401
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Functional nucleic acid nanostructures and DNA machines. Curr Opin Biotechnol 2010; 21:376-91. [PMID: 20727732 DOI: 10.1016/j.copbio.2010.06.001] [Citation(s) in RCA: 187] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 06/15/2010] [Accepted: 06/15/2010] [Indexed: 12/11/2022]
Abstract
The information encoded in the base sequence of DNA provides instructions for the structural and functional properties of this biopolymer. Structural information includes the formation of duplexes, supramolecular crossover tiles, G-quadruplexes, i-motifs, base-metal-ion complexes, and more. Functional information encoded in the DNA is reflected by specific binding (aptamers) or catalytic properties (DNAzymes). Recent advances in tailoring supramolecular DNA structures for DNA-based machinery and for amplified biosensing are reviewed. Different DNA machines that perform 'tweezer', 'walker' or 'metronome' functions are discussed, and the control of macroscopic surface properties or the motility of micro-objects by molecular DNA devices is introduced. Furthermore, the design of DNA machines for the ultrasensitive detection of DNA, low-molecular-weight substrates, and macromolecules is discussed. Supramolecular aptamer and DNAzyme structures are used as molecular tools for amplified sensing.
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402
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New strategy for the synthesis of chemically modified RNA constructs exemplified by hairpin and hammerhead ribozymes. Proc Natl Acad Sci U S A 2010; 107:15329-34. [PMID: 20713730 DOI: 10.1073/pnas.1006447107] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The CuAAC reaction (click chemistry) has been used in conjunction with solid-phase synthesis to produce catalytically active hairpin ribozymes around 100 nucleotides in length. Cross-strand ligation through neighboring nucleobases was successful in covalently linking presynthesized RNA strands with high efficiency (trans-ligation). In an alternative strategy, intrastrand click ligation was employed to produce a functional hammerhead ribozyme containing a novel nucleic acid backbone mimic at the catalytic site (cis-ligation). The ability to synthesize long RNA strands by a combination of solid-phase synthesis and click ligation is an important addition to RNA chemistry. It is compatible with a plethora of site-specific modifications and is applicable to the synthesis of many biologically important RNA molecules.
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403
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Baaske P, Wienken CJ, Reineck P, Duhr S, Braun D. Optical thermophoresis for quantifying the buffer dependence of aptamer binding. Angew Chem Int Ed Engl 2010; 49:2238-41. [PMID: 20186894 DOI: 10.1002/anie.200903998] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Philipp Baaske
- Ludwig-Maximilians-Universität München, Systems Biophysics, Department of Physics, Center for NanoScience (CeNS), 80799 Munich, Germany.
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404
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Lünse C, Michlewski G, Hopp C, Rentmeister A, Cáceres J, Famulok M, Mayer G. Modulation der pri-miRNA-Reifung durch ein die apikale Schleife bindendes Aptamer. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906919] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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405
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Stengel G, Urban M, Purse BW, Kuchta RD. Incorporation of the fluorescent ribonucleotide analogue tCTP by T7 RNA polymerase. Anal Chem 2010; 82:1082-9. [PMID: 20067253 DOI: 10.1021/ac902456n] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescent RNA is an important analytical tool in medical diagnostics, RNA cytochemistry, and RNA aptamer development. We have synthesized the fluorescent ribonucleotide analogue 1,3-diaza-2-oxophenothiazine-ribose-5'-triphosphate (tCTP) and tested it as substrate for T7 RNA polymerase in transcription reactions, a convenient route for generating RNA in vitro. When transcribing a guanine, T7 RNA polymerase incorporates tCTP with 2-fold higher catalytic efficiency than CTP and efficiently polymerizes additional NTPs onto the tC. Remarkably, T7 RNA polymerase does not incorporate tCTP with the same ambivalence opposite guanine and adenine with which DNA polymerases incorporate the analogous dtCTP. While several DNA polymerases discriminated against a d(tC-A) base pair only by factors <10, T7 RNA polymerase discriminates against tC-A base pair formation by factors of 40 and 300 when operating in the elongation and initiation mode, respectively. These catalytic properties make T7 RNA polymerase an ideal tool for synthesizing large fluorescent RNA, as we demonstrated by generating a approximately 800 nucleotide RNA in which every cytosine was replaced with tC.
