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Nucleic Acid Chemical Biology: An Honorary Issue for Professor Li-He Zhang on the Occasion of His 85th Birthday

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (30 September 2022) | Viewed by 27643

Special Issue Editors

Prof. Dr. Xinjing Tang

E-Mail Website
Guest Editor
State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
Interests: nulceic acid drugs; gene silencing; gene editing; gene photoregulation; oligonucleotide modification
Special Issues, Collections and Topics in MDPI journals
Dr. Changmai Chen

E-Mail Website
Guest Editor
School of Pharmacy, Fujian Medical University, Fuzhou, China
Interests: chemical biology; nucleic acid drugs; self-assembled nanostructures; gene therapy; drug delivery system

Special Issue Information

Dear Colleagues,

In recent years, an increasing number of nucleic acid drugs have been used in clinical applications. Nucleic acids have been hot research targets for both chemists and biologists. Many types of functional oligonucleotides have been developed, including CRISPR gRNA, lncRNA, miRNA, aptamers, siRNA, antisense ODN, etc., and their precise modifications have also been achieved for both scientific research and pharmaceutical applications in vivo and in clinic. At the same time, we still face unsolved key problems for nucleic acid drugs, such as off-target effects, enzymatic stability and immunoreaction, etc.

Professor Li-He Zhang (born in 1937) is a key player in nucleic acid chemistry and chemical biology in China. He is a Professor at State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, and an Academician of the Chinese Academy of Sciences (1995). He graduated from the Department of Pharmacy in 1958 and obtained his graduate diploma on medicinal chemistry in 1967 from Beijing Medical College. He worked as a research associate from 1981 to 1983 in the Department of Chemistry, University of Virginia, USA. In 1985, he became professor of medicinal chemistry at the School of Pharmaceutical Sciences, Beijing Medical University, and was appointed as Dean of the School of Pharmaceutical Sciences, Beijing Medical University (1987–1999) and Director of the Chemistry Division of the National Natural Science Foundation of China (1999-2006). He is the Associate Editor of Eur. J. Med. Chem. and J. Chem. Chin. Univ.; Editor in Chief of J. Chin. Med. Chem., and he is also on the Editorial Boards of a number of scientific journals, including Med. Res. Rev., Curr. Top. Med. Chem., and Org. Biomol. Chem., ChemMedChem. His main research areas include chemistry and chemical biology of nucleosides, nucleotides, and oligonucleotides. He has conducted systematic studies on the chemical and biological activity of intracellular messenger cADPR and cAMP. He has also made outstanding contributions to the research areas of ribozyme cleavage mechanism, the nature and recognition of artificial oligonucleotides, and anticancer and antiviral drugs of nucleosides and nucleotides.

The journal is pleased to be publishing an honorary Special Issue in honor of Professor Li-He Zhang for his outstanding contributions on nucleosides, nucleotides, and oligonucleotides on the occasion of his 85th birthday in 2022. This Special Issue of Molecules welcomes the submission of unpublished manuscripts of original work or reviews on “Nucleosides, Nucleotides, and Oligonucleotides”.

Prof. Dr. Xinjing Tang
Dr. Changmai Chen
Guest Editors

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Related Special Issue

Published Papers (11 papers)

