, USA
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238
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Saladino R, Crestini C, Ciciriello F, Pino S, Costanzo G, Di Mauro E. From formamide to RNA: the roles of formamide and water in the evolution of chemical information. Res Microbiol 2009; 160:441-8. [DOI: 10.1016/j.resmic.2009.06.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 05/22/2009] [Accepted: 06/03/2009] [Indexed: 11/24/2022]
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239
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A DNAzyme with Three Protein-Like Functional Groups: Enhancing Catalytic Efficiency of M2+-Independent RNA Cleavage. Chembiochem 2009; 10:1988-92. [DOI: 10.1002/cbic.200900314] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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240
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Gorin DJ, Kamlet AS, Liu DR. Reactivity-dependent PCR: direct, solution-phase in vitro selection for bond formation. J Am Chem Soc 2009; 131:9189-91. [PMID: 19522494 PMCID: PMC2710857 DOI: 10.1021/ja903084a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Indexed: 11/30/2022]
Abstract
In vitro selection is a key component of efforts to discover functional nucleic acids and small molecules from libraries of DNA, RNA, and DNA-encoded small molecules. Such selections have been widely used to evolve RNA and DNA catalysts and, more recently, to discover new reactions from DNA-encoded libraries of potential substrates. While effective, current strategies for selections of bond-forming and bond-cleaving reactivity are generally indirect, require the synthesis of biotin-linked substrates, and involve multiple solution-phase and solid-phase manipulations. In this work we report the successful development and validation of reactivity-dependent PCR (RDPCR), a new method that more directly links bond formation or bond cleavage with the amplification of desired sequences and that obviates the need for solid-phase capture, washing, and elution steps. We show that RDPCR can be used to select for bond formation in the context of reaction discovery and for bond cleavage in the context of protease activity profiling.
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Affiliation(s)
- David J. Gorin
- Howard Hughes Medical Institute and Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Adam S. Kamlet
- Howard Hughes Medical Institute and Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - David R. Liu
- Howard Hughes Medical Institute and Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
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241
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Talini G, Gallori E, Maurel MC. Natural and unnatural ribozymes: back to the primordial RNA world. Res Microbiol 2009; 160:457-65. [PMID: 19539027 DOI: 10.1016/j.resmic.2009.05.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 05/27/2009] [Accepted: 05/29/2009] [Indexed: 10/20/2022]
Abstract
We review natural and in vitro selected ribozymes, for which combined studies could provide us with both insight into the functions performed by ancient RNA molecules in a primitive RNA world and a hypothesis about evolutionary steps that led to the contemporary world.
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Affiliation(s)
- Giulia Talini
- Department of Astronomy and Space Science, University of Florence, Largo E. Fermi 2, 50125 Florence, Italy.
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242
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Abstract
The paradigm of gene regulation was forever changed by the discovery that short RNA duplexes could directly regulate gene expression. Most regulatory roles attributed to noncoding RNA were often repressive. Recent observations are beginning to reveal that duplex RNA molecules can stimulate gene transcription. These RNA activators employ a wide array of mechanisms to up-regulate transcription of target genes, including functioning as DNA-tethered activation domains, as coactivators and modulators of general transcriptional machinery, and as regulators of other noncoding transcripts. The discoveries over the past few years defy "Moore's law" in the breath-taking rapidity with which new roles for noncoding RNA in gene expression are being revealed. As gene regulatory networks are reconstructed to accommodate the influence of noncoding RNAs, their importance in maintenance of cellular health will become increasingly apparent. In fact, a new generation of therapeutic agents will focus on modulating the function of noncoding RNA.
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Affiliation(s)
- Aseem Z Ansari
- Department of Biochemistry & The Genome Center of Wisconsin, University of Wisconsin-Madison, 53706, USA.
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243
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Brudno Y, Liu DR. Recent progress toward the templated synthesis and directed evolution of sequence-defined synthetic polymers. ACTA ACUST UNITED AC 2009; 16:265-76. [PMID: 19318208 DOI: 10.1016/j.chembiol.2009.02.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 01/20/2009] [Accepted: 02/16/2009] [Indexed: 12/21/2022]
Abstract
Biological polymers such as nucleic acids and proteins are ubiquitous in living systems, but their ability to address problems beyond those found in nature is constrained by factors such as chemical or biological instability, limited building-block functionality, bioavailability, and immunogenicity. In principle, sequence-defined synthetic polymers based on nonbiological monomers and backbones might overcome these constraints; however, identifying the sequence of a synthetic polymer that possesses a specific desired functional property remains a major challenge. Molecular evolution can rapidly generate functional polymers but requires a means of translating amplifiable templates such as nucleic acids into the polymer being evolved. This review covers recent advances in the enzymatic and nonenzymatic templated polymerization of nonnatural polymers and their potential applications in the directed evolution of sequence-defined synthetic polymers.
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Affiliation(s)
- Yevgeny Brudno
- Department of Chemistry and Chemical Biology and the Howard Hughes Medical Institute, 12 Oxford Street, Harvard University, Cambridge, MA 02138, USA
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244
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Affiliation(s)
- Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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245
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Briones C, Stich M, Manrubia SC. The dawn of the RNA World: toward functional complexity through ligation of random RNA oligomers. RNA (NEW YORK, N.Y.) 2009; 15:743-9. [PMID: 19318464 PMCID: PMC2673073 DOI: 10.1261/rna.1488609] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Accepted: 01/31/2009] [Indexed: 05/23/2023]
Abstract
A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation-based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered.
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Affiliation(s)
- Carlos Briones
- Centro de Astrobiología (CSIC-INTA), 28850 Torrejón de Ardoz, Madrid, Spain.
