1
|
Cheng C, Cheng Q, Zhou W, Chen Y, Xiao P. Highly accurate single-color fluorogenic DNA decoding sequencing for mutational genotyping. J Pharm Biomed Anal 2024; 249:116397. [PMID: 39111245 DOI: 10.1016/j.jpba.2024.116397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/30/2024] [Accepted: 08/03/2024] [Indexed: 08/20/2024]
Abstract
We proposed a single-color fluorogenic DNA decoding sequencing method designed to improve sequencing accuracy, increase read length and throughput, as well as decrease scanning time. This method involves the incorporation of a mixture of four types of 3'-O-modified nucleotide reversible terminators into each reaction. Among them, two nucleotides are labeled with the same fluorophore, while the remaining two are unlabeled. Only one nucleotide can be extended in each reaction, and an encoding that partially defines base composition can be obtained. Through cyclic interrogation of a template twice with different nucleotide combinations, two sets of encodings are sequentially obtained, enabling the determination of the sequence. We demonstrate the feasibility of this method using established sequencing chemistry, achieving a cycle efficiency of approximately 99.5 %. Notably, this strategy exhibits remarkable efficacy in the detection and correction of sequencing errors, achieving a theoretical error rate of 0.00016 % at a sequencing depth of ×2, which is lower than Sanger sequencing. This method is theoretically compatible with the existing sequencing-by-synthesis (SBS) platforms, and the instrument is simpler, which may facilitate further reductions in sequencing costs, thereby broadening its applications in biology and medicine. Moreover, we demonstrate the capability to detect known mutation sites using information from only a single sequencing run. We validate this approach by accurately identifying a mutation site in the human mitochondrial DNA.
Collapse
Affiliation(s)
- Chu Cheng
- College of Medicine and Health Science, Wuhan Polytechnic University, Wuhan, China.
| | - Qingzhou Cheng
- College of Medicine and Health Science, Wuhan Polytechnic University, Wuhan, China
| | - Wei Zhou
- College of Medicine and Health Science, Wuhan Polytechnic University, Wuhan, China
| | - Yulong Chen
- College of Medicine and Health Science, Wuhan Polytechnic University, Wuhan, China
| | - Pengfeng Xiao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| |
Collapse
|
2
|
Pichon M, Hollenstein M. Controlled enzymatic synthesis of oligonucleotides. Commun Chem 2024; 7:138. [PMID: 38890393 PMCID: PMC11189433 DOI: 10.1038/s42004-024-01216-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Oligonucleotides are advancing as essential materials for the development of new therapeutics, artificial genes, or in storage of information applications. Hitherto, our capacity to write (i.e., synthesize) oligonucleotides is not as efficient as that to read (i.e., sequencing) DNA/RNA. Alternative, biocatalytic methods for the de novo synthesis of natural or modified oligonucleotides are in dire need to circumvent the limitations of traditional synthetic approaches. This Perspective article summarizes recent progress made in controlled enzymatic synthesis, where temporary blocked nucleotides are incorporated into immobilized primers by polymerases. While robust protocols have been established for DNA, RNA or XNA synthesis is more challenging. Nevertheless, using a suitable combination of protected nucleotides and polymerase has shown promises to produce RNA oligonucleotides even though the production of long DNA/RNA/XNA sequences (>1000 nt) remains challenging. We surmise that merging ligase- and polymerase-based synthesis would help to circumvent the current shortcomings of controlled enzymatic synthesis.
Collapse
Affiliation(s)
- Maëva Pichon
- Institut Pasteur, Université 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, France
| | - Marcel Hollenstein
- Institut Pasteur, Université 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, France.
| |
Collapse
|
3
|
Wang B, Bradley KM, Kim MJ, Laos R, Chen C, Gerloff DL, Manfio L, Yang Z, Benner SA. Enzyme-assisted high throughput sequencing of an expanded genetic alphabet at single base resolution. Nat Commun 2024; 15:4057. [PMID: 38744910 PMCID: PMC11094070 DOI: 10.1038/s41467-024-48408-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
With just four building blocks, low sequence information density, few functional groups, poor control over folding, and difficulties in forming compact folds, natural DNA and RNA have been disappointing platforms from which to evolve receptors, ligands, and catalysts. Accordingly, synthetic biology has created "artificially expanded genetic information systems" (AEGIS) to add nucleotides, functionality, and information density. With the expected improvements seen in AegisBodies and AegisZymes, the task for synthetic biologists shifts to developing for expanded DNA the same analytical tools available to natural DNA. Here we report one of these, an enzyme-assisted sequencing of expanded genetic alphabet (ESEGA) method to sequence six-letter AEGIS DNA. We show how ESEGA analyses this DNA at single base resolution, and applies it to optimized conditions for six-nucleotide PCR, assessing the fidelity of various DNA polymerases, and extending this to AEGIS components with functional groups. This supports the renewed exploitation of expanded DNA alphabets in biotechnology.
Collapse
Affiliation(s)
- Bang Wang
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | | | | | - Roberto Laos
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | - Cen Chen
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | | | - Luran Manfio
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, Alachua, FL, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA.