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Affiliation(s)
- Gudrun Stengel
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 30309-0215, USA
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406
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Niemeyer CM. Semisynthetic DNA-protein conjugates for biosensing and nanofabrication. Angew Chem Int Ed Engl 2010; 49:1200-16. [PMID: 20091721 DOI: 10.1002/anie.200904930] [Citation(s) in RCA: 300] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Conjugation with artificial nucleic acids allows proteins to be modified with a synthetically accessible, robust tag. This attachment is addressable in a highly specific manner by means of molecular recognition events, such as Watson-Crick hybridization. Such DNA-protein conjugates, with their combined properties, have a broad range of applications, such as in high-performance biomedical diagnostic assays, fundamental research on molecular recognition, and the synthesis of DNA nanostructures. This Review surveys current approaches to generate DNA-protein conjugates as well as recent advances in their applications. For example, DNA-protein conjugates have been assembled into model systems for the investigation of catalytic cascade reactions and light-harvesting devices. Such hybrid conjugates are also used for the biofunctionalization of planar surfaces for micro- and nanoarrays, and for decorating inorganic nanoparticles to enable applications in sensing, materials science, and catalysis.
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Affiliation(s)
- Christof M Niemeyer
- Technische Universität Dortmund, Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto-Hahn Strasse 6, 44227 Dortmund, Germany.
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407
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Tera M, Iida K, Ikebukuro K, Seimiya H, Shin-Ya K, Nagasawa K. Visualization of G-quadruplexes by using a BODIPY-labeled macrocyclic heptaoxazole. Org Biomol Chem 2010; 8:2749-55. [PMID: 20414484 DOI: 10.1039/c002117b] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A BODIPY-labeled macrocyclic heptaoxazole, L1BOD-7OTD, was developed as a fluorescent ligand for G-quadruplexes. The results of the study show that L1BOD-7OTD both selectively induces the formation of intramolecular G-quadruplexes from some G-quadruplex forming oligonucleotides (GFOs). In addition, the labelled macrocyclic heptaozaxole strongly binds to and stabilizes intramolecular G-quadruplexes. Moreover, this substance can be used to directly visualize the G-quadruplexes in the form of green fluorescence. Finally, the possibility that G-quadruplexes form in the cells was demonstrated by using of L1BOD-7OTD.
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Affiliation(s)
- Masayuki Tera
- Department of Biotechnology and Life Science Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), Koganei, Tokyo 184-8588, Japan
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408
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Ahmed MSL, Mayer G. Evolution of specific RNA motifs derived from pan-protein interacting precursors. Bioorg Med Chem Lett 2010; 20:3793-6. [PMID: 20471261 DOI: 10.1016/j.bmcl.2010.04.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 04/09/2010] [Accepted: 04/13/2010] [Indexed: 11/24/2022]
Abstract
In vitro evolution of nucleic acid aptamers is a powerful tool to investigate the structure-function relationship of natural occurring RNA-protein interaction motifs. Otherwise, it also allows the identification of novel RNA-based ligands that can be used to investigate a target's function in its native environment. However, artifacts have been described during in vitro selection procedures hampering the successful enrichment of aptamers. Here we describe a novel observation, namely the enrichment of pan-protein binding RNA sequences. We demonstrate that evolution of specific target binding sequences originating from a pan-protein binding RNA precursor is possible in general. Our data demonstrate that the mutual co-variation of an ancestor molecule can be applied for the evolution of specific target binding RNA sequences. These results might have implications in the context of the RNA world theory, exemplifying a possible evolutionary route towards protein-specific RNA molecules from a common ancestor.
