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Yudkina AV, Kim DV, Zharkov TD, Zharkov DO, Endutkin AV. Probing the Conformational Restraints of DNA Damage Recognition with β-L-Nucleotides. Int J Mol Sci 2024; 25:6006. [PMID: 38892193 PMCID: PMC11172447 DOI: 10.3390/ijms25116006] [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: 04/25/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
The DNA building blocks 2'-deoxynucleotides are enantiomeric, with their natural β-D-configuration dictated by the sugar moiety. Their synthetic β-L-enantiomers (βLdNs) can be used to obtain L-DNA, which, when fully substituted, is resistant to nucleases and is finding use in many biosensing and nanotechnology applications. However, much less is known about the enzymatic recognition and processing of individual βLdNs embedded in D-DNA. Here, we address the template properties of βLdNs for several DNA polymerases and the ability of base excision repair enzymes to remove these modifications from DNA. The Klenow fragment was fully blocked by βLdNs, whereas DNA polymerase κ bypassed them in an error-free manner. Phage RB69 DNA polymerase and DNA polymerase β treated βLdNs as non-instructive but the latter enzyme shifted towards error-free incorporation on a gapped DNA substrate. DNA glycosylases and AP endonucleases did not process βLdNs. DNA glycosylases sensitive to the base opposite their cognate lesions also did not recognize βLdNs as a correct pairing partner. Nevertheless, when placed in a reporter plasmid, pyrimidine βLdNs were resistant to repair in human cells, whereas purine βLdNs appear to be partly repaired. Overall, βLdNs are unique modifications that are mostly non-instructive but have dual non-instructive/instructive properties in special cases.
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Affiliation(s)
- Anna V. Yudkina
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Daria V. Kim
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
| | - Timofey D. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Anton V. Endutkin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.V.Y.); (D.V.K.); (T.D.Z.)
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Anwar A, Sun P, Rong X, Arkin A, Elham A, Yalkun Z, Li X, Iminjan M. Process analytical technology as in-process control tool in semi-continuous manufacturing of PLGA/PEG-PLGA microspheres. Heliyon 2023; 9:e15753. [PMID: 37153380 PMCID: PMC10160502 DOI: 10.1016/j.heliyon.2023.e15753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/09/2023] Open
Abstract
Nowadays, among 3rd generation drug delivery systems, biodegradable polymeric based long-acting injectable depot has achieved tremendous success in clinical application. So far, there have been two dozen of commercial products of Poly (lactic-co-glycolic acid) microspheres available in the market. Recently, continuous manufacturing concept has been successfully applied on oral solid formulation from buzzword to reality. However, the polymeric injectable microspheres are still stayed at batch manufacturing phase due to the lack of understanding of knowledge matrix. In this study, micro-mixer as a plug-and-play emulsification modules, Raman spectroscopy and focused beam reflectance measurement as real-time monitoring modules are integrated into a novel semi-continuous manufacturing streamline to provides more efficient upscaling flexibility in microspheres production. In this end to end semi-continuous manufacturing process, amphiphilic block polymer monomethoxy-poly (ethylene glycol) modified PLGA (mPEG-PLGA) was used for encapsulating Gallic acid. Additionally, with guarantee of good robustness, the correlation relationship between critical process parameters, critical material attributes and critical quality attributes were investigated. The time-space evolution process and mechanism for formation of PEG-PLGA microsphere with particular morphology were elaborated. Altogether, this study firstly established semi-continuous manufacturing streamline for PLGA/PEG-PLGA microspheres, which would not only lower the cost of production, narrow process variability and smaller equipment/environmental footprint but also applied in-process control (IPC) and QbD principle on complicated production process of microspheres. Therefore, this study build confidence in the industrial development of PLGA/PEG-PLGA microspheres and establish best practice standards, which might be a quantum leap for developing PLGA microspheres in the future.