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA.
| |
Collapse
|
4
|
Wang B, Bradley KM, Kim MJ, Laos R, Chen C, Gerloff DL, Manfio L, Yang Z, Benner SA. Enzyme-Assisted High Throughput Sequencing of an Expanded Genetic Alphabet at Single Base Resolution. RESEARCH SQUARE 2023:rs.3.rs-3678081. [PMID: 38196584 PMCID: PMC10775363 DOI: 10.21203/rs.3.rs-3678081/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Many efforts have sought to apply laboratory in vitro evolution (LIVE) to natural nucleic acid (NA) scaffolds to directly evolve functional molecules. However, synthetic biology can move beyond natural NA scaffolds to create molecular systems whose libraries are far richer reservoirs of functionality than natural NAs. For example, "artificially expanded genetic information systems" (AEGIS) add up to eight nucleotides to the four found in standard NA. Even in its simplest 6-letter versions, AEGIS adds functional groups, information density, and folding motifs that natural NA libraries lack. To complete this vision, however, tools are needed to sequence molecules that are created by AEGIS LIVE. Previous sequencing approaches, including approaches from our laboratories, exhibited limited performance and lost many sequences in diverse library mixtures. Here, we present a new approach that enzymatically transforms the target AEGIS DNA. With higher transliteration efficiency and fidelity, this Enzyme-Assisted Sequencing of Expanded Genetic Alphabet (ESEGA) approach produces substantially better sequences of 6-letter (AGCTZP) DNA than previous transliteration approaches. Therefore, ESEGA facilitates precise analysis of libraries, allowing 'next-generation deep sequencing' to accurately quantify the sequences of 6-letter DNA molecules at single base resolution. We then applied ESEGA to three tasks: (a) defining optimal conditions to perform 6-nucleotide PCR (b) evaluating the fidelity of 6-nucleotide PCR with various DNA polymerases, and (c) extending that evaluation to AEGIS components functionalized with alkynyl and aromatic groups. No other approach at present has this scope, allowing this work to be the next step towards exploiting the potential of expanded DNA alphabets in biotechnology.
Collapse
Affiliation(s)
- Bang Wang
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
- Department of Chemistry, University of Florida, Gainesville, FL, USA, 32611
| | | | - Myong-Jung Kim
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA, 32615
| | - Roberto Laos
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
| | - Cen Chen
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
| | - Dietlind L. Gerloff
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
| | - Luran Manfio
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA, 32615
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA, 32615
| |
Collapse
|
5
|
Downs IL, David Ordonez Luna A, Kota KP, Rubin SK, Shirsekar SS, Ward MD, Panchal RG, Litosh VA. Modification of N-hydroxycytidine yields a novel lead compound exhibiting activity against the Venezuelan equine encephalitis virus. Bioorg Med Chem Lett 2023; 94:129432. [PMID: 37591319 DOI: 10.1016/j.bmcl.2023.129432] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/27/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
Nucleoside and nucleobase analogs capable of interfering with nucleic acid synthesis have played essential roles in fighting infectious diseases. However, many of these agents are associated with important and potentially lethal off-target intracellular effects that limit their use. Based on the previous discovery of base-modified 2'-deoxyuridines, which showed high anticancer activity while exhibiting lower toxicity toward rapidly dividing normal human cells compared to antimetabolite chemotherapeutics, we hypothesized that a similar modification of the N4-hydroxycytidine (NHC) molecule would provide novel antiviral compounds with diminished side effects. This presumption is due to the substantial structural difference with natural cytidine leading to less recognizability by host cell enzymes. Among the 42 antimetabolite species that have been synthesized and screened against VEEV, one hit compound was identified. The structural features of the modifying moiety were similar to those of the anticancer lead 2'-deoxyuridine derivative reported previously, providing an opportunity to pursue further structure-activity relationship (SAR) studies directed to lead improvement, and obtain insight into the mechanism of action, which can lead to identifying drug candidates against a broad spectrum of RNA viral infections.
Collapse
Affiliation(s)
- Isaac L Downs
- US Army Medical Research Institute of Infectious Diseases, 1425 Porter St., Fort Detrick, MD 21702, USA
| | - A David Ordonez Luna
- US Army Medical Research Institute of Infectious Diseases, 1425 Porter St., Fort Detrick, MD 21702, USA
| | - Krishna P Kota
- US Army Medical Research Institute of Infectious Diseases, 1425 Porter St., Fort Detrick, MD 21702, USA
| | - Sarah K Rubin
- US Army Medical Research Institute of Infectious Diseases, 1425 Porter St., Fort Detrick, MD 21702, USA
| | - Serena S Shirsekar
- US Army Medical Research Institute of Infectious Diseases, 1425 Porter St., Fort Detrick, MD 21702, USA
| | - Michael D Ward
- US Army Medical Research Institute of Infectious Diseases, 1425 Porter St., Fort Detrick, MD 21702, USA
| | - Rekha G Panchal
- US Army Medical Research Institute of Infectious Diseases, 1425 Porter St., Fort Detrick, MD 21702, USA
| | - Vladislav A Litosh
- US Army Medical Research Institute of Infectious Diseases, 1425 Porter St., Fort Detrick, MD 21702, USA.
| |
Collapse
|
6
|
Hoose A, Vellacott R, Storch M, Freemont PS, Ryadnov MG. DNA synthesis technologies to close the gene writing gap. Nat Rev Chem 2023; 7:144-161. [PMID: 36714378 PMCID: PMC9869848 DOI: 10.1038/s41570-022-00456-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2022] [Indexed: 01/24/2023]
Abstract
Synthetic DNA is of increasing demand across many sectors of research and commercial activities. Engineering biology, therapy, data storage and nanotechnology are set for rapid developments if DNA can be provided at scale and low cost. Stimulated by successes in next generation sequencing and gene editing technologies, DNA synthesis is already a burgeoning industry. However, the synthesis of >200 bp sequences remains unaffordable. To overcome these limitations and start writing DNA as effectively as it is read, alternative technologies have been developed including molecular assembly and cloning methods, template-independent enzymatic synthesis, microarray and rolling circle amplification techniques. Here, we review the progress in developing and commercializing these technologies, which are exemplified by innovations from leading companies. We discuss pros and cons of each technology, the need for oversight and regulatory policies for DNA synthesis as a whole and give an overview of DNA synthesis business models.
