1
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Zuo L, Ren K, Guo X, Pokhrel P, Pokhrel B, Hossain MA, Chen ZX, Mao H, Shen H. Amalgamation of DNAzymes and Nanozymes in a Coronazyme. J Am Chem Soc 2023; 145:5750-5758. [PMID: 36795472 PMCID: PMC10325850 DOI: 10.1021/jacs.2c12367] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Artificial enzymes such as nanozymes and DNAzymes are economical and stable alternatives to natural enzymes. By coating Au nanoparticles (AuNPs) with a DNA corona (AuNP@DNA), we amalgamated nanozymes and DNAzymes into a new artificial enzyme with catalytic efficiency 5 times higher than AuNP nanozymes, 10 times higher than other nanozymes, and significantly greater than most of the DNAzymes on the same oxidation reaction. The AuNP@DNA demonstrates excellent specificity as its reactivity on a reduction reaction does not change with respect to pristine AuNP. Single-molecule fluorescence and force spectroscopies and density functional theory (DFT) simulations indicate a long-range oxidation reaction initiated by radical production on the AuNP surface, followed by radical transport to the DNA corona, where the binding and turnover of substrates take place. The AuNP@DNA is named coronazyme because of its natural enzyme mimicking capability through the well-orchestrated structures and synergetic functions. By incorporating different nanocores and corona materials beyond DNAs, we anticipate that the coronazymes represent generic enzyme mimics to carry out versatile reactions in harsh environments.
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Affiliation(s)
- Li Zuo
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Kehao Ren
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | - Xianming Guo
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Pravin Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | - Bishal Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | | | - Zhao-Xu Chen
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | - Hao Shen
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
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2
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Perrin D, Paul S, Wong AAWL, Liu LT. Selection of M2+-independent RNA-cleaving DNAzymes with Sidechains Mimicking Arginine and Lysine. Chembiochem 2021; 23:e202100600. [PMID: 34881502 DOI: 10.1002/cbic.202100600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/04/2021] [Indexed: 11/07/2022]
Abstract
Sequence-specific cleavage of RNA by nucleic acid catalysts in the absence of a divalent metal cation (M 2+ ) has remained an important goal in biomimicry with potential therapeutic applications. Given the lack of functional group diversity in canonical nucleotides, modified nucleotides with amino acid-like side chains were used to enhance self-cleavage rates at a single embedded ribonucleoside site. Previous works relied on three functional groups: an amine, a guanidine and an imidazole ensconced on three different nucleosides. However, to date, few studies have systematically addressed the necessity of all three modifications, as the value of any single modified nucleoside is contextualized at the outset of selection. Herein, we report on the use of only two modified dNTPs, excluding an imidazole, i.e. 5-(3-guanidinoallyl)-2'-dUTP (dU ga TP) and 5-aminoallyl-2'-dCTP (dC aa TP), to select in-vitro self-cleaving DNAzymes that cleave in the absence of M 2+ in a pH-independent fashion. Cleavage shows biphasic kinetics with rate constants that are significantly higher than in unmodified DNAzymes and compare favorably to certain DNAzymes involving an imidazole. This work is the first report of a M2+-independent DNAzyme with two cationic modifications; as such it shows appreciable self-cleaving activity in the absence of an imidazole modification.
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Affiliation(s)
- David Perrin
- U. British Columbia, Chemistry, 2036 Main Mall, V6T-1Z1, Vancouver, CANADA
| | - Somdeb Paul
- The University of British Columbia, Chemistry, 2036 Main Mall, Vancouver, V6T1Z1, Vancouver, CANADA
| | - Antonio A W L Wong
- The University of British Columbia, Chemistry, 2036 Main Mall, Vancouver, V6T1Z1, Vancouver, CANADA
| | - Leo T Liu
- The University of British Columbia, Chemistry, 2036 Main Mall, UBC, Vancouver, V6T-1Z1, Vancouver, CANADA
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3
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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4
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Huang PJ, Liu J. In vitro Selection of Chemically Modified DNAzymes. ChemistryOpen 2020; 9:1046-1059. [PMID: 33101831 PMCID: PMC7570446 DOI: 10.1002/open.202000134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
DNAzymes are in vitro selected DNA oligonucleotides with catalytic activities. RNA cleavage is one of the most extensively studied DNAzyme reactions. To expand the chemical functionality of DNA, various chemical modifications have been made during and after selection. In this review, we summarize examples of RNA-cleaving DNAzymes and focus on those modifications introduced during in vitro selection. By incorporating various modified nucleotides via polymerase chain reaction (PCR) or primer extension, a few DNAzymes were obtained that can be specifically activated by metal ions such as Zn2+ and Hg2+. In addition, some modifications were introduced to mimic RNase A that can cleave RNA substrates in the absence of divalent metal ions. In addition, single modifications at the fixed regions of DNA libraries, especially at the cleavage junctions, have been tested, and examples of DNAzymes with phosphorothioate and histidine-glycine modified tertiary amine were successfully obtained specific for Cu2+, Cd2+, Zn2+, and Ni2+. Labeling fluorophore/quencher pair right next to the cleavage junction was also used to obtain signaling DNAzymes for detecting various metal ions and cells. Furthermore, we reviewed work on the cleavage of 2'-5' linked RNA and L-RNA substrates. Finally, applications of these modified DNAzymes as biosensors, RNases, and biochemical probes are briefly described with a few future research opportunities outlined at the end.