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Affiliation(s)
- Marie-Sophie L Ahmed
- Strathclyde Institute for Pharmacy and Biological Sciences, University of Strathclyde, Glasgow, Scotland, UK
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409
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Baaske P, Wienken C, Reineck P, Duhr S, Braun D. Quantifizierung der Puffer-Abhängigkeit von Aptamer-Bindungsreaktionen mit optischer Thermophorese. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200903998] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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410
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Niemeyer C. Halbsynthetische DNA-Protein-Konjugate für Biosensorik und Nanofabrikation. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200904930] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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411
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Zhou J, Rossi JJ. Aptamer-targeted cell-specific RNA interference. SILENCE 2010; 1:4. [PMID: 20226078 PMCID: PMC2835998 DOI: 10.1186/1758-907x-1-4] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 02/01/2010] [Indexed: 11/10/2022]
Abstract
This potent ability of small interfering (si)RNAs to inhibit the expression of complementary RNA transcripts is being exploited as a new class of therapeutics for a variety of diseases. However, the efficient and safe delivery of siRNAs into specific cell populations is still the principal challenge in the clinical development of RNAi therapeutics. With the increasing enthusiasm for developing targeted delivery vehicles, nucleic acid-based aptamers targeting cell surface proteins are being explored as promising delivery vehicles to target a distinct disease or tissue in a cell-type-specific manner. The aptamer-based delivery of siRNAs can often enhance the therapeutic efficacy and reduce the unwanted off-target effects of siRNAs. In particular, for RNA interference-based therapeutics, aptamers represent an efficient agent for cell type-specific, systemic delivery of these oligonucleotides. In this review, we summarize recent attractive developments in creatively using cell-internalizing aptamers to deliver siRNAs to target cells. The optimization and improvement of aptamer-targeted siRNAs for clinical translation are further highlighted.
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Affiliation(s)
- Jiehua Zhou
- Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, City of Hope, Duarte, CA 91010, USA.
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412
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Zeng Z, Hoshino Y, Rodriguez A, Yoo H, Shea KJ. Synthetic polymer nanoparticles with antibody-like affinity for a hydrophilic peptide. ACS NANO 2010; 4:199-204. [PMID: 20014822 PMCID: PMC2815330 DOI: 10.1021/nn901256s] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Synthetic polymer nanoparticles with antibody-like affinity for a hydrophilic peptide have been prepared by inverse microemulsion polymerization. Peptide affinity was achieved in part by incorporating the target (imprint) peptide in the polymerization reaction mixture. Incorporation of the imprint peptide assists in the creation of complementary binding sites in the resulting polymer nanoparticle (NP). To orient the imprint peptide at the interface of the water and oil domains during polymerization, the peptide target was coupled with fatty acid chains of varying length. The peptide--NP binding affinities (ca. 90-900 nM) were quantitatively evaluated by a quartz crystal microbalance (QCM). The optimal chain length was established that created high affinity peptide binding sites on the surface of the nanoparticles. This method can be used for the preparation of nanosized synthetic polymers with antibody-like affinity for hydrophilic peptides and proteins ("plastic antibodies").
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Affiliation(s)
- Zhiyang Zeng
- Department of Chemistry, University of California, Irvine, California 92697, USA
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413
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414
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Caruana DJ, Howorka S. Biosensors and biofuel cells with engineered proteins. MOLECULAR BIOSYSTEMS 2010; 6:1548-56. [DOI: 10.1039/c004951d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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415
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Immunoaffinity column clean-up techniques in food analysis: A review. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:115-32. [DOI: 10.1016/j.jchromb.2009.05.042] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 05/16/2009] [Accepted: 05/19/2009] [Indexed: 11/15/2022]
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416
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Chiu TC, Huang CC. Aptamer-functionalized nano-biosensors. SENSORS 2009; 9:10356-88. [PMID: 22303178 PMCID: PMC3267226 DOI: 10.3390/s91210356] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 12/03/2009] [Accepted: 12/03/2009] [Indexed: 12/12/2022]
Abstract
Nanomaterials have become one of the most interesting sensing materials because of their unique size- and shape-dependent optical properties, high surface energy and surface-to-volume ratio, and tunable surface properties. Aptamers are oligonucleotides that can bind their target ligands with high affinity. The use of nanomaterials that are bioconjugated with aptamers for selective and sensitive detection of analytes such as small molecules, metal ions, proteins, and cells has been demonstrated. This review focuses on recent progress in the development of biosensors by integrating functional aptamers with different types of nanomaterials, including quantum dots, magnetic nanoparticles (NPs), metallic NPs, and carbon nanotubes. Colorimetry, fluorescence, electrochemistry, surface plasmon resonance, surface-enhanced Raman scattering, and magnetic resonance imaging are common detection modes for a broad range of analytes with high sensitivity and selectivity when using aptamer bioconjugated nanomaterials (Apt-NMs). We highlight the important roles that the size and concentration of nanomaterials, the secondary structure and density of aptamers, and the multivalent interactions play in determining the specificity and sensitivity of the nanosensors towards analytes. Advantages and disadvantages of the Apt-NMs for bioapplications are focused.
