1
|
Wang LJ, Liu Q, Lu YY, Liang L, Zhang CY. Silver-Coordinated Watson-Crick Pairing-Driven Three-Dimensional DNA Walker for Locus-Specific Detection of Genomic N6-Methyladenine and N4-Methylcytosine at the Single-Molecule Level. Anal Chem 2024; 96:2191-2198. [PMID: 38282288 DOI: 10.1021/acs.analchem.3c05184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
N6-Methyladenine (6mdA) and N4-methylcytosine (4mdC) are the two most dominant DNA modifications in both prokaryotes and eukaryotes, but standard hybridization-based techniques cannot be applied for the 6mdA/4mdC assay. Herein, we demonstrate the silver-coordinated Watson-Crick pairing-driven three-dimensional (3D) DNA walker for locus-specific detection of genomic 6mdA/4mdC at the single-molecule level. 6mdA-DNA and 4mdC-DNA can selectively hybridize with the binding probes (BP1 and BP2) to form 6mdA-DNA-BP1 and 4mdC-DNA-BP2 duplexes. The 6mdA-C/4mdC-A mismatches cannot be stabilized by AgI, and thus, 18-nt BP1/BP2 cannot be extended by the catalysis of KF exonuclease. Through toehold-mediated strand displacement (TMSD), the signal probe (SP1/SP2) functionalized on the gold nanoparticles (AuNPs) can competitively bind to BP1/BP2 in 6mdA-DNA-BP1/4mdC-DNA-BP2 duplex to obtain SP1-18-nt BP1 and SP2-18-nt BP2 duplexes. The resulting DNA duplexes can act as the substrates of lambda exonuclease, leading to the cleavage of SP1/SP2 and the release of Cy3/Cy5 and 18-nt BP1/BP2. The released 18-nt BP1/BP2 can subsequently serve as the walker DNA, moving along the surface of the AuNP to activate dynamic 3D DNA walking and releasing abundant Cy3/Cy5. The released Cy3/Cy5 can be quantified by single-molecule imaging. This nanosensor exhibits high sensitivity with a limit of detection (LOD) of 9.80 × 10-15 M for 6mdA-DNA and 9.97 × 10-15 M for 4mdC-DNA. It can discriminate 6mdA-/4mdC-DNA from unmodified genomic DNAs, distinguish 0.01% 6mdA-/4mdC-DNA from excess unmethylated DNAs, and quantify 6mdA-/4mdC-DNA at specific sites in genomic DNAs of liver cancer cells and Escherichia coli plasmid cloning vector, providing a new platform for locus-specific analysis of 6mdA/4mdC in genomic DNAs.
Collapse
Affiliation(s)
- Li-Juan Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Qian Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Ying-Ying Lu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Le Liang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| |
Collapse
|
2
|
Schaudy E, Lietard J. In situ enzymatic template replication on DNA microarrays. Methods 2023; 213:33-41. [PMID: 37001684 DOI: 10.1016/j.ymeth.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
DNA microarrays are very useful tools to study the realm of nucleic acids interactions at high throughput. The conventional approach to microarray synthesis employs phosphoramidite chemistry and yields unmodified DNA generally attached to a surface at the 3' terminus. Having a freely accessible 3'-OH instead of 5'-OH is desirable too, and being able to introduce nucleoside analogs in a combinatorial manner is highly relevant in the context of nucleic acid therapeutics and in aptamer research. Here, we describe an enzymatic approach to the synthesis of high-density DNA microarrays that can also contain chemical modifications. The method uses a standard DNA microarray, to which a DNA primer is covalently bound through photocrosslinking. The extension of the primer with a DNA polymerase yields double-stranded DNA but is also amenable to the incorporation of modified dNTPs. Further processing with T7 exonuclease, which catalyzes the degradation of DNA in a specific (5'→3') direction, results in template strand removal. Overall, the method produces surface-bound natural and non-natural DNA oligonucleotides, is applicable to commercial microarrays and paves the way for the preparation of combinatorial, chemically modified aptamer libraries.
Collapse
|
3
|
Dalla Pozza M, Abdullrahman A, Cardin CJ, Gasser G, Hall JP. Three's a crowd - stabilisation, structure, and applications of DNA triplexes. Chem Sci 2022; 13:10193-10215. [PMID: 36277639 PMCID: PMC9473520 DOI: 10.1039/d2sc01793h] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/02/2022] [Indexed: 12/16/2022] Open
Abstract
DNA is a strikingly flexible molecule and can form a variety of secondary structures, including the triple helix, which is the subject of this review. The DNA triplex may be formed naturally, during homologous recombination, or can be formed by the introduction of a synthetic triplex forming oligonucleotide (TFO) to a DNA duplex. As the TFO will bind to the duplex with sequence specificity, there is significant interest in developing TFOs with potential therapeutic applications, including using TFOs as a delivery mechanism for compounds able to modify or damage DNA. However, to combine triplexes with functionalised compounds, a full understanding of triplex structure and chemical modification strategies, which may increase triplex stability or in vivo degradation, is essential - these areas will be discussed in this review. Ruthenium polypyridyl complexes, which are able to photooxidise DNA and act as luminescent DNA probes, may serve as a suitable photophysical payload for a TFO system and the developments in this area in the context of DNA triplexes will also be reviewed.