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Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
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5
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Du S, Li Y, Chai Z, Shi W, He J. Site-specific functionalization with amino, guanidinium, and imidazolyl groups enabling the activation of 10–23 DNAzyme. RSC Adv 2020; 10:19067-19075. [PMID: 35518333 PMCID: PMC9053948 DOI: 10.1039/d0ra02226h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/01/2020] [Indexed: 12/16/2022] Open
Abstract
10–23 DNAzyme has been extensively explored as a therapeutic and biotechnological tool, as well as in DNA computing. Faster cleavage or transformation is always needed. The present research displays a rational modification approach for a more efficient DNAzyme. In the catalytic core, amino, guanidinium and imidazolyl groups were introduced for its chemical activation through the adenine base. Among the six adenine residues, A9 is the unique residue that realizes all the positive effects; the 6-amino and 8-position of adenine and the 7-position of 8-aza-7-deaza-adenine could be used for the introduction of the functional groups. A12 is a new choice for catalytic improvement with an 8-substituent. Therefore, more active DNAzymes could be expected by this nucleobase-modified activation approach. Chemical activation of 10–23 DNAzyme was realized at A9 modified with active functional groups amino, guanidinium, and imidazolyl groups.![]()
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Affiliation(s)
- Shanshan Du
- State Key Laboratory of Toxicology and Medical Countermeasures
- Beijing Institute of Pharmacology and Toxicology
- Beijing 100850
- China
| | - Yang Li
- State Key Laboratory of Toxicology and Medical Countermeasures
- Beijing Institute of Pharmacology and Toxicology
- Beijing 100850
- China
| | - Zhilong Chai
- School of Pharmaceutical Sciences
- Guizhou University
- China
| | - Weiguo Shi
- State Key Laboratory of Toxicology and Medical Countermeasures
- Beijing Institute of Pharmacology and Toxicology
- Beijing 100850
- China
| | - Junlin He
- State Key Laboratory of Toxicology and Medical Countermeasures
- Beijing Institute of Pharmacology and Toxicology
- Beijing 100850
- China
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6
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Du S, Li Y, Chai Z, Shi W, He J. Functionalization of 8-17 DNAzymes modulates catalytic efficiency and divalent metal ion preference. Bioorg Chem 2019; 94:103401. [PMID: 31711763 DOI: 10.1016/j.bioorg.2019.103401] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/17/2019] [Accepted: 10/24/2019] [Indexed: 11/26/2022]
Abstract
8-17 and 17E DNAzyme are being explored as biosensors for metal ions and RNA motifs of interest, more sensitive and efficient DNAzymes are required to meet the practical applications. Their similarity in the catalytic cores and differences in catalytic efficiency and metal ion dependence initiated great interest about the contribution of the catalytic residues. Functionalization of four adenine residues in the catalytic cores of 8-17 DNAzyme and 17E was conducted with amino, guanidinium, and imidazolyl groups. In the bulge loops of 8-17 and 17E, N6-(3-aminopropyl)-2'-deoxyadenosine (residue 1) at A15 led to new DNAzymes 8-17DZ-A15-1 and 17E-A15-1, with much more efficient cleavage ability in the Ca2+-mediated reaction and the greater preference for Ca2+ over Mg2+ than 8-17 DNAzyme and 17E, respectively, especially with a concentration-dependent increase of the selectivity, which is different from most DNAzymes with the similar dependence on both Mg2+ and Ca2+. With this kind of post-selection modification on 8-17 DNAzymes, for the first time, the catalytic efficiency and metal ion selectivity could be positively modulated. It is also helpful for the catalyic mechanistic studies of these DNAzymes, especially, the role of the unconserved A15 should be emphasized.
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Affiliation(s)
- Shanshan Du
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Yang Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Zhilong Chai
- School of Pharmaceutical Sciences, Guizhou University, Guizhou 550025, China
| | - Weiguo Shi
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
| | - Junlin He
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
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7
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Indole-nitroimidazole conjugates as efficient manipulators to decrease the genes expression of methicillin-resistant Staphylococcus aureus. Eur J Med Chem 2019; 179:723-735. [DOI: 10.1016/j.ejmech.2019.06.093] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/28/2019] [Accepted: 06/28/2019] [Indexed: 12/28/2022]
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8
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Nucleic acid enzymes based on functionalized nucleosides. Curr Opin Chem Biol 2019; 52:93-101. [PMID: 31307007 DOI: 10.1016/j.cbpa.2019.06.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/28/2019] [Accepted: 06/06/2019] [Indexed: 12/29/2022]
Abstract
Nucleic acid-based enzymes have recently joined their proteinaceous counterparts as important biocatalysts. While RNA enzymes (ribozymes) are found in nature, deoxyribozymes or DNAzymes are man-made entities. Numerous ribozymes and DNAzymes have been identified by Darwinian selection methods to catalyze a broad array of chemical transformations. Despite these important advances, practical applications involving nucleic acid enzymes are often plagued by relatively poor pharmacokinetic properties and cellular uptake, rapid degradation by nucleases and/or by the limited chemical arsenal carried by natural DNA and RNA. In this review, the two main chemical approaches for the modification of nucleic acid-based catalysts, particularly DNAzymes, are described. These methods aim at improving the functional properties of nucleic acid enzymes by mitigating some of these shortcomings. In this context, recent developments in the post-SELEX processing of existing nucleic acid catalysts as well as efforts for the selection of DNAzymes and ribozymes with modified nucleoside triphosphates are summarized.
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9
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Röthlisberger P, Levi-Acobas F, Sarac I, Marlière P, Herdewijn P, Hollenstein M. Towards the enzymatic formation of artificial metal base pairs with a carboxy-imidazole-modified nucleotide. J Inorg Biochem 2018; 191:154-163. [PMID: 30529723 DOI: 10.1016/j.jinorgbio.2018.11.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/08/2018] [Accepted: 11/13/2018] [Indexed: 01/13/2023]
Abstract
The identification of synthetic nucleotides that sustain the formation of orthogonal, unnatural base pairs is an important goal in synthetic biology. Such artificial synthons have been used for the generation of semi-synthetic organisms as well as functional nucleic acids with enhanced binding properties. The enzymatic formation of artificial metal-base pairs is a vastly underexplored and alluring alternative to existing systems. Here, we report the synthesis and biochemical characterization of 1‑(2-deoxy‑β‑d‑ribofuranosyl) imidazole‑4‑carboxylate nucleoside triphosphate (dImCTP) which is equipped with a carboxylic acid moiety on the imidazole moiety in order to increase the coordination environment to [2 + 2] and [2 + 1]. A clear metal dependence was observed for the single incorporation of the modified nucleotide into DNA by the DNA polymerase from Thermus aquaticus (Taq). The presence of AgI in primer extension reactions conducted with combinations of 1‑(2‑deoxy‑β‑d‑ribofuranosyl) imidazole nucleoside triphosphate (dImTP) and dImCTP supported the unusual [2 + 1] coordination pattern. The efficiency of the tailing reactions mediated by the terminal deoxynucleotidyl transferase (TdT) was markedly improved when using dImCTP instead of dImTP. Even though products with multiple modified nucleotides were not observed, the appendage of additional metal binding ligands on the imidazole nucleobase appears to be a valid approach to improve the biochemical properties of modified triphosphates in the context of an expansion of the genetic alphabet with metal base pairs.
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Affiliation(s)
- Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Ivo Sarac
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Philippe Marlière
- University of Paris Saclay, CNRS, iSSB, UEVE, Genopole, 5 Rue Henri Desbrueres, 91030 Evry, France
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat, 3000 Leuven, Belgium
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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10
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Röthlisberger P, Hollenstein M. Aptamer chemistry. Adv Drug Deliv Rev 2018; 134:3-21. [PMID: 29626546 DOI: 10.1016/j.addr.2018.04.007] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/12/2022]
Abstract
Aptamers are single-stranded DNA or RNA molecules capable of tightly binding to specific targets. These functional nucleic acids are obtained by an in vitro Darwinian evolution method coined SELEX (Systematic Evolution of Ligands by EXponential enrichment). Compared to their proteinaceous counterparts, aptamers offer a number of advantages including a low immunogenicity, a relative ease of large-scale synthesis at affordable costs with little or no batch-to-batch variation, physical stability, and facile chemical modification. These alluring properties have propelled aptamers into the forefront of numerous practical applications such as the development of therapeutic and diagnostic agents as well as the construction of biosensing platforms. However, commercial success of aptamers still proceeds at a weak pace. The main factors responsible for this delay are the susceptibility of aptamers to degradation by nucleases, their rapid renal filtration, suboptimal thermal stability, and the lack of functional group diversity. Here, we describe the different chemical methods available to mitigate these shortcomings. Particularly, we describe the chemical post-SELEX processing of aptamers to include functional groups as well as the inclusion of modified nucleoside triphosphates into the SELEX protocol. These methods will be illustrated with successful examples of chemically modified aptamers used as drug delivery systems, in therapeutic applications, and as biosensing devices.