Collapse
Affiliation(s)
- Alex Hoose
- National Physical Laboratory, Teddington, Middlesex UK
| | | | - Marko Storch
- London Biofoundry, Translation and Innovation Hub, Imperial College White City Campus, London, UK
- Section of Structural and Synthetic Biology, Faculty of Medicine, Imperial College London, London, UK
| | - Paul S. Freemont
- London Biofoundry, Translation and Innovation Hub, Imperial College White City Campus, London, UK
- Section of Structural and Synthetic Biology, Faculty of Medicine, Imperial College London, London, UK
| | | |
Collapse
|
7
|
Cheng C, Xiao P. Evaluation of the correctable decoding sequencing as a new powerful strategy for DNA sequencing. Life Sci Alliance 2022; 5:5/8/e202101294. [PMID: 35422436 PMCID: PMC9012935 DOI: 10.26508/lsa.202101294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/01/2022] [Accepted: 04/01/2022] [Indexed: 12/01/2022] Open
Abstract
This article proposed the correctable decoding sequencing technology with conservative theoretical error rate of 0.0009%, and evaluated its robustness by simulation. This technology can provide a powerful new protocol for NGS platforms, enabling accurate identification of rare mutations in medicine. Next-generation sequencing (NGS) promises to revolutionize precision medicine, but the existing sequencing technologies are limited in accuracy. To overcome this limitation, we propose the correctable decoding sequencing strategy, which is a duplex sequencing protocol with conservative theoretical error rates of 0.0009%. This rate is lower than that for Sanger sequencing. Here, we simulate the sequencing reactions by the self-developed software, and find that this approach has great potential in NGS in terms of sequence decoding, reassembly, error correction, and sequencing accuracy. Besides, this approach can be compatible with most SBS-based sequencing platforms, and also has the ability to compensate for some of the shortcomings of NGS platforms, thereby broadening its application for researchers. Hopefully, it can provide a powerful new protocol that can be used as an alternative to the existing NGS platforms, enabling accurate identification of rare mutations in a variety of applications in biology and medicine.
Collapse
Affiliation(s)
- Chu Cheng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Pengfeng Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| |
Collapse
|
8
|
Bollu A, Sharma NK. Biased photo cleavage of N-/N-nitrobenzyl from 2’-hydroxyethyl-adenosine and their DNA/RNA Caged-analogues. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.112864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
9
|
Takeshita L, Yamada Y, Masaki Y, Seio K. Synthesis of Deoxypseudouridine 5'-Triphosphate Bearing the Photoremovable Protecting Group at the N1 Position Capable of Enzymatic Incorporation to DNA. J Org Chem 2020; 85:1861-1870. [PMID: 31910013 DOI: 10.1021/acs.joc.9b02194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymatic incorporation of deoxynucleoside 5'-triphosphate bearing the photocleavable protecting group is a useful method for the preparation of photocaged oligodeoxynucleotides. Here, we describe the synthesis of new photocaged deoxynucleoside triphosphates N1-(2-nitrobenzyl)-deoxypseudouridine triphosphate (dNBΨTP) and N1-(6-nitropiperonyloxymethyl)-deoxypseudouridine triphosphate (dNPOMΨTP). We successfully synthesized dNBΨTP and dNPOMΨTP and applied them to enzymatic synthesis of photocaged oligonucleotides. In addition, we also synthesized phosphoramidites of N1-(2-nitrobenzyl)- and N1-(6-nitropiperonyloxymethyl)-deoxypseudouridine to enable chemical synthesis of photocaged oligonucleotides incorporating them. The photocleavable 2-nitrobenzyl and 6-nitropiperonyloxymethyl in oligonucleotides were cleaved by irradiation at 365 nm for 30 and 10 s, respectively. We also studied the enzymatic incorporation of dNBΨTP and dNPOMΨTP using the Klenow fragment exo-. As a result, it was clarified that dNPOMΨTP could be incorporated to oligonucleotide 193 times more efficiently than dNBΨTP, as judged by Vmax/Km. We also performed the incorporation of at least eight dNPOMΨ residues in a 35-mer oligodeoxynucleotide. It has also been revealed that the oligodeoxynucleotides incorporating photocaged deoxypseudouridine were useful for photocontrol of DNA triplex formation.
Collapse
Affiliation(s)
- Leo Takeshita
- Department of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta-cho , Midori-ku, Yokohama 226-8501 , Japan
| | - Yuji Yamada
- Department of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta-cho , Midori-ku, Yokohama 226-8501 , Japan
| | - Yoshiaki Masaki
- Department of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta-cho , Midori-ku, Yokohama 226-8501 , Japan
| | - Kohji Seio
- Department of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta-cho , Midori-ku, Yokohama 226-8501 , Japan
| |
Collapse
|
10
|
Chen Z, Zhou W, Qiao S, Kang L, Duan H, Xie XS, Huang Y. Highly accurate fluorogenic DNA sequencing with information theory-based error correction. Nat Biotechnol 2017; 35:1170-1178. [PMID: 29106407 DOI: 10.1038/nbt.3982] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 08/30/2017] [Indexed: 11/09/2022]
Abstract
Eliminating errors in next-generation DNA sequencing has proved challenging. Here we present error-correction code (ECC) sequencing, a method to greatly improve sequencing accuracy by combining fluorogenic sequencing-by-synthesis (SBS) with an information theory-based error-correction algorithm. ECC embeds redundancy in sequencing reads by creating three orthogonal degenerate sequences, generated by alternate dual-base reactions. This is similar to encoding and decoding strategies that have proved effective in detecting and correcting errors in information communication and storage. We show that, when combined with a fluorogenic SBS chemistry with raw accuracy of 98.1%, ECC sequencing provides single-end, error-free sequences up to 200 bp. ECC approaches should enable accurate identification of extremely rare genomic variations in various applications in biology and medicine.