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Affiliation(s)
- Tai-Chia Chiu
- Department of Applied Science, National Taitung University, 684, Section 1, Chunghua Road, Taitung, 95002, Taiwan
- Authors to whom correspondence should be addressed; E-Mails: (T.C.C.); (C.C.H.); Tel.: +886-89-318855 Ext. 3801; Fax: +886-89-342-539
| | - Chih-Ching Huang
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, 2 Beining Road, Keelung, 20224, Taiwan
- Authors to whom correspondence should be addressed; E-Mails: (T.C.C.); (C.C.H.); Tel.: +886-89-318855 Ext. 3801; Fax: +886-89-342-539
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417
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Choi EW, Nayak LV, Bates PJ. Cancer-selective antiproliferative activity is a general property of some G-rich oligodeoxynucleotides. Nucleic Acids Res 2009; 38:1623-35. [PMID: 20008101 PMCID: PMC2836550 DOI: 10.1093/nar/gkp1088] [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] [Indexed: 12/03/2022] Open
Abstract
Oligodeoxynucleotide libraries containing randomly incorporated bases are used to generate DNA aptamers by systematic evolution of ligands by exponential enrichment (SELEX). We predicted that combinatorial libraries with alternative base compositions might have innate properties different from the standard library containing equimolar A + C + G + T bases. In particular, we hypothesized that G-rich libraries would contain a higher proportion of quadruplex-forming sequences, which may impart desirable qualities, such as increased nuclease resistance and enhanced cellular uptake. Here, we report on 11 synthetic oligodeoxynucleotide libraries of various base combinations and lengths, with regard to their circular dichroism, stability in serum-containing medium, cellular uptake, protein binding and antiproliferative activity. Unexpectedly, we found that some G-rich libraries (composed of G + T or G + C nucleotides) strongly inhibited cancer cell growth while sparing non-malignant cells. These libraries had spectral features consistent with G-quadruplex formation, were significantly more stable in serum than inactive libraries and showed enhanced cellular uptake. Active libraries generally had strong protein binding, while the pattern of protein binding suggested that G/T and G/C libraries have distinct mechanisms of action. In conclusion, cancer-selective antiproliferative activity may be a general feature of certain G-rich oligodeoxynucleotides and is associated with quadruplex formation, nuclease resistance, efficient cellular uptake and protein binding.
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Affiliation(s)
- Enid W Choi
- Department of Biochemistry and Molecular Biology and Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
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418
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Buff MCR, Schäfer F, Wulffen B, Müller J, Pötzsch B, Heckel A, Mayer G. Dependence of aptamer activity on opposed terminal extensions: improvement of light-regulation efficiency. Nucleic Acids Res 2009; 38:2111-8. [PMID: 20007153 PMCID: PMC2847219 DOI: 10.1093/nar/gkp1148] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aptamers that can be regulated with light allow precise control of protein activity in space and time and hence of biological function in general. In a previous study, we showed that the activity of the thrombin-binding aptamer HD1 can be turned off by irradiation using a light activatable 'caged' intramolecular antisense-domain. However, the activity of the presented aptamer in its ON state was only mediocre. Here we studied the nature of this loss in activity in detail and found that switching from 5'- to 3'-extensions affords aptamers that are even more potent than the unmodified HD1. In particular we arrived at derivatives that are now more active than the aptamer NU172 that is currently in phase 2 clinical trials as an anticoagulant. As a result, we present light-regulatable aptamers with a superior activity in their ON state and an almost digital ON/OFF behavior upon irradiation.