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11
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Abstract
The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an 'RNA world', notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pK a values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.
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12
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Röthlisberger P, Levi-Acobas F, Sarac I, Baron B, England P, Marlière P, Herdewijn P, Hollenstein M. Facile immobilization of DNA using an enzymatic his-tag mimic. Chem Commun (Camb) 2018; 53:13031-13034. [PMID: 29164188 DOI: 10.1039/c7cc07207d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Methods for immobilization of DNA on solid supports are in high demand. Herein, we present a generally applicable enzymatic method for the immobilization of DNA without any prior chemical derivatization. This strategy relies on the homopolymerization of the modified triphosphate dImTP by the TdT. The resulting enzymatic his-tag mimic ensures binding of DNA on Ni-NTA agarose. The usefulness of this method is highlighted by the immobilization of functional nucleic acids without impairing their specific activities.
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Affiliation(s)
- Pascal Röthlisberger
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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13
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Wang Y, Ng N, Liu E, Lam CH, Perrin DM. Systematic study of constraints imposed by modified nucleoside triphosphates with protein-like side chains for use in in vitro selection. Org Biomol Chem 2018; 15:610-618. [PMID: 27942671 DOI: 10.1039/c6ob02335e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Successful selection of modified DNAzymes depends on the potential for modified nucleoside triphosphates (dNTPs) to replace their unmodified counterparts in enzyme catalyzed primer extension reactions and, once incorporated, to serve as template bases for information transfer prior to PCR amplification. To date, the most densely modified DNAzymes have been selected from three modified dNTPs: 8-histaminyl-deoxyadenosine (dAimTP), 5-guanidinoallyl-deoxyuridine (dUgaTP), and 5-aminoallyl-deoxycytidine (dCaaTP) to provide several RNA-cleaving DNAzymes with greatly enhanced rate constants compared to unmodified counterparts. Here we report biophysical and enzymatic properties of these three modified nucleosides in the context of specific oligonucleotide sequences to understand how these three modified nucleobases function in combinatorial selection. The base-pairing abilities of oligonucleotides bearing one or three modified nucleosides were investigated by thermal denaturation studies and as templates for enzymatic polymerization with both modified and unmodified dNTPs. While we address certain shortcomings in the use of modified dNTPs, we also provide key evidence of faithful incorporation and enzymatic read-out, which strongly supports their continued use in in vitro selection.
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Affiliation(s)
- Yajun Wang
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - Nicole Ng
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - Erkai Liu
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - Curtis H Lam
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - David M Perrin
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
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14
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Chen Z, Lichtor PA, Berliner AP, Chen JC, Liu DR. Evolution of sequence-defined highly functionalized nucleic acid polymers. Nat Chem 2018; 10:420-427. [PMID: 29507367 PMCID: PMC5866196 DOI: 10.1038/s41557-018-0008-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/08/2017] [Indexed: 11/09/2022]
Abstract
The evolution of sequence-defined synthetic polymers made of building blocks beyond those compatible with polymerase enzymes or the ribosome has the potential to generate new classes of receptors, catalysts, and materials. Here we describe a ligase-mediated DNA-templated polymerization system and in vitro selection to evolve highly functionalized nucleic acid polymers (HFNAPs) made from 32 building blocks containing eight chemically diverse side-chains on a DNA backbone. Through iterated cycles of polymer translation, selection, and reverse translation, we discovered HFNAPs that bind PCSK9 and IL-6, two protein targets implicated in human diseases. Mutation and reselection of an active PCSK9-binding polymer yielded evolved polymers with high affinity (KD = 3 nM). This evolved polymer potently inhibited binding between PCSK9 and the LDL receptor. Structure-activity relationship studies revealed that specific side-chains at defined positions in the polymers are required for binding to their respective targets. Our findings expand the chemical space of evolvable polymers to include densely functionalized nucleic acids with diverse, researcher-defined chemical repertoires.
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Affiliation(s)
- Zhen Chen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Phillip A Lichtor
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adrian P Berliner
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan C Chen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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15
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Wang Y, Liu E, Lam CH, Perrin DM. A densely modified M 2+-independent DNAzyme that cleaves RNA efficiently with multiple catalytic turnover. Chem Sci 2018; 9:1813-1821. [PMID: 29675226 PMCID: PMC5890787 DOI: 10.1039/c7sc04491g] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/04/2018] [Indexed: 12/12/2022] Open
Abstract
Sequence-specific cleavage of RNA targets in the absence of a divalent metal cation (M2+) has been a long-standing goal in bioorganic chemistry. Herein, we report the in vitro selection of novel RNA cleaving DNAzymes that are selected using 8-histaminyl-deoxyadenosine (dAimTP), 5-guanidinoallyl-deoxyuridine (dUgaTP), and 5-aminoallyl-deoxycytidine (dCaaTP) along with dGTP. These modified dNTPs provide key functionalities reminiscent of the active sites of ribonucleases, notably RNase A. Of several such M2+-free DNAymes, DNAzyme 7-38-32 cleaves a 19 nt all-RNA substrate with multiple-turnover, under simulated physiological conditions wherein only 0.5 mM Mg2+ was present, attaining values of kcat of 1.06 min-1 and a KM of 1.37 μM corresponding to a catalytic efficiency of ∼106 M-1 min-1. Therefore, Dz7-38-32 represents a promising candidate towards the development of therapeutically efficient DNAzymes.
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Affiliation(s)
- Yajun Wang
- Chemistry Dept. , UBC , 2036 Main Mall , Vancouver , BC V6T1Z1 , Canada .
| | - Erkai Liu
- Chemistry Dept. , UBC , 2036 Main Mall , Vancouver , BC V6T1Z1 , Canada .
| | - Curtis H Lam
- Chemistry Dept. , UBC , 2036 Main Mall , Vancouver , BC V6T1Z1 , Canada .
| | - David M Perrin
- Chemistry Dept. , UBC , 2036 Main Mall , Vancouver , BC V6T1Z1 , Canada .