Collapse
Affiliation(s)
- Zitian Chen
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.,Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, China.,College of Engineering, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Wenxiong Zhou
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.,Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shuo Qiao
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.,Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Li Kang
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.,Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Haifeng Duan
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.,Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - X Sunney Xie
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.,Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.,Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, China.,College of Engineering, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| |
Collapse
|
11
|
Ohno K, Sugiyama D, Takeshita L, Kanamori T, Masaki Y, Sekine M, Seio K. Synthesis of photocaged 6-O-(2-nitrobenzyl)guanosine and 4-O-(2-nitrobenzyl) uridine triphosphates for photocontrol of the RNA transcription reaction. Bioorg Med Chem 2017; 25:6007-6015. [PMID: 28986114 DOI: 10.1016/j.bmc.2017.09.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/15/2017] [Accepted: 09/20/2017] [Indexed: 11/27/2022]
Abstract
6-O-(2-Nitrobenzyl)guanosine and 4-O-(2-nitrobenzyl)uridine triphosphates (NBGTP, NBUTP) were synthesized, and their biochemical and photophysical properties were evaluated. We synthesized NBUTP using the canonical triphosphate synthesis method and NBGTP from 2',3'-O-TBDMS guanosine via a triphosphate synthesis method by utilizing mild acidic desilylation conditions. Deprotection of the nitrobenzyl group in NBGTP and NBUTP proceeded within 60s by UV irradiation at 365nm. Experiments using NBGTP or NBUTP in T7-RNA transcription reactions showed that NBGTP could be useful for the photocontrol of transcription by UV irradiation.
Collapse
Affiliation(s)
- Kentaro Ohno
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Daiki Sugiyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Leo Takeshita
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Takashi Kanamori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Mitsuo Sekine
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| |
Collapse
|
12
|
Seio K, Ohno Y, Ohno K, Takeshita L, Kanamori T, Masaki Y, Sekine M. Photo-controlled binding of MutS to photo-caged DNA duplexes incorporating 4- O -(2-nitrobenzyl) or 4- O -[2-(2-nitrophenyl)propyl]thymidine. Bioorg Med Chem Lett 2016; 26:4861-4863. [DOI: 10.1016/j.bmcl.2016.07.075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 07/14/2016] [Accepted: 07/29/2016] [Indexed: 10/21/2022]
|
13
|
Mathews AS, Yang H, Montemagno C. Photo-cleavable nucleotides for primer free enzyme mediated DNA synthesis. Org Biomol Chem 2016; 14:8278-88. [PMID: 27527494 DOI: 10.1039/c6ob01371f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis, characterization and potential application of eight 3'-O modified 2'-deoxyribonucleoside triphosphates (dNTPs) are discussed. These nucleotide analogues are modified by capping the 3'-OH with a photolabile protecting group which can temporarily cease DNA strand growth and can smoothly reinitiate the growth by the photodecomposition of the protecting group and setting the 3'-OH of dNTPs free to propagate. The synthesis of 3'-O-(2-nitrobenzyl)-2'-deoxyribonucleoside triphosphates (NB-dNTPs) and 3'-O-(4,5-dimethoxy-2-nitrobenzyl)-2'-deoxyribonucleoside triphosphates (DMNB-dNTPs) is discussed in detail with structural confirmation using NMR. The UV-cleaving studies are monitored and quantified using LCMS and (1)H NMR spectral traces. The synthesised nucleotides are employed for terminating and reinitiating template-less DNA synthesis, using primer independent Terminal Deoxynucleotidyl Transferase (TdT) enzyme. The use of this photolabile nucleotide in one step stop-start DNA synthesis is a novel strategy towards the precise assembly of dNTPs with the potential to reinforce present technologies.
Collapse
Affiliation(s)
- Anu Stella Mathews
- Ingenuity Lab, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 3M9, Canada.
| | | | | |
Collapse
|
14
|
Gade CR, Dixit M, Sharma NK. Dideoxy nucleoside triphosphate (ddNTP) analogues: Synthesis and polymerase substrate activities of pyrrolidinyl nucleoside triphosphates (prNTPs). Bioorg Med Chem 2016; 24:4016-4022. [PMID: 27377861 DOI: 10.1016/j.bmc.2016.06.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 01/05/2023]
Abstract
The dideoxynucleoside triphosphates (ddNTPs) terminate the bio-polymerization of DNA and become essential chemical component of DNA sequencing technology which is now basic tool for molecular biology research. In this method the radiolabeled or fluorescent dye labeled ddNTP analogues are being used for DNA sequencing by detection of the terminated DNA fragment after single labeled ddNTP incorporation into DNA under PCR conditions. This report describes the syntheses of rationally designed novel amino-functionalized ddNTP analogue such as Pyrrolidine nucleoside triphosphates (prNTPs), and their polymerase activities with DNA polymerase by LC-MS and Gel-electrophoretic techniques. The Mass and PAGE analyses strongly support the incorporation of prNTPs into DNA oligonucleotide with Therminator DNA polymerase as like control substrate ddNTP. As resultant the DNA oligonucleotide are functionalized as amine group by prNTP incorporation with polymerase. Hence prNTPs provide opportunities to prepare demandable conjugated DNA with other biomolecules/dyes/fluorescence molecule without modifying nucleobase structure.
Collapse
Affiliation(s)
- Chandrasekhar Reddy Gade
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, Jatni 752050, Odisha, India
| | - Manjusha Dixit
- School of Biological Sciences, NISER, Bhubaneswar, Jatni 752050, Odisha, India
| | - Nagendra K Sharma
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, Jatni 752050, Odisha, India.
| |
Collapse
|
15
|
Chen Z, Duan H, Qiao S, Zhou W, Qiu H, Kang L, Xie XS, Huang Y. Fluorogenic sequencing using halogen-fluorescein-labeled nucleotides. Chembiochem 2015; 16:1153-7. [PMID: 25846104 DOI: 10.1002/cbic.201500117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 01/23/2023]
Abstract
Fluorogenic sequencing is a sequencing-by-synthesis technology that combines the advantages of pyrosequencing and fluorescence detection. With native duplex DNA as the major product, we employ polymerase to incorporate the complement- arily matched terminal phosphate-labeled fluorogenic nucleotides into the DNA template and release halogen-fluorescein as the reporter. This red-emitting fluorophore successfully avoids spectral overlap with the autofluorescence background of the flow chip. We fully characterized the enzymatic reaction kinetics of the new substrates, and performed a 35-base sequencing experiment with 60 reaction cycles. Our achievement expands the substrate repertoire for fluorogenic sequencing, and extends the spectral range to obtain better signal-to-background performance.