Collapse
Affiliation(s)
- Maria Dalla Pozza
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology F-75005 Paris France www.gassergroup.com
| | - Ahmad Abdullrahman
- Department of Pharmacy, Chemistry and Pharmacy Building, University of Reading Whiteknights Campus Reading Berkshire RG6 6AD UK
| | - Christine J Cardin
- Department of Chemistry, University of Reading Whiteknights Reading RG6 6AD UK
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology F-75005 Paris France www.gassergroup.com
| | - James P Hall
- Department of Pharmacy, Chemistry and Pharmacy Building, University of Reading Whiteknights Campus Reading Berkshire RG6 6AD UK
| |
Collapse
|
4
|
Zhao F, Wei Y, Wang X, Zhou Y, Tong Y, Ang EL, Liu S, Zhao H, Zhang Y. Enzymatic Synthesis of the Unnatural Nucleotide 2'-Deoxyisoguanosine 5'-Monophosphate. Chembiochem 2022; 23:e202200295. [PMID: 35959532 DOI: 10.1002/cbic.202200295] [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: 05/24/2022] [Revised: 08/05/2022] [Indexed: 11/05/2022]
Abstract
Naturally occurring DNA contains four canonical bases, forming two Watson-Crick base pairs (adenine-thymine, guanine-cytosine). Efforts over the past decades have led to the development of several unnatural base pairs, enabling the synthesis of unnatural DNA with an expanded genetic alphabet. The engineering of organisms capable of de novo biosynthesis of unnatural DNA would have significant technological and philosophical implications, but remains a challenge. Here we report the enzymatic conversion of 2'-deoxyxanthosine 5'-monophosphate (dXMP) into deoxyisoguanosine monophosphate (dBMP), a precursor of the unnatural isoguanine-isocytosine base pair. The reaction is catalyzed by the bacteriophage enzyme PurZ and bacterial PurB, and is a key addition to the toolbox for de novo biosynthesis of unnatural DNA.
Collapse
Affiliation(s)
- Fuping Zhao
- Tianjin University, School of Pharmacology Science and Technology, CHINA
| | - Yifeng Wei
- Agency for Science Technology and Research, Singapore Institute of Food and Biotechnology Innovation, SINGAPORE
| | - Xinyu Wang
- Tianjin University, School of Pharmacology Science and Technology, CHINA
| | - Yan Zhou
- Tianjin University, School of Pharmacology Science and Technology, CHINA
| | - Yang Tong
- Tianjin University, School of Pharmacology Science and Technology, CHINA
| | - Ee Lui Ang
- Agency for Science Technology and Research, Singapore Institute of Food and Biotechnology Innovation, SINGAPORE
| | - Shengnan Liu
- Tianjin University, Institute of Molecular Plus, CHINA
| | - Huimin Zhao
- Agency for Science Technology and Research, Singapore Institute of Food and Biotechnology Innovation, SINGAPORE
| | - Yan Zhang
- Tianjin University, School of Pharmaceutical Science and Technology, Office 417-4, 92 Weijin Rd, Nankai District, 300072, Tianjin, CHINA
| |
Collapse
|
5
|
Flamme M, Hanlon S, Marzuoli I, Püntener K, Sladojevich F, Hollenstein M. Evaluation of 3'-phosphate as a transient protecting group for controlled enzymatic synthesis of DNA and XNA oligonucleotides. Commun Chem 2022; 5:68. [PMID: 36697944 PMCID: PMC9814670 DOI: 10.1038/s42004-022-00685-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/12/2022] [Indexed: 01/28/2023] Open
Abstract
Chemically modified oligonucleotides have advanced as important therapeutic tools as reflected by the recent advent of mRNA vaccines and the FDA-approval of various siRNA and antisense oligonucleotides. These sequences are typically accessed by solid-phase synthesis which despite numerous advantages is restricted to short sequences and displays a limited tolerance to functional groups. Controlled enzymatic synthesis is an emerging alternative synthetic methodology that circumvents the limitations of traditional solid-phase synthesis. So far, most approaches strived to improve controlled enzymatic synthesis of canonical DNA and no potential routes to access xenonucleic acids (XNAs) have been reported. In this context, we have investigated the possibility of using phosphate as a transient protecting group for controlled enzymatic synthesis of DNA and locked nucleic acid (LNA) oligonucleotides. Phosphate is ubiquitously employed in natural systems and we demonstrate that this group displays most characteristics required for controlled enzymatic synthesis. We have devised robust synthetic pathways leading to these challenging compounds and we have discovered a hitherto unknown phosphatase activity of various DNA polymerases. These findings open up directions for the design of protected DNA and XNA nucleoside triphosphates for controlled enzymatic synthesis of chemically modified nucleic acids.