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246
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Brown AK, Liu J, He Y, Lu Y. Biochemical characterization of a uranyl ion-specific DNAzyme. Chembiochem 2009; 10:486-92. [PMID: 19142882 DOI: 10.1002/cbic.200800632] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Uranyl ion-specific DNAzyme: A DNAzyme (lower strand) cleaves the substrate (upper strand) in the presence of the uranyl ion. The enzyme folds into a bulged three-way-junction structure with catalytically important nucleotides residing in the bulge. A highly conserved GA mismatch is also crucial for the enzyme's activity.The biochemical characterization of a DNAzyme that is highly specific for uranyl (UO(2) (2+)) ions is described. Sequence alignment, enzyme truncation, and mutation studies have resulted in a conserved sequence that folds into a bulged stem-loop structure. Interestingly, a GA pair next to the scissile site is important for the uranyl ion-specific DNAzyme; this is reminiscent of the GT wobble base pair adjacent to the cleavage site that is crucial for the Pb(II)-specific 8-17 DNAzyme activity. Therefore wobble pairs might be important for formation of metal-specific metal-binding sites in DNAzymes. The DNAzyme binds the uranyl ion with a dissociation constant of 469 nM, which is among the strongest metal-binding affinities in nucleic acid enzymes reported to date. This explains why a catalytic beacon fluorescent sensor based on this enzyme has a detection limit (45 pM) that rivals the most-sensitive analytical instrument. It also has over 1 000 000-fold specificity for the uranyl ion over other metal ions. The DNAzyme can carry out multiple turnover reactions that follow the Michaelis-Menten equation, with a k(cat) of 1.46 min(-1) and a K(M) of 463 nM, similar to that of the 8-17 DNAzyme. The pH profile shows a bell-shaped curve that reaches a maximum at pH 5.5, at which the in vitro selection was carried out; this suggests that in vitro selection can be performed to obtain DNAzymes with optimal performance under specific conditions under which practical applications are required. These findings enrich our fundamental understanding of metal-binding sites in nucleic acids and allow the design of sensors with better performance.
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Affiliation(s)
- Andrea K Brown
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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247
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Li F, Zhang J, Cao X, Wang L, Li D, Song S, Ye B, Fan C. Adenosine detection by using gold nanoparticles and designed aptamer sequences. Analyst 2009; 134:1355-60. [PMID: 19562201 DOI: 10.1039/b900900k] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Based on gold nanoparticles (AuNPs) and engineered DNA aptamers, we designed a novel bioassay strategy for the detection of adenosine as a small target molecule. In this design, an aptamer is engineered to consist of two pieces of random-coil like ssDNA which are respectively attached to AuNPs through their 5'-thiol-modified end. They can reassemble into the intact aptamer tertiary structure and induce nanoparticle aggregation in the presence of the specific target. Results have demonstrated that gold nanoparticles can effectively differentiate these two different DNA structures via their characteristic surface plasmon resonance-based color change. With this method, adenosine can be selectively detected in the low micromolar range, which means that the strategy reported here can be applicable to the detection of several other small target molecules.
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Affiliation(s)
- Fan Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
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248
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Hollenstein M, Hipolito CJ, Lam CH, Perrin DM. A self-cleaving DNA enzyme modified with amines, guanidines and imidazoles operates independently of divalent metal cations (M2+). Nucleic Acids Res 2009; 37:1638-49. [PMID: 19153138 PMCID: PMC2655665 DOI: 10.1093/nar/gkn1070] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 12/18/2008] [Accepted: 12/19/2008] [Indexed: 12/04/2022] Open
Abstract
The selection of modified DNAzymes represents an important endeavor in expanding the chemical and catalytic properties of catalytic nucleic acids. Few examples of such exist and to date, there is no example where three different modified bases have been simultaneously incorporated for catalytic activity. Herein, dCTP, dATP and dUTP bearing, respectively, a cationic amine, an imidazole and a cationic guanidine, were enzymatically polymerized on a DNA template for the selection of a highly functionalized DNAzyme, called DNAzyme 9-86, that catalyzed (M(2+))-independent self-cleavage under physiological conditions at a single ribo(cytosine)phosphodiester linkage with a rate constant of (0.134 +/- 0.026) min(-1). A pH rate profile analysis revealed pK(a)'s of 7.4 and 8.1, consistent with both general acid and base catalysis. The presence of guanidinium cations permits cleavage at significantly higher temperatures than previously observed for DNAzymes with only amines and imidazoles. Qualitatively, DNAzyme 9-86 presents an unprecedented ensemble of synthetic functionalities while quantitatively it expresses one of the highest reported values for any self-cleaving nucleic acid when investigated under M(2+)-free conditions at 37 degrees C.
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Affiliation(s)
| | | | | | - David M. Perrin
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T 1Z1, Canada
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Díaz Arenas C, Lehman N. Darwin’s concepts in a test tube: Parallels between organismal and in vitro evolution. Int J Biochem Cell Biol 2009; 41:266-73. [PMID: 18809507 DOI: 10.1016/j.biocel.2008.08.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 08/13/2008] [Accepted: 08/20/2008] [Indexed: 11/27/2022]
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250
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Zelin E, Silverman SK. Efficient control of group I intron ribozyme catalysis by DNA constraints. Chem Commun (Camb) 2009:767-9. [PMID: 19322435 DOI: 10.1039/b820676g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Double-stranded DNA constraints enable efficient control of catalysis by a large multi-domain group I intron ribozyme.
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Affiliation(s)
- Elena Zelin
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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