Collapse
Affiliation(s)
- Zitian Chen
- College of Engineering, Peking University, Beijing 100871 (China) http://www.gene.pku.edu.cn.,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China)
| | - Haifeng Duan
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China).
| | - Shuo Qiao
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China)
| | - Wenxiong Zhou
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China)
| | - Haiwei Qiu
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China)
| | - Li Kang
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China)
| | - X Sunney Xie
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China).,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138 (USA)
| | - Yanyi Huang
- College of Engineering, Peking University, Beijing 100871 (China) http://www.gene.pku.edu.cn. .,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China).
| |
Collapse
|
16
|
Borland KM, AbdulSalam SF, Solivio MJ, Burke MP, Wolfkiel PR, Lawson SM, Stockman CA, Andersen JM, Smith S, Tolstolutskaya JN, Gurjar PN, Bercz AP, Merino EJ, Litosh VA. Base-modified thymidines capable of terminating DNA synthesis are novel bioactive compounds with activity in cancer cells. Bioorg Med Chem 2015; 23:1869-81. [PMID: 25778768 DOI: 10.1016/j.bmc.2015.01.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 01/22/2015] [Accepted: 01/30/2015] [Indexed: 10/24/2022]
Abstract
Current FDA-approved chemotherapeutic antimetabolites elicit severe side effects that warrant their improvement; therefore, we designed compounds with mechanisms of action focusing on inhibiting DNA replication rather than targeting multiple pathways. We previously discovered that 5-(α-substituted-2-nitrobenzyloxy)methyluridine-5'-triphosphates were exquisite DNA synthesis terminators; therefore, we synthesized a library of 35 thymidine analogs and evaluated their activity using an MTT cell viability assay of MCF7 breast cancer cells chosen for their vulnerability to these nucleoside derivatives. Compound 3a, having an α-tert-butyl-2-nitro-4-(phenyl)alkynylbenzyloxy group, showed an IC50 of 9±1μM. The compound is more selective for cancer cells than for fibroblast cells compared with 5-fluorouracil. Treatment of MCF7 cells with 3a elicits the DNA damage response as indicated by phosphorylation of γ-H2A. A primer extension assay of the 5'-triphosphate of 3a revealed that 3aTP is more likely to inhibit DNA polymerase than to lead to termination events upon incorporation into the DNA replication fork.
Collapse
Affiliation(s)
- Kayla M Borland
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Safnas F AbdulSalam
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Morwena J Solivio
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Matthew P Burke
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Patrick R Wolfkiel
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Sean M Lawson
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Courtney A Stockman
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Joel M Andersen
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Skyler Smith
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Julia N Tolstolutskaya
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Purujit N Gurjar
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Aron P Bercz
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Edward J Merino
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Vladislav A Litosh
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA.
| |
Collapse
|
17
|
Laos R, Thomson JM, Benner SA. DNA polymerases engineered by directed evolution to incorporate non-standard nucleotides. Front Microbiol 2014; 5:565. [PMID: 25400626 PMCID: PMC4215692 DOI: 10.3389/fmicb.2014.00565] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/07/2014] [Indexed: 11/13/2022] Open
Abstract
DNA polymerases have evolved for billions of years to accept natural nucleoside triphosphate substrates with high fidelity and to exclude closely related structures, such as the analogous ribonucleoside triphosphates. However, polymerases that can accept unnatural nucleoside triphosphates are desired for many applications in biotechnology. The focus of this review is on non-standard nucleotides that expand the genetic "alphabet." This review focuses on experiments that, by directed evolution, have created variants of DNA polymerases that are better able to accept unnatural nucleotides. In many cases, an analysis of past evolution of these polymerases (as inferred by examining multiple sequence alignments) can help explain some of the mutations delivered by directed evolution.
Collapse
Affiliation(s)
- Roberto Laos
- Foundation for Applied Molecular Evolution Gainesville, FL, USA
| | | | - Steven A Benner
- Foundation for Applied Molecular Evolution Gainesville, FL, USA
| |
Collapse
|
18
|
Wu L, Pei F, Zhang J, Wu J, Feng M, Wang Y, Jin H, Zhang L, Tang X. Synthesis of Site-Specifically Phosphate-Caged siRNAs and Evaluation of Their RNAi Activity and Stability. Chemistry 2014; 20:12114-22. [DOI: 10.1002/chem.201403430] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Indexed: 01/17/2023]
|
19
|
Wu J, Wang J, Tang X. Synthesis of photolabile dUTP analogues and their enzymatic incorporation for DNA labeling. Sci China Chem 2013. [DOI: 10.1007/s11426-013-5034-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
20
|
Kim DR, Kim TS, Kim E, Min SJ, Shin D, Ahn DR. Synthesis of 3'-O-fluorescently mono-modified reversible terminators and their uses in sequencing-by-synthesis. Bioorg Med Chem Lett 2013; 24:209-13. [PMID: 24332495 DOI: 10.1016/j.bmcl.2013.11.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 11/13/2013] [Accepted: 11/15/2013] [Indexed: 11/18/2022]
Abstract
Next-generation sequencing (NGS) technologies recently developed are now used for study of genomes from various organisms. Sequencing-by-synthesis (SBS) is a key strategy in the NGS. The SBS uses nucleotides so-called dual-modified reversible terminators (DRTs) in which bases are labeled with fluorophores and 3'-OH is protected with a reversibly cleavable chemical group, respectively. In this study, we examined the possibility of performing SBS with mono-modified reversible terminators (MRTs), in which the reversible blocking group on the 3'-OH plays a dual role as a fluorescent signal report as well as a chemical protection. We studied cyclic reversible termination by using two MRTs (dA and dT), wherein the modifications were two different fluorophores and cleavable to regenerate a free 3'-OH. We here demonstrated that SBS could be achieved with incorporation of MRTs by a DNA polymerase and correct base-calls based on the two different colors from the fluorophores.
