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Afari MNK, Lönnberg T. Base-Filling in Double-Helical Nucleic Acids. ChemistryOpen 2024:e202400088. [PMID: 38709096 DOI: 10.1002/open.202400088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/10/2024] [Indexed: 05/07/2024] Open
Abstract
Base-filling, i. e., post-synthetic furnishing of an oligonucleotide scaffold with base moieties or their analogues, is an interesting alternative to the conventional approach of sequential coupling of building blocks (modified or otherwise). Reversible attachment of the base moieties is particularly attractive as it allows the use of dynamic combinatorial chemistry and usually leads to higher fidelity. This concept article summarizes the various backbones and coupling reactions used for base-filling over the past fifteen years, discusses the impact of base stacking and pairing on efficiency and fidelity and highlights potential and realized applications.
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Affiliation(s)
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
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Baranda Pellejero L, Mahdifar M, Ercolani G, Watson J, Brown T, Ricci F. Using antibodies to control DNA-templated chemical reactions. Nat Commun 2020; 11:6242. [PMID: 33288745 PMCID: PMC7721721 DOI: 10.1038/s41467-020-20024-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/11/2020] [Indexed: 11/09/2022] Open
Abstract
DNA-templated synthesis takes advantage of the programmability of DNA-DNA interactions to accelerate chemical reactions under diluted conditions upon sequence-specific hybridization. While this strategy has proven advantageous for a variety of applications, including sensing and drug discovery, it has been so far limited to the use of nucleic acids as templating elements. Here, we report the rational design of DNA templated synthesis controlled by specific IgG antibodies. Our approach is based on the co-localization of reactants induced by the bivalent binding of a specific IgG antibody to two antigen-conjugated DNA templating strands that triggers a chemical reaction that would be otherwise too slow under diluted conditions. This strategy is versatile, orthogonal and adaptable to different IgG antibodies and can be employed to achieve the targeted synthesis of clinically-relevant molecules in the presence of specific IgG biomarker antibodies.
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Affiliation(s)
- Lorena Baranda Pellejero
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Malihe Mahdifar
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Gianfranco Ercolani
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Jonathan Watson
- ATDBio Ltd, Magdalen Centre, Oxford Science Park, Robert Robinson Avenue, Oxford, OX4 4GA, UK
| | - Tom Brown
- ATDBio Ltd, Magdalen Centre, Oxford Science Park, Robert Robinson Avenue, Oxford, OX4 4GA, UK
| | - Francesco Ricci
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy.
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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4
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Tamura K. Beyond the Frozen Accident: Glycine Assignment in the Genetic Code. J Mol Evol 2015; 81:69-71. [PMID: 26289730 DOI: 10.1007/s00239-015-9694-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
Abstract
tRNA with a terminal UCCA-3' forms a structure in which the 3'-sequence folds back. The adenine of glycyl-AMP can base-pair with the uridine of the UCCA-3' region, which places the glycine residue in close proximity to the 3'-terminal adenosine of tRNA, possibly enabling the transfer of glycine from glycyl-AMP to tRNA. Thus, the UCCA-3'-containing tRNA (as seen in eubacterial tRNA(Gly)s) would possess an intrinsic property of glycylation by glycyl-AMP. This model provides a new perspective on the origins of the glycine assignment in the genetic code, beyond the "frozen accident" hypothesis.
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Affiliation(s)
- Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan. .,Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
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5
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Strazewski P. Omne Vivum Ex Vivo … Omne? How to Feed an Inanimate Evolvable Chemical System so as to Let it Self-evolve into Increased Complexity and Life-like Behaviour. Isr J Chem 2015. [DOI: 10.1002/ijch.201400175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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6
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7
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Garcia M, Kempe K, Haddleton DM, Khan A, Marsh A. Templated polymerizations on solid supports mediated by complementary nucleoside interactions. Polym Chem 2015. [DOI: 10.1039/c4py01783h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The preparation of immobilized poly(methacryloyl nucleosides) and their abilities for template polymerizations is discussed.
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Affiliation(s)
| | | | | | - Afzal Khan
- Department of Chemistry
- University of Warwick
- Coventry
- UK
| | - Andrew Marsh
- Department of Chemistry
- University of Warwick
- Coventry
- UK
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8
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Umehara T, Kitagawa T, Nakazawa Y, Yoshino H, Nemoto R, Tamura K. RNA tetraplex as a primordial peptide synthesis scaffold. Biosystems 2012; 109:145-50. [PMID: 22465151 DOI: 10.1016/j.biosystems.2012.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 03/02/2012] [Accepted: 03/08/2012] [Indexed: 11/29/2022]
Abstract
Peptide bond formation at the peptidyl transferase center on the ribosome is a crucial phenomenon in life systems. In this study, we conceptually propose possible roles of the RNA tetraplex as a scaffold for two aminoacyl minihelices that enable peptide bond formation. The basic rationale of this model is that "parallel" complementary templates composed of only 10-mer nucleotides can position two amino acids in close proximity, which is conceptually and essentially similar to the situation observed in ribosomes. Using supportive experimental data, we discuss the origin and evolution of peptide bond formation in early biological systems.