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16
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Chen T, Romesberg FE. Enzymatic Synthesis, Amplification, and Application of DNA with a Functionalized Backbone. Angew Chem Int Ed Engl 2017; 56:14046-14051. [PMID: 28914996 DOI: 10.1002/anie.201707367] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/04/2017] [Indexed: 12/29/2022]
Abstract
The ability to amplify DNA along with its unprecedented sequence control has led to its use for different applications, but all are limited by the properties available to natural nucleotides. We previously reported the evolution of polymerase SFM4-3, which better tolerates 2'-modified substrates. To explore the utility of SFM4-3, we now report the characterization of its recognition of substrates with 2'-azido, 2'-chloro, 2'-amino, or arabinose sugars. We find that SFM4-3 can efficiently synthesize polymers composed of these nucleotides, and most interestingly, that SFM4-3 can also PCR amplify these modified oligonucleotides. When combined with post-amplification modification, the latter allows for the exponential amplification of polymers that may be functionalized with desired moieties arrayed in a controlled fashion, the utility of which we demonstrate with extensive small molecule functionalization and the production and initial characterization of a novel DNA hydrogel.
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Affiliation(s)
- Tingjian Chen
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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17
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Chen T, Romesberg FE. Enzymatic Synthesis, Amplification, and Application of DNA with a Functionalized Backbone. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Tingjian Chen
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Floyd E. Romesberg
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
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18
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Kong D, Yeung W, Hili R. In Vitro Selection of Diversely Functionalized Aptamers. J Am Chem Soc 2017; 139:13977-13980. [PMID: 28938065 DOI: 10.1021/jacs.7b07241] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We describe the application of T4 DNA ligase-catalyzed DNA templated oligonucleotide polymerization toward the evolution of a diversely functionalized nucleic acid aptamer for human α-thrombin. Using a 256-membered ANNNN comonomer library comprising 16 sublibraries modified with different functional groups, a highly functionalized aptamer for thrombin was raised with a dissociation constant of 1.6 nM. The aptamer was found to be selective for thrombin and required the modifications for binding affinity. This study demonstrates the most differentially functionalized nucleic acid aptamer discovered by in vitro selection and should enable the future exploration of functional group dependence during the evolution of nucleic acid polymer activity.
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Affiliation(s)
- Dehui Kong
- Department of Chemistry, University of Georgia , 140 Cedar Street, Athens, Georgia 30602, United States
| | - Wayland Yeung
- Department of Chemistry, University of Georgia , 140 Cedar Street, Athens, Georgia 30602, United States
| | - Ryan Hili
- Department of Chemistry, University of Georgia , 140 Cedar Street, Athens, Georgia 30602, United States.,Department Chemistry, York University , 4700 Keele Street, Toronto, ON M3J 1P3, Canada
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Liu M, Zhang Q, Chang D, Gu J, Brennan JD, Li Y. A DNAzyme Feedback Amplification Strategy for Biosensing. Angew Chem Int Ed Engl 2017; 56:6142-6146. [PMID: 28370773 DOI: 10.1002/anie.201700054] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/05/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
| | - Qiang Zhang
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - John D. Brennan
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
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21
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Minagawa H, Onodera K, Fujita H, Sakamoto T, Akitomi J, Kaneko N, Shiratori I, Kuwahara M, Horii K, Waga I. Selection, Characterization and Application of Artificial DNA Aptamer Containing Appended Bases with Sub-nanomolar Affinity for a Salivary Biomarker. Sci Rep 2017; 7:42716. [PMID: 28256555 PMCID: PMC5335659 DOI: 10.1038/srep42716] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/12/2017] [Indexed: 12/21/2022] Open
Abstract
We have attained a chemically modified DNA aptamer against salivary α-amylase (sAA), which attracts researchers’ attention as a useful biomarker for assessing human psychobiological and social behavioural processes, although high affinity aptamers have not been isolated from a random natural DNA library to date. For the selection, we used the base-appended base (BAB) modification, that is, a modified-base DNA library containing (E)-5-(2-(N-(2-(N6-adeninyl)ethyl))carbamylvinyl)-uracil in place of thymine. After eight rounds of selection, a 75 mer aptamer, AMYm1, which binds to sAA with extremely high affinity (Kd < 1 nM), was isolated. Furthermore, we have successfully determined the 36-mer minimum fragment, AMYm1-3, which retains target binding activity comparable to the full-length AMYm1, by surface plasmon resonance assays. Nuclear magnetic resonance spectral analysis indicated that the minimum fragment forms a specific stable conformation, whereas the predicted secondary structures were suggested to be disordered forms. Thus, DNA libraries with BAB-modifications can achieve more diverse conformations for fitness to various targets compared with natural DNA libraries, which is an important advantage for aptamer development. Furthermore, using AMYm1, a capillary gel electrophoresis assay and lateral flow assay with human saliva were conducted, and its feasibility was demonstrated.
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Affiliation(s)
- Hirotaka Minagawa
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Kentaro Onodera
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Hiroto Fujita
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino 275-0016, Japan
| | - Joe Akitomi
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Naoto Kaneko
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Ikuo Shiratori
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Katsunori Horii
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Iwao Waga
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
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Abstract
DNAzymes are catalytically active DNA molecules that are obtained via in vitro selection. RNA-cleaving DNAzymes have attracted significant attention for both therapeutic and diagnostic applications due to their excellent programmability, stability, and activity. They can be designed to cleave a specific mRNA to down-regulate gene expression. At the same time, DNAzymes can sense a broad range of analytes. By combining these two functions, theranostic DNAzymes are obtained. This review summarizes the progress of DNAzyme for theranostic applications. First, in vitro selection of DNAzymes is briefly introduced, and some representative DNAzymes related to biological applications are summarized. Then, the applications of DNAzyme for RNA cleaving are reviewed. DNAzymes have been used to cleave RNA for treating various diseases, such as viral infection, cancer, inflammation and atherosclerosis. Several formulations have entered clinical trials. Next, the use of DNAzymes for detecting metal ions, small molecules and nucleic acids related to disease diagnosis is summarized. Finally, the theranostic applications of DNAzyme are reviewed. The challenges to be addressed include poor DNAzyme activity under biological conditions, mRNA accessibility, delivery, and quantification of gene expression. Possible solutions to overcome these challenges are discussed, and future directions of the field are speculated.
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Kong D, Lei Y, Yeung W, Hili R. Enzymatic Synthesis of Sequence-Defined Synthetic Nucleic Acid Polymers with Diverse Functional Groups. Angew Chem Int Ed Engl 2016; 55:13164-13168. [PMID: 27633832 PMCID: PMC5330676 DOI: 10.1002/anie.201607538] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 08/23/2016] [Indexed: 12/21/2022]
Abstract
The development and in-depth analysis of T4 DNA ligase-catalyzed DNA templated oligonucleotide polymerization toward the generation of diversely functionalized nucleic acid polymers is described. The NNNNT codon set enables low codon bias, high fidelity, and high efficiency for the polymerization of ANNNN libraries comprising various functional groups. The robustness of the method was highlighted in the copolymerization of a 256-membered ANNNN library comprising 16 sub-libraries modified with different functional groups. This enabled the generation of diversely functionalized synthetic nucleic acid polymer libraries with 93.8 % fidelity. This process should find ready application in DNA nanotechnology, DNA computing, and in vitro evolution of functional nucleic acid polymers.