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Affiliation(s)
- Maximilian C R Buff
- University of Frankfurt, Cluster of Excellence Macromolecular Complexes, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
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419
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Appella DH. Non-natural nucleic acids for synthetic biology. Curr Opin Chem Biol 2009; 13:687-96. [PMID: 19879178 PMCID: PMC3152792 DOI: 10.1016/j.cbpa.2009.09.030] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2009] [Revised: 09/24/2009] [Accepted: 09/29/2009] [Indexed: 11/29/2022]
Abstract
Genetic manipulation is an important facet of synthetic biology but can be complicated by undesired nuclease degradation. Incorporating non-natural nucleic acids into a gene could convey resistance to nucleases and promote expression. The compatibility of non-natural nucleosides with polymerases is reviewed with a focus on results from the past two years. Details are provided about how the different systems could be useful in synthetic biology.
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Affiliation(s)
- Daniel H Appella
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA.
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420
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Mayer G, Faulhammer D, Grättinger M, Fessele S, Blind M. A RNA-based approach towards small-molecule inhibitors. Chembiochem 2009; 10:1993-6. [PMID: 19575374 DOI: 10.1002/cbic.200900325] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Günter Mayer
- LIMES, University of Bonn, c/o Kekulé-Institut für Org. Chemie und Biochemie, 53121 Bonn (Germany).
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421
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Mayer G, Lohberger A, Butzen S, Pofahl M, Blind M, Heckel A. From selection to caged aptamers: identification of light-dependent ssDNA aptamers targeting cytohesin. Bioorg Med Chem Lett 2009; 19:6561-4. [PMID: 19854646 DOI: 10.1016/j.bmcl.2009.10.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 10/07/2009] [Accepted: 10/07/2009] [Indexed: 11/25/2022]
Abstract
Caged aptamers represent valuable tools for the spatiotemporal control of protein function by light. Here we describe a general route starting with the de novo selection process targeting cytohesin-1 and aiming at the synthesis of caged aptamers without the prior knowledge of detailed structural determinants of aptamer-target binding.
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Affiliation(s)
- Günter Mayer
- Strathclyde Institute for Pharmacy and Biological Sciences, University of Strathclyde, Glasgow G4 0NR, Scotland, United Kingdom.
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422
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Hernandez FJ, Kalra N, Wengel J, Vester B. Aptamers as a model for functional evaluation of LNA and 2'-amino LNA. Bioorg Med Chem Lett 2009; 19:6585-7. [PMID: 19864131 DOI: 10.1016/j.bmcl.2009.10.039] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 10/06/2009] [Accepted: 10/07/2009] [Indexed: 10/20/2022]
Abstract
The affinity change upon incorporation of LNA and 2'-amino-LNA monomers into an avidin binding DNA aptamer is described. The kinetic profile of selected modified-aptamer was obtained by surface plasmon resonance experiments and compared with the profile of the parent unmodified DNA aptamer. We report significant improvement of avidin binding affinity by the incorporation of single LNA modifications into the aptamer, and successful incorporation of 2'-amino LNA as a novel monomer in aptamers with potential function as carrier unit for additional molecular entities.
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Affiliation(s)
- Frank J Hernandez
- Biochemistry and Molecular Biology Department, Nucleic Acid Center, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
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423
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Weigand JE, Suess B. Aptamers and riboswitches: perspectives in biotechnology. Appl Microbiol Biotechnol 2009; 85:229-36. [PMID: 19756582 DOI: 10.1007/s00253-009-2194-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 08/05/2009] [Accepted: 08/05/2009] [Indexed: 01/03/2023]
Abstract
Aptamers are short, single stranded nucleic acids which bind a wide range of different ligands with extraordinary high binding affinity and specificity. The steadily increasing number of aptamers is accompanied by an expanding range of applications in biotechnology. We will describe new developments in the field including the use of aptamers for conditional gene regulation and as biosensors. In addition, we will discuss the potential of aptamers as tags to visualize RNA and protein distribution in living cells and as therapeutics. Furthermore, we will consider biotechnological applications of riboswitches for gene regulation and as drug target.