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Affiliation(s)
- Takuya Umehara
- Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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9
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Oligonucleotide-templated reactions for sensing nucleic acids. Molecules 2012; 17:2446-63. [PMID: 22374329 PMCID: PMC6268776 DOI: 10.3390/molecules17032446] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 02/23/2012] [Accepted: 02/24/2012] [Indexed: 02/07/2023] Open
Abstract
Oligonucleotide-templated reactions are useful for applying nucleic acid sensing. Various chemistries for oligonucleotide-templated reaction have been reported so far. Major scientific interests are focused on the development of signal amplification systems and signal generation systems. We introduce the recent advances of oligonucleotide-templated reaction in consideration of the above two points.
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Derr J, Manapat ML, Rajamani S, Leu K, Xulvi-Brunet R, Joseph I, Nowak MA, Chen IA. Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences. Nucleic Acids Res 2012; 40:4711-22. [PMID: 22319215 PMCID: PMC3378899 DOI: 10.1093/nar/gks065] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
During the origin of life, the biological information of nucleic acid polymers must have increased to encode functional molecules (the RNA world). Ribozymes tend to be compositionally unbiased, as is the vast majority of possible sequence space. However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences. While natural selection could lead to complex sequences, molecules with some activity are required to begin this process. Was the emergence of compositionally diverse sequences a matter of chance, or could prebiotically plausible reactions counter chemical biases to increase the probability of finding a ribozyme? Our in silico simulations using a two-letter alphabet show that template-directed ligation and high concatenation rates counter compositional bias and shift the pool toward longer sequences, permitting greater exploration of sequence space and stable folding. We verified experimentally that unbiased DNA sequences are more efficient templates for ligation, thus increasing the compositional diversity of the pool. Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules. Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life.
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Affiliation(s)
- Julien Derr
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
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Lin J, Surin M, Beljonne D, Lou X, van Dongen JLJ, Schenning APHJ. On the mechanism of dynamic polymerization via recycled ss-DNA templated assembly of non-natural bases. Chem Sci 2012. [DOI: 10.1039/c2sc20389h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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12
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Mukae M, Ihara T, Tabara M, Jyo A. Anthracene–DNA conjugates as building blocks of designed DNA structures constructed by photochemical reactions. Org Biomol Chem 2009; 7:1349-54. [DOI: 10.1039/b821869b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Liu Y, Wang R, Ding L, Sha R, Lukeman PS, Canary JW, Seeman NC. Thermodynamic analysis of nylon nucleic acids. Chembiochem 2008; 9:1641-8. [PMID: 18543259 PMCID: PMC2976662 DOI: 10.1002/cbic.200800032] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Indexed: 11/08/2022]
Abstract
The stability and structure of nylon nucleic acid duplexes with complementary DNA and RNA strands was examined. Thermal denaturing studies of a series of oligonucleotides that contained nylon nucleic acids (1-5 amide linkages) revealed that the amide linkage significantly enhanced the binding affinity of nylon nucleic acids towards both complementary DNA (up to 26 degrees C increase in the thermal transition temperature (T(m)) for five linkages) and RNA (around 15 degrees C increase in T(m) for five linkages) compared with nonamide linked precursor strands. For both DNA and RNA complements, increasing derivatization decreased the melting temperatures of uncoupled molecules relative to unmodified strands; by contrast, increasing lengths of coupled copolymer raised T(m) from less to slightly greater than T(m) of unmodified strands. Thermodynamic data extracted from melting curves and CD spectra of nylon nucleic acid duplexes were consistent with loss of stability due to incorporation of pendent groups on the 2'-position of ribose and recovery of stability upon linkage of the side chains.
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Affiliation(s)
- Yu Liu
- Department of Chemistry New York University 100 Washington Square E., New York, NY 10003 (USA) Fax: (+1) 212-260-7905
| | - Risheng Wang
- Department of Chemistry New York University 100 Washington Square E., New York, NY 10003 (USA) Fax: (+1) 212-260-7905
| | - Liang Ding
- Department of Chemistry New York University 100 Washington Square E., New York, NY 10003 (USA) Fax: (+1) 212-260-7905
| | - Ruojie Sha
- Department of Chemistry New York University 100 Washington Square E., New York, NY 10003 (USA) Fax: (+1) 212-260-7905
| | - Philip S. Lukeman
- Department of Chemistry New York University 100 Washington Square E., New York, NY 10003 (USA) Fax: (+1) 212-260-7905
| | - James W. Canary
- Department of Chemistry New York University 100 Washington Square E., New York, NY 10003 (USA) Fax: (+1) 212-260-7905
| | - Nadrian C. Seeman
- Department of Chemistry New York University 100 Washington Square E., New York, NY 10003 (USA) Fax: (+1) 212-260-7905
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14
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Abstract
In modern academic and industrial laboratories, evolutionary strategies are used routinely to identify biopolymers with novel activities. Large libraries of nucleic acids (approximately 10(15)) or peptides and proteins (approximately 10(13)) can be subjected to multiple rounds of selective pressure, amplification, and diversification, yielding individual sequences with desirable properties. Although the evolutionary approach is a powerful search tool, the chemical nature of biopolymers is not suited for all purposes. Application of evolutionary strategies to libraries of arbitrary chemical composition would overcome this problem, and radically change traditional small-molecule discovery. The chemical make-up of in vitro evolution libraries has necessarily been limited, because library synthesis relies on enzymes. A great deal of current research focuses on expanding the chemical repertoire of in vitro evolution by (a) broadening enzyme substrate specificities to include unnatural building blocks, or (b) developing methods to translate DNA sequences into multistep organic syntheses. We discuss the strengths and weaknesses of the approaches, review the successes, and consider the future of chemical evolution as a tool.