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Affiliation(s)
- Dehui Kong
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
| | - Yi Lei
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
| | - Wayland Yeung
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
| | - Ryan Hili
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA.
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24
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Kong D, Lei Y, Yeung W, Hili R. Enzymatic Synthesis of Sequence-Defined Synthetic Nucleic Acid Polymers with Diverse Functional Groups. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607538] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Dehui Kong
- Department of Chemistry; University of Georgia; Athens GA 30602 USA
| | - Yi Lei
- Department of Chemistry; University of Georgia; Athens GA 30602 USA
| | - Wayland Yeung
- Department of Chemistry; University of Georgia; Athens GA 30602 USA
| | - Ryan Hili
- Department of Chemistry; University of Georgia; Athens GA 30602 USA
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25
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Zhu J, Li Z, Wang Q, Liu Y, He J. The contribution of adenines in the catalytic core of 10-23 DNAzyme improved by the 6-amino group modifications. Bioorg Med Chem Lett 2016; 26:4462-4465. [DOI: 10.1016/j.bmcl.2016.07.076] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 07/13/2016] [Accepted: 07/29/2016] [Indexed: 10/21/2022]
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26
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Zhang W, Feng Q, Chang D, Tram K, Li Y. In vitro selection of RNA-cleaving DNAzymes for bacterial detection. Methods 2016; 106:66-75. [DOI: 10.1016/j.ymeth.2016.03.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 12/23/2022] Open
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Kong D, Yeung W, Hili R. Generation of Synthetic Copolymer Libraries by Combinatorial Assembly on Nucleic Acid Templates. ACS COMBINATORIAL SCIENCE 2016; 18:355-70. [PMID: 27275512 DOI: 10.1021/acscombsci.6b00059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent advances in nucleic acid-templated copolymerization have expanded the scope of sequence-controlled synthetic copolymers beyond the molecular architectures witnessed in nature. This has enabled the power of molecular evolution to be applied to synthetic copolymer libraries to evolve molecular function ranging from molecular recognition to catalysis. This Review seeks to summarize different approaches available to generate sequence-defined monodispersed synthetic copolymer libraries using nucleic acid-templated polymerization. Key concepts and principles governing nucleic acid-templated polymerization, as well as the fidelity of various copolymerization technologies, will be described. The Review will focus on methods that enable the combinatorial generation of copolymer libraries and their molecular evolution for desired function.
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Affiliation(s)
- Dehui Kong
- Department of Chemistry, University of Georgia, 140 Cedar
Street, Athens, Georgia 30602, United States
| | - Wayland Yeung
- Department of Chemistry, University of Georgia, 140 Cedar
Street, Athens, Georgia 30602, United States
| | - Ryan Hili
- Department of Chemistry, University of Georgia, 140 Cedar
Street, Athens, Georgia 30602, United States
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28
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Meek KN, Rangel AE, Heemstra JM. Enhancing aptamer function and stability via in vitro selection using modified nucleic acids. Methods 2016; 106:29-36. [PMID: 27012179 DOI: 10.1016/j.ymeth.2016.03.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 11/29/2022] Open
Abstract
Nucleic acid aptamers have emerged as a promising alternative to antibodies for use as recognition elements in therapeutics, bioimaging, and analytical applications. A key benefit that aptamers possess relative to antibodies is their ability to be chemically synthesized. This advantage, coupled with the broad range of modified nucleotide building blocks that can be constructed using chemical synthesis, has enabled the discovery and development of modified aptamers having extraordinary affinity, specificity, and biostability. Early efforts to generate modified aptamers focused on selection of a native DNA or RNA aptamer, followed by post-selection trial-and-error testing of modifications. However, recent advances in polymerase engineering and templated nucleic acid synthesis have enabled the direct selection of aptamers having modified backbones and nucleobases. This review will discuss these technological advances and highlight the improvements in aptamer function that have been realized through in vitro selection of non-natural nucleic acids.
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Affiliation(s)
- Kirsten N Meek
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, 315 S 1400 E, Salt Lake City, UT 84112, United States
| | - Alexandra E Rangel
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, 315 S 1400 E, Salt Lake City, UT 84112, United States
| | - Jennifer M Heemstra
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, 315 S 1400 E, Salt Lake City, UT 84112, United States.
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29
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Tolle F, Rosenthal M, Pfeiffer F, Mayer G. Click Reaction on Solid Phase Enables High Fidelity Synthesis of Nucleobase-Modified DNA. Bioconjug Chem 2016; 27:500-3. [PMID: 26850226 DOI: 10.1021/acs.bioconjchem.5b00668] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The post-synthetic functionalization of nucleic acids via click chemistry (CuAAC) has seen tremendous implementation, extending the applicability of nucleobase-modified nucleic acids in fields like fluorescent labeling, nanotechnology, and in vitro selection. However, the production of large quantities of high-density functionalized material via solid phase synthesis has been hampered by oxidative by-product formation associated with the alkaline workup conditions. Herein, we describe a rapid and cost-effective protocol for the high fidelity large-scale production of nucleobase-modified nucleic acids, exemplified with a recently described nucleobase-modified aptamer.
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Affiliation(s)
- Fabian Tolle
- Life and Medical Sciences Institute, University of Bonn , Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Malte Rosenthal
- Life and Medical Sciences Institute, University of Bonn , Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Franziska Pfeiffer
- Life and Medical Sciences Institute, University of Bonn , Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute, University of Bonn , Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
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30
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Räz MH, Hollenstein M. Probing the effect of minor groove interactions on the catalytic efficiency of DNAzymes 8-17 and 10-23. MOLECULAR BIOSYSTEMS 2016; 11:1454-61. [PMID: 25854917 DOI: 10.1039/c5mb00102a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNAzymes (Dz) 8-17 and 10-23 are two widely studied and well-characterized RNA-cleaving DNA catalysts. In an effort to further improve the understanding of the fragile interactions and dynamics of the enzymatic mechanism, this study examines the catalytic efficiency of minimally modified DNAzymes. Five single mutants of Dz8-17 and Dz10-23 were prepared by replacing the adenine residues in the corresponding catalytic cores with 3-deazaadenine units. Kinetic assays were used to assess the effect on the catalytic activity and thereby identify the importance of hydrogen bonding that arises from the N3 atoms. The results suggest that modifications at A15 and A15.0 of Dz8-17 have a significant influence and show a reduction in catalytic activity. Modification at each location in Dz10-23 results in a decrease of the observed rate constants, with A12 appearing to be the most affected with a reduction of ∼80% of kobs and ∼25% of the maximal cleavage rate compared to the wild-type DNAzyme. On the other hand, modification of A12 in Dz8-17 showed an ∼130% increase in kobs, thus unraveling a new potential site for the introduction of chemical modifications. A pH-profile analysis showed that the chemical cleavage step is rate-determining, regardless of the presence and/or location of the mutation. These findings point towards the importance of the N3-nitrogens of certain adenine nucleotides located within the catalytic cores of the DNAzymes for efficient catalytic activity and further suggest that they might directly partake in maintaining the appropriate tertiary structure. Therefore, it appears that minor groove interactions constitute an important feature of DNAzymes as well as ribozymes.