Collapse
Affiliation(s)
- Da-Rae Kim
- Center for Theragnosis, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Taek-Soo Kim
- College of Pharmacy, Gachon University, 191 Hambakmoero, Yoensu-Gu, Incheon, Republic of Korea
| | - Eunsun Kim
- Center for Neuro-medicine, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Sun-Joon Min
- Center for Neuro-medicine, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea; Department of Biological Chemistry, University of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Dongyun Shin
- College of Pharmacy, Gachon University, 191 Hambakmoero, Yoensu-Gu, Incheon, Republic of Korea.
| | - Dae-Ro Ahn
- Center for Theragnosis, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea; Department of Biological Chemistry, University of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea.
| |
Collapse
|
21
|
Tang X, Zhang J, Sun J, Wang Y, Wu J, Zhang L. Caged nucleotides/nucleosides and their photochemical biology. Org Biomol Chem 2013; 11:7814-24. [PMID: 24132515 DOI: 10.1039/c3ob41735b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleotides and nucleosides are not only key units of DNA/RNA that store genetic information, but are also the regulators of many biological events of our lives. By caging the key functional groups or key residues of nucleotides with photosensitive moieties, it will be possible to trigger biological events of target nucleotides with spatiotemporal resolution and amplitude upon light activation or photomodulate polymerase reactions with the caged nucleotide analogues for next-generation sequencing (NGS) and bioorthogonal labeling. This review highlights three different caging strategies for nucleotides and demonstrates the photochemical biology of these caged nucleotides.
Collapse
Affiliation(s)
- Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Rd., Beijing 100191, China.
| | | | | | | | | | | |
Collapse
|
22
|
Chen F, Dong M, Ge M, Zhu L, Ren L, Liu G, Mu R. The history and advances of reversible terminators used in new generations of sequencing technology. GENOMICS PROTEOMICS & BIOINFORMATICS 2013; 11:34-40. [PMID: 23414612 PMCID: PMC4357665 DOI: 10.1016/j.gpb.2013.01.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 01/06/2013] [Accepted: 01/10/2013] [Indexed: 02/06/2023]
Abstract
DNA sequencing using reversible terminators, as one sequencing by synthesis strategy, has garnered a great deal of interest due to its popular application in the second-generation high-throughput DNA sequencing technology. In this review, we provided its history of development, classification, and working mechanism of this technology. We also outlined the screening strategies for DNA polymerases to accommodate the reversible terminators as substrates during polymerization; particularly, we introduced the "REAP" method developed by us. At the end of this review, we discussed current limitations of this approach and provided potential solutions to extend its application.
Collapse
Affiliation(s)
- Fei Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | | | | | | | | | | | | |
Collapse
|
23
|
Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Light-controlled tools. Angew Chem Int Ed Engl 2012; 51:8446-76. [PMID: 22829531 DOI: 10.1002/anie.201202134] [Citation(s) in RCA: 738] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Indexed: 12/21/2022]
Abstract
Spatial and temporal control over chemical and biological processes plays a key role in life, where the whole is often much more than the sum of its parts. Quite trivially, the molecules of a cell do not form a living system if they are only arranged in a random fashion. If we want to understand these relationships and especially the problems arising from malfunction, tools are necessary that allow us to design sophisticated experiments that address these questions. Highly valuable in this respect are external triggers that enable us to precisely determine where, when, and to what extent a process is started or stopped. Light is an ideal external trigger: It is highly selective and if applied correctly also harmless. It can be generated and manipulated with well-established techniques, and many ways exist to apply light to living systems--from cells to higher organisms. This Review will focus on developments over the last six years and includes discussions on the underlying technologies as well as their applications.
Collapse
Affiliation(s)
- Clara Brieke
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, 60438 Frankfurt/Main, Germany
| | | | | | | | | |
Collapse
|
24
|
Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Lichtgesteuerte Werkzeuge. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202134] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Clara Brieke
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
| | - Falk Rohrbach
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Gottschalk
- Buchmann‐Institut für Molekulare Lebenswissenschaften, Institut für Biochemie, Max‐von‐Laue‐Straße 15, 60438 Frankfurt/Main (Deutschland)
| | - Günter Mayer
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Heckel
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
| |
Collapse
|
25
|
Gardner AF, Wang J, Wu W, Karouby J, Li H, Stupi BP, Jack WE, Hersh MN, Metzker ML. Rapid incorporation kinetics and improved fidelity of a novel class of 3'-OH unblocked reversible terminators. Nucleic Acids Res 2012; 40:7404-15. [PMID: 22570423 PMCID: PMC3424534 DOI: 10.1093/nar/gks330] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Recent developments of unique nucleotide probes have expanded our understanding of DNA polymerase function, providing many benefits to techniques involving next-generation sequencing (NGS) technologies. The cyclic reversible termination (CRT) method depends on efficient base-selective incorporation of reversible terminators by DNA polymerases. Most terminators are designed with 3′-O-blocking groups but are incorporated with low efficiency and fidelity. We have developed a novel class of 3′-OH unblocked nucleotides, called Lightning Terminators™, which have a terminating 2-nitrobenzyl moiety attached to hydroxymethylated nucleobases. A key structural feature of this photocleavable group displays a ‘molecular tuning’ effect with respect to single-base termination and improved nucleotide fidelity. Using Therminator™ DNA polymerase, we demonstrate that these 3′-OH unblocked terminators exhibit superior enzymatic performance compared to two other reversible terminators, 3′-O-amino-TTP and 3′-O-azidomethyl-TTP. Lightning Terminators™ show maximum incorporation rates (kpol) that range from 35 to 45 nt/s, comparable to the fastest NGS chemistries, yet with catalytic efficiencies (kpol/KD) comparable to natural nucleotides. Pre-steady-state kinetic studies of thymidine analogs revealed that the major determinant for improved nucleotide selectivity is a significant reduction in kpol by >1000-fold over TTP misincorporation. These studies highlight the importance of structure–function relationships of modified nucleotides in dictating polymerase performance.