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Affiliation(s)
- Arfidin Anwar
- Department of Pharmaceutics and Physical Chemistry, College of Pharmacy, Xinjiang Medical University, Urumqi, 830017, China
| | - Pengfei Sun
- University of Wisconsin-Madison, Department of Educational Psychology, Madison, USA
| | - Xiaoxu Rong
- University of Wisconsin-Madison, Department of Educational Psychology, Madison, USA
| | - Abdulaziz Arkin
- Department of Pharmaceutics and Physical Chemistry, College of Pharmacy, Xinjiang Medical University, Urumqi, 830017, China
| | - Aliya Elham
- Department of Pharmaceutics and Physical Chemistry, College of Pharmacy, Xinjiang Medical University, Urumqi, 830017, China
| | - Zilala Yalkun
- College of Pharmacy, Dalian Medical University, Dalian, 116000, China
| | - Xun Li
- Chinese Academy of Science, Department of Chemical Engineering, Beijing, 100190, China
- Corresponding author.
| | - Mubarak Iminjan
- Department of Pharmaceutics and Physical Chemistry, College of Pharmacy, Xinjiang Medical University, Urumqi, 830017, China
- Corresponding author.
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Kan Y, Jin Z, Ke Y, Lin D, Yan L, Wu L, He Y. Replicative bypass studies of l-deoxyribonucleosides in Vitro and in E. coli cell. Sci Rep 2022; 12:21183. [PMID: 36476762 PMCID: PMC9729220 DOI: 10.1038/s41598-022-24802-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
L-nucleosides were the most important antiviral lead compounds because they can inhibit viral DNA polymerase and DNA synthesis of many viruses, whereas they may lead to mutations in DNA replication and cause genomic instability. In this study, we reported the replicative bypass of L-deoxynucleosides in recombinant DNA by restriction enzyme-mediated assays to examine their impact on DNA replication in vitro and in E. coli cells. The results showed that a template L-dC inhibited Taq DNA polymerase reaction, whereas it can be bypassed by Vent (exo-) DNA polymerase as well as in cell replication, inserting correct nucleotides opposite L-dC. L-dG can be bypassed by Taq DNA polymerase and in E. coli cells, maintaining insertion of correct incoming nucleotides, and L-dG induced mutagenic replication by Vent (exo-) DNA polymerase. In contrast, L-dA can induced mutagenic replication in vitro and in E. coli cells. MD simulations were performed to investigate how DNA polymerase affected replicative bypass and mutations when D-nucleosides replaced with L-nucleosides. This study will provide a basis for the ability to assess the cytotoxic and mutagenic properties of the L-nucleoside drugs.
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Affiliation(s)
- Yuhe Kan
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China ,grid.411643.50000 0004 1761 0411School of Life Sciences, Inner Mongolia University, Hohhot, 010021 Inner Mongolia People’s Republic of China ,Qilu Pharmaceutical (Inner Mongolia) CO., LTD., Hohhot, 010080 Inner Mongolia People’s Republic of China
| | - Zhaoyang Jin
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yongqi Ke
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Dao Lin
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Liang Yan
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Li Wu
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China ,grid.11135.370000 0001 2256 9319State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191 People’s Republic of China
| | - Yujian He
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China ,grid.11135.370000 0001 2256 9319State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191 People’s Republic of China ,grid.410726.60000 0004 1797 8419School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
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Wu Y, Bu X, Ke Y, Sun H, Li J, Chen L, Cui W, He Y, Wu L. Insight into the Stereocontrol of DNA Polymerase‐Catalysed Reaction by Chiral Cobalt Complexes. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ya Wu
- College of Chemistry and Chemical Engineering Xi'an Shiyou University Xi'an 710065 People's Republic of China
| | - Xinya Bu
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Yongqi Ke
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Huaming Sun
- School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710065 People's Republic of China
| | - Jingyao Li
- College of Chemistry and Chemical Engineering Xi'an Shiyou University Xi'an 710065 People's Republic of China
| | - Lu Chen
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Wei Cui
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Yujian He
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Li Wu
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Beijing 100191 People's Republic of China
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Liu Q, Ke Y, Kan Y, Tang X, Li X, He Y, Wu L. Compatibility and Fidelity of Mirror-Image Thymidine in Transcription Events by T7 RNA Polymerase. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:604-613. [PMID: 32721880 PMCID: PMC7390857 DOI: 10.1016/j.omtn.2020.06.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/15/2020] [Accepted: 06/23/2020] [Indexed: 11/16/2022]
Abstract
Due to highly enzymatic d-stereoselectivity, l-nucleotides (l-2'-deoxynucleoside 5'-triphosphates [l-dNTPs]) are not natural targets of polymerases. In this study, we synthesized series of l-thymidine (l-T)-modified DNA strands and evaluated the processivity of nucleotide incorporation for transcription by T7 RNA polymerase (RNAP) with an l-T-containing template. When single l-T was introduced into the transcribed region, transcription proceeded to afford the full-length transcript with different efficiencies. However, introduction of l-T into the non-transcribed region did not exhibit a noticeable change in the transcription efficiency. Surprisingly, when two consecutive or internal l-Ts were introduced into the transcribed region, no transcripts were detected. Compared to natural template, significant lags in NTP incorporation into the template T+4/N and T+7/N (where the number corresponds to the site of l-T position, and + means downstream of the transcribed region) were detected by kinetic analysis. Furthermore, affinity of template T+4/N was almost the same with T/N, whereas affinity of T+7/N was apparently increased. Furthermore, no mismatch opposite to l-T in the template was detected in transcription reactions via gel fidelity analysis. These results demonstrate the effects of chiral l-T in DNA on the efficiency and fidelity of RNA transcription mediated by T7 RNAP, which provides important knowledge about how mirror-image thymidine perturbs the flow of genetic information during RNA transcription and development of diseases caused by gene mutation.