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Affiliation(s)
- Michael H Räz
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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31
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Hollenstein M. DNA Catalysis: The Chemical Repertoire of DNAzymes. Molecules 2015; 20:20777-804. [PMID: 26610449 PMCID: PMC6332124 DOI: 10.3390/molecules201119730] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 12/24/2022] Open
Abstract
Deoxyribozymes or DNAzymes are single-stranded catalytic DNA molecules that are obtained by combinatorial in vitro selection methods. Initially conceived to function as gene silencing agents, the scope of DNAzymes has rapidly expanded into diverse fields, including biosensing, diagnostics, logic gate operations, and the development of novel synthetic and biological tools. In this review, an overview of all the different chemical reactions catalyzed by DNAzymes is given with an emphasis on RNA cleavage and the use of non-nucleosidic substrates. The use of modified nucleoside triphosphates (dN*TPs) to expand the chemical space to be explored in selection experiments and ultimately to generate DNAzymes with an expanded chemical repertoire is also highlighted.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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32
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Renders M, Miller E, Hollenstein M, Perrin D. A method for selecting modified DNAzymes without the use of modified DNA as a template in PCR. Chem Commun (Camb) 2015; 51:1360-2. [PMID: 25487111 DOI: 10.1039/c4cc07588a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Modified DNAzyme selections typically depend on recopying catalytically active modified DNA (mDNA) into cDNA in a PCR amplification step. However mDNA is often a poor template in PCR. Herein we propose a selection method in which the catalytically active, mDNA strand is covalently linked to the unmodified DNA template strand from which it was polymerized. Following selection, the unmodified DNA template is amplified in a PCR instead of the mDNA. This method circumvents the PCR amplification of mDNA.
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Affiliation(s)
- Marleen Renders
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T 1Z1, Canada.
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33
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Abstract
To expand the chemical functionality of DNAzymes and aptamers, several new modified deoxyuridine triphosphates have been synthesized. An important precursor that enables this aim is 5-aminomethyl dUTP, whereby the pendent amine serves as a handle for further synthetic functionalization. Five functional groups were conjugated to 5-aminomethyl dUTP. Incorporation assays were performed on several templates that demand 2-5 sequential incorporation events using several commercially available DNA polymerases. It was found that Vent (exo-) DNA polymerase efficiently incorporates all five modified dUTPs. In addition, all nucleoside triphosphates were capable of supporting a double-stranded exponential PCR amplification. Modified PCR amplicons were PCR amplified into unmodified DNA and sequenced to verify that genetic information was conserved through incorporation, amplification, and reamplification. Overall these modified dUTPs represent new candidate substrates for use in selections using modified nucleotide libraries.
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34
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Tolle F, Brändle GM, Matzner D, Mayer G. Ein universeller Zugang zu Nucleobasen-modifizierten Aptameren. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503652] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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35
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Tolle F, Brändle GM, Matzner D, Mayer G. A Versatile Approach Towards Nucleobase-Modified Aptamers. Angew Chem Int Ed Engl 2015. [PMID: 26224087 DOI: 10.1002/anie.201503652] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A novel and versatile method has been developed for modular expansion of the chemical space of nucleic acid libraries, thus enabling the generation of nucleobase-modified aptamers with unprecedented recognition properties. Reintroduction of the modification after enzymatic replication gives broad access to many chemical modifications. This wide applicability, which is not limited to a single modification, will rapidly advance the application of in vitro selection approaches beyond what is currently feasible and enable the generation of aptamers to many targets that have so far not been addressable.
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Affiliation(s)
- Fabian Tolle
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn (Germany)
| | - Gerhard M Brändle
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn (Germany)
| | - Daniel Matzner
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn (Germany)
| | - Günter Mayer
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn (Germany).
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36
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Buyst D, Gheerardijn V, Fehér K, Van Gasse B, Van Den Begin J, Martins JC, Madder A. Identification of a pKa-regulating motif stabilizing imidazole-modified double-stranded DNA. Nucleic Acids Res 2014; 43:51-62. [PMID: 25520197 PMCID: PMC4288195 DOI: 10.1093/nar/gku1306] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The predictable 3D structure of double-stranded DNA renders it ideally suited as a template for the bottom-up design of functionalized nucleic acid-based active sites. We here explore the use of a 14mer DNA duplex as a scaffold for the precise and predictable positioning of catalytic functionalities. Given the ubiquitous participation of the histidine-based imidazole group in protein recognition and catalysis events, single histidine-like modified duplexes were investigated. Tethering histamine to the C5 of the thymine base via an amide bond, allows the flexible positioning of the imidazole function in the major groove. The mutual interactions between the imidazole and the duplex and its influence on the imidazolium pKaH are investigated by placing a single modified thymine at four different positions in the center of the 14mer double helix. Using NMR and unrestrained molecular dynamics, a structural motif involving the formation of a hydrogen bond between the imidazole and the Hoogsteen side of the guanine bases of two neighboring GC base pairs is established. The motif contributes to a stabilization against thermal melting of 6°C and is key in modulating the pKaH of the imidazolium group. The general features, prerequisites and generic character of the new pKaH-regulating motif are described.
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Affiliation(s)
- Dieter Buyst
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Unit, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Vicky Gheerardijn
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Krisztina Fehér
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Unit, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Bjorn Van Gasse
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Unit, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Jos Van Den Begin
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - José C Martins
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Unit, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
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37
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Gheerardijn V, Van den Begin J, Madder A. Versatile synthesis of amino acid functionalized nucleosides via a domino carboxamidation reaction. Beilstein J Org Chem 2014; 10:2566-72. [PMID: 25383128 PMCID: PMC4222392 DOI: 10.3762/bjoc.10.268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/23/2014] [Indexed: 12/23/2022] Open
Abstract
Functionalized oligonucleotides have recently gained increased attention for incorporation in modified nucleic acid structures both for the design of aptamers with enhanced binding properties as well as the construction of catalytic DNA and RNA. As a shortcut alternative to the incorporation of multiple modified residues, each bearing one extra functional group, we present here a straightforward method for direct linking of functionalized amino acids to the nucleoside base, thus equipping the nucleoside with two extra functionalities at once. As a proof of principle, we have introduced three amino acids with functional groups frequently used as key-intermediates in DNA- and RNAzymes via an efficient and straightforward domino carboxamidation reaction.