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Affiliation(s)
- Julia E Weigand
- Institut für Molekulare Biowissenschaften, Aventis Foundation Endowed Professorship, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str 9, 60438 Frankfurt am Main, Germany
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424
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Pollet J, Delport F, Janssen KPF, Jans K, Maes G, Pfeiffer H, Wevers M, Lammertyn J. Fiber optic SPR biosensing of DNA hybridization and DNA-protein interactions. Biosens Bioelectron 2009; 25:864-9. [PMID: 19775884 DOI: 10.1016/j.bios.2009.08.045] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 08/26/2009] [Accepted: 08/28/2009] [Indexed: 10/20/2022]
Abstract
In this paper we present a fiber optic surface plasmon resonance (SPR) sensor as a reusable, cost-effective and label free biosensor for measuring DNA hybridization and DNA-protein interactions. This is the first paper that combines the concept of a fiber-based SPR system with DNA aptamer bioreceptors. The fibers were sputtered with a 50nm gold layer which was then covered with a protein repulsive self-assembled monolayer of mixed polyethylene glycol (PEG). Streptavidin was attached to the PEG's carboxyl groups to serve as a versatile binding element for biotinylated ssDNA. The ssDNA coated SPR fibers were first evaluated as a nucleic acid biosensor through a DNA-DNA hybridization assay for a random 37-mer ssDNA. This single stranded DNA showed a 15 nucleotides overlap with the receptor ssDNA on the SPR fiber. A linear calibration curve was observed in 0.5-5 microM range. A negative control test did not reveal any significant non-specific binding, and the biosensor was easily regenerated. In a second assay the fiber optic SPR biosensor was functionalized with ssDNA aptamers against human immunoglobulin E. Limits of detection (2nM) and quantification (6nM) in the low nanomolar range were observed. The presented biosensor was not only useful for DNA and protein quantification purposes, but also to reveal the binding kinetics occurring at the sensor surface. The dissociation constant between aptamer and hIgE was equal to 30.9+/-2.9nM. The observed kinetics fully comply with most data from the literature and were also confirmed by own control measurements.
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Affiliation(s)
- Jeroen Pollet
- BIOSYST-MeBioS, Katholieke Universiteit Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium.
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425
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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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426
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Li Y, Shi J, Luo Z, Jiang H, Chen X, Wang F, Wu X, Guo Q. Photoregulation of thrombin aptamer activity using Bhc caging strategy. Bioorg Med Chem Lett 2009; 19:5368-71. [PMID: 19682894 DOI: 10.1016/j.bmcl.2009.07.128] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 07/26/2009] [Accepted: 07/28/2009] [Indexed: 11/28/2022]
Abstract
Thrombin aptamer was attempted to cage with Bhc (6-bromo-7-hydroxycoumarin-4-ylmethyl) group for controlling its specific affinity to target molecular through photolysis. By multiple-caging strategy, aptamer could be rendered biologically inert and partially restored with subsequently illumination. This provides a convenient method for photoregulating aptamer activity with exact spatiotemporal resolution.
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Affiliation(s)
- Yiming Li
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
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Knudsen SM, Robertson MP, Ellington AD. In vitro selection using modified or unnatural nucleotides. ACTA ACUST UNITED AC 2008; Chapter 9:Unit 9.6. [PMID: 18428900 DOI: 10.1002/0471142700.nc0906s07] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The use of modified nucleotides in an RNA or DNA pool to be used for in vitro selection offers many potential advantages, such as the increased stability of the selected nucleic acid against nuclease degradation. This unit provides useful information and protocols for in vitro selection using modified nucleotides. It includes a discussion of when to use modified nucleotides; protocols for preparing a modified RNA pool and verifying its suitability for in vitro selection; and protocols for selecting and amplifying a functionally enriched pool.
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