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Affiliation(s)
- S Jarrett Wrenn
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA.
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15
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Affiliation(s)
- Clinton R. South
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| | - Marcus Weck
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
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16
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Luisi PL, Chiarabelli C, Stano P. From Never Born Proteins to Minimal Living Cells: two projects in synthetic biology. ORIGINS LIFE EVOL B 2006; 36:605-16. [PMID: 17131092 DOI: 10.1007/s11084-006-9033-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The Never Born Proteins (NBPs) and the Minimal Cell projects are two currently developed research lines belonging to the field of synthetic biology. The first deals with the investigation of structural and functional properties of de novo proteins with random sequences, selected and isolated using phage display methods. The minimal cell is the simplest cellular construct which displays living properties, such as self-maintenance, self-reproduction and evolvability. The semi-synthetic approach to minimal cells involves the use of extant genes and proteins in order to build a supramolecular construct based on lipid vesicles. Results and outlooks on these two research lines are shortly discussed, mainly focusing on their relevance to the origin of life studies.
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Affiliation(s)
- Pier Luigi Luisi
- Biology Department, University of RomaTre, Viale G. Marconi 446, 00146 Rome, Italy.
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Luisi PL, Ferri F, Stano P. Approaches to semi-synthetic minimal cells: a review. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2005; 93:1-13. [PMID: 16292523 DOI: 10.1007/s00114-005-0056-z] [Citation(s) in RCA: 338] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Following is a synthetic review on the minimal living cell, defined as an artificial or a semi-artificial cell having the minimal and sufficient number of components to be considered alive. We describe concepts and experiments based on these constructions, and we point out that an operational definition of minimal cell does not define a single species, but rather a broad family of interrelated cell-like structures. The relevance of these researches, considering that the minimal cell should also correspond to the early simple cell in the origin of life and early evolution, is also explained. In addition, we present detailed data in relation to minimal genome, with observations cited by several authors who agree on setting the theoretical full-fledged minimal genome to a figure between 200 and 300 genes. However, further theoretical assumptions may significantly reduce this number (i.e. by eliminating ribosomal proteins and by limiting DNA and RNA polymerases to only a few, less specific molecular species). Generally, the experimental approach to minimal cells consists in utilizing liposomes as cell models and in filling them with genes/enzymes corresponding to minimal cellular functions. To date, a few research groups have successfully induced the expression of single proteins, such as the green fluorescence protein, inside liposomes. Here, different approaches are described and compared. Present constructs are still rather far from the minimal cell, and experimental as well as theoretical difficulties opposing further reduction of complexity are discussed. While most of these minimal cell constructions may represent relatively poor imitations of a modern full-fledged cell, further studies will begin precisely from these constructs. In conclusion, we give a brief outline of the next possible steps on the road map to the minimal cell.
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Affiliation(s)
- Pier Luigi Luisi
- Biology Department, University of RomaTre, Viale G. Marconi 446, 00146 Rome, Italy.
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Stains CI, Porter JR, Ooi AT, Segal DJ, Ghosh I. DNA Sequence-Enabled Reassembly of the Green Fluorescent Protein. J Am Chem Soc 2005; 127:10782-3. [PMID: 16076155 DOI: 10.1021/ja051969w] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe a general methodology for the direct detection of DNA by the design of a split-protein system that reassembles to form an active complex only in the presence of a targeted DNA sequence. This approach, called SEquence Enabled Reassembly (SEER) of proteins, combines the ability to rationally dissect proteins to construct oligomerization-dependent protein reassembly systems and the availability of DNA binding Cys2-His2 zinc-finger motifs for the recognition of specific DNA sequences. We demonstrate the feasibility of the SEER approach utilizing the split green fluorescent protein appended to appropriate zinc fingers, such that chromophore formation is only catalyzed in the presence of DNA sequences that incorporate binding sites for both zinc fingers.
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Affiliation(s)
- Cliff I Stains
- Department of Chemistry and Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721, USA
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