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Affiliation(s)
- Vicky Gheerardijn
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium
| | - Jos Van den Begin
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium
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38
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Therapeutic potential of siRNA and DNAzymes in cancer. Tumour Biol 2014; 35:9505-21. [PMID: 25149153 DOI: 10.1007/s13277-014-2477-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/07/2014] [Indexed: 02/07/2023] Open
Abstract
Cancer is characterized by uncontrolled cell growth, invasion, and metastasis and possess threat to humans worldwide. The scientific community is facing numerous challenges despite several efforts to cure cancer. Though a number of studies were done earlier, the molecular mechanism of cancer progression is not completely understood. Currently available treatments like surgery resection, adjuvant chemotherapy, and radiotherapy are not completely effective in curing all the cancers. Recent advances in the antisense technology provide a powerful tool to investigate various cancer pathways and target them. Small interfering RNAs (siRNAs) could be effective in downregulating the cancer-associated genes, but their in vivo delivery is the main obstacle. DNA enzymes (DNAzymes) have great potential in the treatment of cancer due to high selectivity and significant catalytic efficiency. In this review, we are focusing on antisense molecules such as siRNA and DNAzymes in cancer therapeutics development. This review also describes the challenges and approaches to overcome obstacles involved in using siRNA and DNAzymes in the treatment of cancers.
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39
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Hollenstein M, Leumann CJ. Synthesis and biochemical characterization of tricyclothymidine triphosphate (tc-TTP). Chembiochem 2014; 15:1901-4. [PMID: 25044722 DOI: 10.1002/cbic.201402116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Indexed: 01/03/2023]
Abstract
Tricyclo-DNA (tc-DNA) is a conformationally restricted oligonucleotide analogue that exhibits promising properties as a robust antisense agent. Here we report on the synthesis and biochemical characterization of tc-TTP, the triphosphate of a tc-DNA nucleoside containing the base thymine. Tc-TTP turned out to be a substrate for the Vent (exo(-) ) DNA polymerase, a polymerase that allows for multiple incorporations of tc-T nucleotides under primer extension reaction conditions. However, the substrate acceptance is rather low, as also observed for other sugar-modified analogues. Tc-TTP and tc-nucleotide-containing templates do not sustain enzymatic polymerization under physiological conditions; this indicates that tc-DNA-based antisense agents will not enter natural metabolic pathways that lead to long-term toxicity.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern (Switzerland).
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40
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Pinheiro VB, Holliger P. Towards XNA nanotechnology: new materials from synthetic genetic polymers. Trends Biotechnol 2014; 32:321-8. [PMID: 24745974 PMCID: PMC4039137 DOI: 10.1016/j.tibtech.2014.03.010] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 12/21/2022]
Abstract
Nucleic acids display remarkable properties beyond information storage and propagation. The well-understood base pairing rules have enabled nucleic acids to be assembled into nanostructures of ever increasing complexity. Although nanostructures can be constructed using other building blocks, including peptides and lipids, it is the capacity to evolve that sets nucleic acids apart from all other nanoscale building materials. Nonetheless, the poor chemical and biological stability of DNA and RNA constrain their applications. Recent advances in nucleic acid chemistry and polymerase engineering enable the synthesis, replication, and evolution of a range of synthetic genetic polymers (XNAs) with improved chemical and biological stability. We discuss the impact of this technology on the generation of XNA ligands, enzymes, and nanostructures with tailor-made chemistry.
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Affiliation(s)
- Vitor B Pinheiro
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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41
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Hollenstein M, Smith CC, Räz M. Nucleoside triphosphates--from synthesis to biochemical characterization. J Vis Exp 2014:51385. [PMID: 24747811 PMCID: PMC4162383 DOI: 10.3791/51385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The traditional strategy for the introduction of chemical functionalities is the use of solid-phase synthesis by appending suitably modified phosphoramidite precursors to the nascent chain. However, the conditions used during the synthesis and the restriction to rather short sequences hamper the applicability of this methodology. On the other hand, modified nucleoside triphosphates are activated building blocks that have been employed for the mild introduction of numerous functional groups into nucleic acids, a strategy that paves the way for the use of modified nucleic acids in a wide-ranging palette of practical applications such as functional tagging and generation of ribozymes and DNAzymes. One of the major challenges resides in the intricacy of the methodology leading to the isolation and characterization of these nucleoside analogues. In this video article, we present a detailed protocol for the synthesis of these modified analogues using phosphorous(III)-based reagents. In addition, the procedure for their biochemical characterization is divulged, with a special emphasis on primer extension reactions and TdT tailing polymerization. This detailed protocol will be of use for the crafting of modified dNTPs and their further use in chemical biology.
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Affiliation(s)
| | | | - Michael Räz
- Department of Chemistry and Biochemistry, University of Bern
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42
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Stovall GM, Bedenbaugh RS, Singh S, Meyer AJ, Hatala PJ, Ellington AD, Hall B. In vitro selection using modified or unnatural nucleotides. ACTA ACUST UNITED AC 2014; 56:9.6.1-33. [PMID: 25606981 DOI: 10.1002/0471142700.nc0906s56] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Incorporation of modified nucleotides into in vitro RNA or DNA selections offers many potential advantages, such as the increased stability of selected nucleic acids against nuclease degradation, improved affinities, expanded chemical functionality, and increased library diversity. 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 evaluating and optimizing transcription reactions, as well as confirming the incorporation of the modified nucleotides; protocols for evaluating modified nucleotide transcripts as template in reverse transcription reactions; protocols for the evaluation of the fidelity of modified nucleotides in the replication and the regeneration of the pool; and a protocol to compare modified nucleotide pools and selection conditions.
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Affiliation(s)
- Gwendolyn M Stovall
- The University of Texas at Austin, Austin, Texas; Altermune Technologies LLC, Austin, Texas
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Hollenstein M. Deoxynucleoside triphosphates bearing histamine, carboxylic acid, and hydroxyl residues--synthesis and biochemical characterization. Org Biomol Chem 2013; 11:5162-72. [PMID: 23817514 DOI: 10.1039/c3ob40842f] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Modified nucleoside triphosphates (dA(Hs)TP, dU(POH)TP, and dC(Val)TP) bearing imidazole, hydroxyl, and carboxylic acid residues connected to the purine and pyrimidine bases through alkyne linkers were prepared. These modified dN*TPs were excellent substrates for various DNA polymerases in primer extension reactions. Moreover, the combined use of terminal deoxynucleotidyl transferase (TdT) and the modified dNTPs led to efficient tailing reactions that rival those of natural counterparts. Finally, the triphosphates were tolerated by polymerases under PCR conditions, and the ensuing modified oligonucleotides served as templates for the regeneration of unmodified DNA. Thus, these modified dN*TPs are fully compatible with in vitro selection methods and can be used to develop artificial peptidases based on DNA.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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Gu H, Furukawa K, Weinberg Z, Berenson DF, Breaker RR. Small, highly active DNAs that hydrolyze DNA. J Am Chem Soc 2013; 135:9121-9. [PMID: 23679108 PMCID: PMC3763483 DOI: 10.1021/ja403585e] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
DNA phosphoester bonds are exceedingly resistant to hydrolysis in the absence of chemical or enzymatic catalysts. This property is particularly important for organisms with large genomes, as resistance to hydrolytic degradation permits the long-term storage of genetic information. Here we report the creation and analysis of two classes of engineered deoxyribozymes that selectively and rapidly hydrolyze DNA. Members of class I deoxyribozymes carry a catalytic core composed of only 15 conserved nucleotides and attain an observed rate constant (k(obs)) of ~1 min(-1) when incubated near neutral pH in the presence of Zn(2+). Natural DNA sequences conforming to the class I consensus sequence and structure were found that undergo hydrolysis under selection conditions (2 mM Zn(2+), pH 7), which demonstrates that the inherent structure of certain DNA regions might promote catalytic reactions, leading to genomic instability.