Collapse
|
26
|
Hutter D, Kim MJ, Karalkar N, Leal NA, Chen F, Guggenheim E, Visalakshi V, Olejnik J, Gordon S, Benner SA. Labeled nucleoside triphosphates with reversibly terminating aminoalkoxyl groups. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 29:879-95. [PMID: 21128174 DOI: 10.1080/15257770.2010.536191] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Nucleoside triphosphates having a 3'-ONH₂ blocking group have been prepared with and without fluorescent tags on their nucleobases. DNA polymerases were identified that accepted these, adding a single nucleotide to the 3'-end of a primer in a template-directed extension reaction that then stops. Nitrite chemistry was developed to cleave the 3'-ONH₂ group under mild conditions to allow continued primer extension. Extension-cleavage-extension cycles in solution were demonstrated with untagged nucleotides and mixtures of tagged and untagged nucleotides. Multiple extension-cleavage-extension cycles were demonstrated on an Intelligent Bio-Systems Sequencer, showing the potential of the 3'-ONH₂ blocking group in "next generation sequencing."
Collapse
Affiliation(s)
- Daniel Hutter
- Foundation for Applied Molecular Evolution, Gainesville, FL 32604, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Priebbenow DL, Pfeffer FM, Stewart SG. A One-Pot, Three-Component Approach to Functionalised Tetrahydroisoquinolines Using Domino Heck-aza-Michael Reactions. European J Org Chem 2011. [DOI: 10.1002/ejoc.201001621] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
28
|
Litosh VA, Wu W, Stupi BP, Wang J, Morris SE, Hersh MN, Metzker ML. Improved nucleotide selectivity and termination of 3'-OH unblocked reversible terminators by molecular tuning of 2-nitrobenzyl alkylated HOMedU triphosphates. Nucleic Acids Res 2011; 39:e39. [PMID: 21227920 PMCID: PMC3064798 DOI: 10.1093/nar/gkq1293] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We describe a novel 3′-OH unblocked reversible terminator with the potential to improve accuracy and read-lengths in next-generation sequencing (NGS) technologies. This terminator is based on 5-hydroxymethyl-2′-deoxyuridine triphosphate (HOMedUTP), a hypermodified nucleotide found naturally in the genomes of numerous bacteriophages and lower eukaryotes. A series of 5-(2-nitrobenzyloxy)methyl-dUTP analogs (dU.I–dU.V) were synthesized based on our previous work with photochemically cleavable terminators. These 2-nitrobenzyl alkylated HOMedUTP analogs were characterized with respect to incorporation, single-base termination, nucleotide selectivity and photochemical cleavage properties. Substitution at the α-methylene carbon of 2-nitrobenzyl with alkyl groups of increasing size was discovered as a key structural feature that provided for the molecular tuning of enzymatic properties such as single-base termination and improved nucleotide selectivity over that of natural nucleotides. 5-[(S)-α-tert-Butyl-2-nitrobenzyloxy]methyl-dUTP (dU.V) was identified as an efficient reversible terminator, whereby, sequencing feasibility was demonstrated in a cyclic reversible termination (CRT) experiment using a homopolymer repeat of ten complementary template bases without detectable UV damage during photochemical cleavage steps. These results validate our overall strategy of creating 3′-OH unblocked reversible terminator reagents that, upon photochemical cleavage, transform back into a natural state. Modified nucleotides based on 5-hydroxymethyl-pyrimidines and 7-deaza-7-hydroxymethyl-purines lay the foundation for development of a complete set of four reversible terminators for application in NGS technologies.
Collapse
|
29
|
Kim TS, Kim DR, Ahn HC, Shin D, Ahn DR. Novel 3'-O-fluorescently modified nucleotides for reversible termination of DNA synthesis. Chembiochem 2010; 11:75-8. [PMID: 19904795 DOI: 10.1002/cbic.200900632] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Taek-Soo Kim
- Life Sciences Research Division, Korea Institute of Science and Technology, Cheongryang, Seoul, Korea
| | | | | | | | | |
Collapse
|
30
|
Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection. Proc Natl Acad Sci U S A 2010; 107:1948-53. [PMID: 20080675 DOI: 10.1073/pnas.0908463107] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Any system, natural or human-made, is better understood if we analyze both its history and its structure. Here we combine structural analyses with a "Reconstructed Evolutionary Adaptive Path" (REAP) analysis that used the evolutionary and functional history of DNA polymerases to replace amino acids to enable polymerases to accept a new class of triphosphate substrates, those having their 3'-OH ends blocked as a 3(')-ONH(2) group (dNTP-ONH(2)). Analogous to widely used 2',3'-dideoxynucleoside triphosphates (ddNTPs), dNTP-ONH(2)s terminate primer extension. Unlike ddNTPs, however, primer extension can be resumed by cleaving an O-N bond to restore an -OH group to the 3'-end of the primer. REAP combined with crystallographic analyses identified 35 sites where replacements might improve the ability of Taq to accept dNTP-ONH(2)s. A library of 93 Taq variants, each having replacements at three or four of these sites, held eight variants having improved ability to accept dNTP-ONH(2) substrates. Two of these (A597T, L616A, F667Y, E745H, and E520G, K540I, L616A) performed notably well. The second variant incorporated both dNTP-ONH(2)sand ddNTPs faithfully and efficiently, supporting extension-cleavage-extension cycles applicable in parallel sequencing and in SNP detection through competition between reversible and irreversible terminators. Dissecting these results showed that one replacement (L616A), not previously identified, allows Taq to incorporate both reversible and irreversible terminators. Modeling showed how L616A might open space behind Phe-667, allowing it to move to accommodate the larger 3'-substituent. This work provides polymerases for DNA analyses and shows how evolutionary analyses help explore relationships between structure and function in proteins.