Collapse
Affiliation(s)
- Marie Flamme
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université de Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724 Paris Cedex 15, Paris, France
| | - Steven Hanlon
- grid.417570.00000 0004 0374 1269Pharmaceutical Devision, Synthetic Molecules Technical Development, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Irene Marzuoli
- grid.417570.00000 0004 0374 1269Pharmaceutical Devision, Synthetic Molecules Technical Development, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Kurt Püntener
- grid.417570.00000 0004 0374 1269Pharmaceutical Devision, Synthetic Molecules Technical Development, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Filippo Sladojevich
- grid.417570.00000 0004 0374 1269Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Marcel Hollenstein
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université de Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724 Paris Cedex 15, Paris, France
| |
Collapse
|
6
|
Chan KY, Kinghorn AB, Hollenstein M, Tanner JA. Chemical modifications for a next generation of nucleic acid aptamers. Chembiochem 2022; 23:e202200006. [PMID: 35416400 DOI: 10.1002/cbic.202200006] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/11/2022] [Indexed: 11/08/2022]
Abstract
In the past three decades, in vitro systematic evolution of ligands by exponential enrichment (SELEX) has yielded many aptamers for translational applications in both research and clinical settings. Despite their promise as an alternative to antibodies, the low success rate of SELEX (~ 30%) has been a major bottleneck that hampers the further development of aptamers. One hurdle is the lack of chemical diversity in nucleic acids. To address this, the aptamer chemical repertoire has been extended by introducing exotic chemical groups, which provide novel binding functionalities. This review will focus on how modified aptamers can be selected and evolved, with illustration of some successful examples. In particular, unique chemistries are exemplified. Various strategies of incorporating modified building blocks into the standard SELEX protocol are highlighted, with a comparison of the differences between pre-SELEX and post-SELEX modifications. Nucleic acid aptamers with extended functionality evolved from non-natural chemistries will open up new vistas for function and application of nucleic acids.
Collapse
Affiliation(s)
- Kwing Yeung Chan
- The University of Hong Kong, School of Biomedical Sciences, HONG KONG
| | | | | | - Julian Alexander Tanner
- The University of Hong Kong, School of Biomedical Sciences, 3/F Laboratory Block, 21 Sassoon Road, 000000, Pokfulam, HONG KONG
| |
Collapse
|
7
|
Hu L, Takezawa Y, Shionoya M. Metal-mediated DNA base pairing of easily prepared 2-oxo-imidazole-4-carboxylate nucleotides. Chem Sci 2022; 13:3977-3983. [PMID: 35440985 PMCID: PMC8985573 DOI: 10.1039/d2sc00926a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 11/21/2022] Open
Abstract
Metal-mediated DNA base pairs, which consist of two ligand-type artificial nucleobases and a bridging metal ion, have attracted increasing attention in recent years as a different base pairing mode from natural base pairing. Metal-mediated base pairing has been extensively studied, not only for metal-dependent thermal stabilisation of duplexes, but also for metal assembly by DNA templates and construction of functional DNAs that can be controlled by metals. Here, we report the metal-mediated base paring properties of a novel 2-oxo-imidazole-4-carboxylate (ImOC) nucleobase and a previously reported 2-oxo-imidazole-4-carboxamide (ImOA) nucleobase, both of which can be easily derived from a commercially available uridine analogue. The ImOC nucleobases were found to form stable ImOC–CuII–ImOC and ImOC–HgII–ImOC base pairs in the presence of the corresponding metal ions, leading to an increase in the duplex melting temperature by +20 °C and +11 °C, respectively. The ImOC bases did not react with other divalent metal ions and showed superior metal selectivity compared to similar nucleobase design reported so far. The ImOC–CuII–ImOC base pair was much more stable than mismatch pairs with other natural nucleobases, confirming the base pair specificity in the presence of CuII. Furthermore, we demonstrated the quantitative assembly of three CuII ions inside a DNA duplex with three consecutive ImOC–ImOC pairs, showing great potential of DNA-template based CuII nanoarray construction. The study of easily-prepared ImOC base pairs will provide a new design strategy for metal-responsive DNA materials. A novel 2-oxo-imidazole-4-carboxylate (ImOC) nucleobase, which can be easily derived from a commercially available uridine analogue, was found to form stable CuII- and HgII-mediated base pairs in DNA duplexes.![]()
Collapse
Affiliation(s)
- Lingyun Hu
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| |
Collapse
|
8
|
Levi-Acobas F, McKenzie LK, Hollenstein M. Towards polymerase-mediated synthesis of artificial RNA–DNA metal base pairs. NEW J CHEM 2022. [DOI: 10.1039/d2nj00427e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Polymerase-mediated synthesis of RNA-DNA metal base pairs.
Collapse
Affiliation(s)
- Fabienne Levi-Acobas
- Institut Pasteur, Université de Paris, CNRS UMR3523, Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Luke K. McKenzie
- Institut Pasteur, Université de Paris, CNRS UMR3523, Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Marcel Hollenstein
- Institut Pasteur, Université de Paris, CNRS UMR3523, Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| |
Collapse
|