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Affiliation(s)
- Hongzhou Gu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
- Howard Hughes Medical Institute, New Haven, Connecticut, 06520 United States
| | - Kazuhiro Furukawa
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
| | - Zasha Weinberg
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
- Howard Hughes Medical Institute, New Haven, Connecticut, 06520 United States
| | - Daniel F. Berenson
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520 United States
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
- Howard Hughes Medical Institute, New Haven, Connecticut, 06520 United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520 United States
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45
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Hollenstein M, Hipolito CJ, Lam CH, Perrin DM. Toward the combinatorial selection of chemically modified DNAzyme RNase A mimics active against all-RNA substrates. ACS COMBINATORIAL SCIENCE 2013; 15:174-82. [PMID: 23485334 DOI: 10.1021/co3001378] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The convenient use of SELEX and related combinatorial methods of in vitro selection provides a formidable gateway for the generation of DNA enzymes, especially in the context of improving their potential as gene therapeutic agents. Here, we report on the selection of DNAzyme 12-91, a modified nucleic acid catalyst adorned with imidazole, ammonium, and guanidinium groups that provide for efficient M(2+)-independent cleavage of an all-RNA target sequence (kobs = 0.06 min(-1)). While Dz12-91 was selected for intramolecular cleavage of an all-RNA target, it surprisingly cleaves a target containing a lone ribocytosine unit with even greater efficiency (kobs = 0.27 min(-1)) than Dz9-86 (kobs = 0.13 min(-1)). The sequence composition of Dz12-91 bears a marked resemblance to that of Dz9-86 (kobs = 0.0014 min(-1) with an all-RNA substrate) that was selected from the same library to cleave a target containing a single ribonucleotide. However, small alterations in the sequence composition have a profound impact on the substrate preference and catalytic properties. Indeed, Dz12-91 displays the highest known rate enhancement for the M(2+)-independent cleavage of all-RNA targets. Hence, Dz12-91 represents a step toward the generation of potentially therapeutically active DNAzymes and further underscores the usefulness of modified triphosphates in selection experiments.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
| | - Christopher J. Hipolito
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
| | - Curtis H. Lam
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
| | - David M. Perrin
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
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46
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Hatano A, Kurosu M, Yonaha S, Okada M, Uehara S. One-pot approach to functional nucleosides possessing a fluorescent group using nucleobase-exchange reaction by thymidine phosphorylase. Org Biomol Chem 2013; 11:6900-5. [DOI: 10.1039/c3ob41605d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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47
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Hollenstein M. Nucleoside triphosphates--building blocks for the modification of nucleic acids. Molecules 2012; 17:13569-91. [PMID: 23154273 PMCID: PMC6268876 DOI: 10.3390/molecules171113569] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 11/07/2012] [Accepted: 11/09/2012] [Indexed: 11/16/2022] Open
Abstract
Nucleoside triphosphates are moldable entities that can easily be functionalized at various locations. The enzymatic polymerization of these modified triphosphate analogues represents a versatile platform for the facile and mild generation of (highly) functionalized nucleic acids. Numerous modified triphosphates have been utilized in a broad palette of applications spanning from DNA-tagging and -labeling to the generation of catalytic nucleic acids. This review will focus on the recent progress made in the synthesis of modified nucleoside triphosphates as well as on the understanding of the mechanisms underlying their polymerase acceptance. In addition, the usefulness of chemically altered dNTPs in SELEX and related methods of in vitro selection will be highlighted, with a particular emphasis on the generation of modified DNA enzymes (DNAzymes) and DNA-based aptamers.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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48
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Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets. Proc Natl Acad Sci U S A 2012; 109:19971-6. [PMID: 23139410 DOI: 10.1073/pnas.1213933109] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Selection of aptamers from nucleic acid libraries by in vitro evolution represents a powerful method of identifying high-affinity ligands for a broad range of molecular targets. Nevertheless, a sizeable fraction of proteins remain difficult targets due to inherently limited chemical diversity of nucleic acids. We have exploited synthetic nucleotide modifications that confer protein-like diversity on a nucleic acid scaffold, resulting in a new generation of binding reagents called SOMAmers (Slow Off-rate Modified Aptamers). Here we report a unique crystal structure of a SOMAmer bound to its target, platelet-derived growth factor B (PDGF-BB). The SOMAmer folds into a compact structure and exhibits a hydrophobic binding surface that mimics the interface between PDGF-BB and its receptor, contrasting sharply with mainly polar interactions seen in traditional protein-binding aptamers. The modified nucleotides circumvent the intrinsic diversity constraints of natural nucleic acids, thereby greatly expanding the structural vocabulary of nucleic acid ligands and considerably broadening the range of accessible protein targets.
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49
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Hollenstein M. Synthesis of deoxynucleoside triphosphates that include proline, urea, or sulfonamide groups and their polymerase incorporation into DNA. Chemistry 2012; 18:13320-30. [PMID: 22996052 DOI: 10.1002/chem.201201662] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/21/2012] [Indexed: 01/02/2023]
Abstract
To expand the chemical array available for DNA sequences in the context of in vitro selection, I present herein the synthesis of five nucleoside triphosphate analogues containing side chains capable of organocatalysis. The synthesis involved the coupling of L-proline-containing residues (dU(tP)TP and dU(cP)TP), a dipeptide (dU(FP)TP), a urea derivative (dU(Bpu)TP), and a sulfamide residue (dU(Bs)TP) to a suitably protected common intermediate, followed by triphosphorylation. These modified dNTPs were shown to be excellent substrates for the Vent (exo(-)) and Pwo DNA polymerases, as well as the Klenow fragment of E. coli DNA polymerase I, although they were only acceptable substrates for the 9°N(m) polymerase. All of the modified dNTPs, with the exception of dU(Bpu)TP, were readily incorporated into DNA by the polymerase chain reaction (PCR). Modified oligonucleotides efficiently served as templates for PCR for the regeneration of unmodified DNA. Thermal denaturation experiments showed that these modifications are tolerated in the major groove. Overall, these heavily modified dNTPs are excellent candidates for SELEX.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry & Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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50
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Catalytic cleavage activities of 10–23 DNAzyme analogs functionalized with an amino group in its catalytic core. Acta Pharm Sin B 2012. [DOI: 10.1016/j.apsb.2011.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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