Collapse
|
31
|
|
32
|
Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, Jovanovich SB, Nelson JR, Schloss JA, Schwartz DC, Vezenov DV. The challenges of sequencing by synthesis. Nat Biotechnol 2009; 27:1013-23. [PMID: 19898456 DOI: 10.1038/nbt.1585] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA sequencing-by-synthesis (SBS) technology, using a polymerase or ligase enzyme as its core biochemistry, has already been incorporated in several second-generation DNA sequencing systems with significant performance. Notwithstanding the substantial success of these SBS platforms, challenges continue to limit the ability to reduce the cost of sequencing a human genome to $100,000 or less. Achieving dramatically reduced cost with enhanced throughput and quality will require the seamless integration of scientific and technological effort across disciplines within biochemistry, chemistry, physics and engineering. The challenges include sample preparation, surface chemistry, fluorescent labels, optimizing the enzyme-substrate system, optics, instrumentation, understanding tradeoffs of throughput versus accuracy, and read-length/phasing limitations. By framing these challenges in a manner accessible to a broad community of scientists and engineers, we hope to solicit input from the broader research community on means of accelerating the advancement of genome sequencing technology.
Collapse
Affiliation(s)
- Carl W Fuller
- GE Healthcare Life Sciences, Piscataway, New Jersey, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Virtual terminator nucleotides for next-generation DNA sequencing. Nat Methods 2009; 6:593-5. [PMID: 19620973 PMCID: PMC2719685 DOI: 10.1038/nmeth.1354] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 06/22/2009] [Indexed: 11/14/2022]
Abstract
We synthesized reversible terminators with tethered inhibitors for next generation sequencing. These were efficiently incorporated with high fidelity while preventing incorporation of additional nucleotides and were used to sequence canine bacterial artificial chromosomes in a single-molecule system that provided even coverage for over 99% of the region sequenced. This single-molecule approach generated high quality sequence data without the need for target amplification and thus avoided concomitant biases.
Collapse
|
34
|
Berthet N, Crey-Desbiolles C, Kotera M, Dumy P. Chemical synthesis, DNA incorporation and biological study of a new photocleavable 2'-deoxyadenosine mimic. Nucleic Acids Res 2009; 37:5237-45. [PMID: 19586934 PMCID: PMC2760783 DOI: 10.1093/nar/gkp562] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The phototriggered cleavage of chemical bonds has found numerous applications in biology, particularly in the field of gene sequencing through photoinduced DNA strand scission. However, only a small number of modified nucleosides that are able to cleave DNA at selected positions have been reported in the literature. Herein, we show that a new photoactivable deoxyadenosine analogue, 3-nitro-3-deaza-2'-deoxyadenosine (d(3-NiA)), was able to induce DNA backbone breakage upon irradiation (lambda > 320 nm). The d(3-NiA) nucleoside was chemically incorporated at desired positions into 40-mer oligonucleotides as a phosphoramidite monomer and subsequent hybridization studies confirmed that the resulting modified duplexes display a behaviour that is close to that of the related natural sequence. Enzymatic action of the Klenow fragment exonuclease free revealed the preferential incorporation of dAMP opposite the 3-NiA base. On the other hand, incorporation of the analogous 3-NiA triphosphate to a primer revealed high enzyme efficiency and selectivity for insertion opposite thymine. Furthermore, only the enzymatically synthesized base pair 3-NiA:T was a substrate for further extension by the enzyme. All the hybridization and enzymatic data indicate that this new photoactivable 3-NiA triphosphate can be considered as a photochemically cleavable dATP analogue.
Collapse
Affiliation(s)
- Nathalie Berthet
- Département de Chimie Moléculaire-Equipe Ingénierie et Interactions BioMoléculaires, UMR-5250, ICMG FR-2607, CNRS, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9, France.
| | | | | | | |
Collapse
|
35
|
Four-color DNA sequencing with 3'-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides. Proc Natl Acad Sci U S A 2008; 105:9145-50. [PMID: 18591653 DOI: 10.1073/pnas.0804023105] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA sequencing by synthesis (SBS) on a solid surface during polymerase reaction can decipher many sequences in parallel. We report here a DNA sequencing method that is a hybrid between the Sanger dideoxynucleotide terminating reaction and SBS. In this approach, four nucleotides, modified as reversible terminators by capping the 3'-OH with a small reversible moiety so that they are still recognized by DNA polymerase as substrates, are combined with four cleavable fluorescent dideoxynucleotides to perform SBS. The ratio of the two sets of nucleotides is adjusted as the extension cycles proceed. Sequences are determined by the unique fluorescence emission of each fluorophore on the DNA products terminated by ddNTPs. On removing the 3'-OH capping group from the DNA products generated by incorporating the 3'-O-modified dNTPs and the fluorophore from the DNA products terminated with the ddNTPs, the polymerase reaction reinitiates to continue the sequence determination. By using an azidomethyl group as a chemically reversible capping moiety in the 3'-O-modified dNTPs, and an azido-based cleavable linker to attach the fluorophores to the ddNTPs, we synthesized four 3'-O-azidomethyl-dNTPs and four ddNTP-azidolinker-fluorophores for the hybrid SBS. After sequence determination by fluorescence imaging, the 3'-O-azidomethyl group and the fluorophore attached to the DNA extension product via the azidolinker are efficiently removed by using Tris(2-carboxyethyl)phosphine in aqueous solution that is compatible with DNA. Various DNA templates, including those with homopolymer regions, were accurately sequenced with a read length of >30 bases by using this hybrid SBS method on a chip and a four-color fluorescence scanner.
Collapse
|