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Affiliation(s)
- Qingju Liu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongqi Ke
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhe Kan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiangjun Li
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
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Kan Y, Chen L, Lin D, Bu X, Mo M, Yan L, Yang Z, Yuan L, Wu L, He Y. Replication of DNA Containing Mirror-Image Thymidine in E. coli Cells. Chem Res Toxicol 2020; 33:2276-2285. [PMID: 32812424 DOI: 10.1021/acs.chemrestox.9b00502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
DNA damage can occur naturally or through environmental factors, leading to mutations in DNA replication and genomic instability in cells. Normally, natural d-nucleotides were selected by DNA polymerases. The template l-thymidine (l-T) has been shown to be bypassed by several types of DNA polymerases. However, DNA replication fidelity of nucleotide incorporation opposite l-thymidine in vivo remains unknown. Here, we constructed plasmids containing a restriction enzyme (PstI) recognition site in which the l-T lesion was site-specifically located within the PstI recognition sequence (CTGCAG). Further, we assessed the efficiencies of nucleotide incorporation opposite the l-T site and l-T lesion bypass replication in vitro and in vivo. We found that recombinants containing the l-T lesion site inhibited DNA replication. In addition, A was incorporated opposite the l-T lesion by routine PCR assay, whereas preference for nucleotide incorporation opposite the l-T site was A (13%), T (22%), C (46%), and G (19%), and no nucleotide insertion and deletions were detected in E. coli cells. In particular, a novel restriction enzyme-mediated method for detection of the mutagenic properties of DNA lesion was established, which allows us to readily detect restriction-digestion of the l-T-bearing plasmids. The study provided significant insight into how mirror-image nucleosides perturb the fidelity of DNA replication in vivo and whether they elicit mutagenic effects, which may help to understand both how DNA damage interferes with the flow of genetic information during DNA replication and development of diseases caused by gene mutation.
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Affiliation(s)
- Yuhe Kan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Lu Chen
- School of Applied Chemistry, Shenyang University of Chemical Technology, Shenyang 110000, P. R. China
| | - Dao Lin
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xinya Bu
- School of Applied Chemistry, Shenyang University of Chemical Technology, Shenyang 110000, P. R. China
| | - Mengwu Mo
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Liang Yan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
| | - Longfei Yuan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China.,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
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Gardner AF, Jackson KM, Boyle MM, Buss JA, Potapov V, Gehring AM, Zatopek KM, Corrêa IR, Ong JL, Jack WE. Therminator DNA Polymerase: Modified Nucleotides and Unnatural Substrates. Front Mol Biosci 2019; 6:28. [PMID: 31069234 PMCID: PMC6491775 DOI: 10.3389/fmolb.2019.00028] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/04/2019] [Indexed: 11/13/2022] Open
Abstract
A variant of 9°N DNA polymerase [Genbank ID (AAA88769.1)] with three mutations (D141A, E143A, A485L) and commercialized under the name "Therminator DNA polymerase" has the ability to incorporate a variety of modified nucleotide classes. This Review focuses on how Therminator DNA Polymerase has enabled new technologies in synthetic biology and DNA sequencing. In addition, we discuss mechanisms for increased modified nucleotide incorporation.
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Affiliation(s)
| | | | | | | | | | | | | | - Ivan R Corrêa
- New England Biolabs, Inc., Ipswich, MA, United States
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