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Research

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14 pages, 3409 KiB  
Article
Reversible On-Off Photoswitching of DNA Replication Using a Dumbbell Oligodeoxynucleotide
by Yu Wang, Heming Ji, Jian Ma, Hang Luo, Yujian He, Xinjing Tang and Li Wu
Molecules 2022, 27(24), 8992; https://doi.org/10.3390/molecules27248992 - 16 Dec 2022
Cited by 2 | Viewed by 1755
Abstract
In most organisms, DNA extension is highly regulated; however, most studies have focused on controlling the initiation of replication, and few have been done to control the regulation of DNA extension. In this study, we adopted a new strategy for azODNs to regulate [...] Read more.
In most organisms, DNA extension is highly regulated; however, most studies have focused on controlling the initiation of replication, and few have been done to control the regulation of DNA extension. In this study, we adopted a new strategy for azODNs to regulate DNA extension, which is based on azobenzene oligonucleotide chimeras regulated by substrate binding affinity, and the conformation of the chimera can be regulated by a light source with a light wavelength of 365 nm. The results showed that the primer was extended with Taq DNA polymerase after visible light treatment, and DNA extension could be effectively hindered with UV light treatment. We also verify the reversibility of the photoregulation of primer extension through photoswitching of dumbbell asODNs by alternate irradiation with UV and visible light. Our method has the advantages of fast and simple, green response and reversible operations, providing a new strategy for regulating gene replication. Full article
(This article belongs to the Special Issue Nucleic Acid Chemical Biology: An Honorary Issue for Professor Li-He Zhang on the Occasion of His 85th Birthday)
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11 pages, 1736 KiB  
Article
Ultrasensitive Simultaneous Detection of Multiple Rare Modified Nucleosides as Promising Biomarkers in Low-Put Breast Cancer DNA Samples for Clinical Multi-Dimensional Diagnosis
by Yue Yu, Hui-Yu Pan, Xin Zheng, Fang Yuan, Ying-Lin Zhou and Xin-Xiang Zhang
Molecules 2022, 27(20), 7041; https://doi.org/10.3390/molecules27207041 - 19 Oct 2022
Cited by 5 | Viewed by 1564
Abstract
Early cancer diagnosis is essential for successful treatment and prognosis, and modified nucleosides have attracted widespread attention as a promising group of cancer biomarkers. However, analyzing these modified nucleosides with an extremely low abundance is a great challenge, especially analyzing multiple modified nucleosides [...] Read more.
Early cancer diagnosis is essential for successful treatment and prognosis, and modified nucleosides have attracted widespread attention as a promising group of cancer biomarkers. However, analyzing these modified nucleosides with an extremely low abundance is a great challenge, especially analyzing multiple modified nucleosides with a different abundance simultaneously. In this work, an ultrasensitive quantification method based on chemical labeling, coupled with LC-MS/MS analysis, was established for the simultaneous quantification of 5hmdC, 5fdC, 5hmdU and 5fdU. Additionally, the contents of 5mdC and canonical nucleosides could be obtained at the same time. Upon derivatization, the detection sensitivities of 5hmdC, 5fdC, 5hmdU and 5fdU were dramatically enhanced by several hundred times. The established method was further applied to the simultaneous detection of nine nucleosides with different abundances in about 2 μg genomic DNA of breast tissues from 20 breast cancer patients. The DNA consumption was less than other overall reported quantification methods, thereby providing an opportunity to monitor rare, modified nucleosides in precious samples and biology processes that could not be investigated before. The contents of 5hmdC, 5hmdU and 5fdU in tumor tissues and normal tissues adjacent to the tumor were significantly changed, indicating that these three modified nucleosides may play certain roles in the formation and development of tumors and be potential cancer biomarkers. While the detection rates of 5hmdC, 5hmdU and 5fdU alone as a biomarker for breast cancer samples were 95%, 75% and 85%, respectively, by detecting these three cancer biomarkers simultaneously, two of the three were 100% consistent with the overall trend. Therefore, simultaneous detection of multiple cancer biomarkers in clinical samples greatly improved the accuracy of cancer diagnosis, indicating that our method has great application potential in clinical multidimensional diagnosis. Full article
(This article belongs to the Special Issue Nucleic Acid Chemical Biology: An Honorary Issue for Professor Li-He Zhang on the Occasion of His 85th Birthday)
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12 pages, 2278 KiB  
Article
Multiple-Gene Regulation for Enhanced Antitumor Efficacy with Branch-PCR-Assembled TP53 and MYC Gene Nanovector
by Longhuai Cheng, Liqing Lu, Ziyi Chen, Dejun Ma and Zhen Xi
Molecules 2022, 27(20), 6943; https://doi.org/10.3390/molecules27206943 - 16 Oct 2022
Cited by 3 | Viewed by 2068
Abstract
Multiple proteins are involved in network regulation through the crosstalk of different signaling pathways in cancers. Here, we propose a novel strategy of genome therapy with branch-PCR-assembled gene nanovectors to perform network-based gene regulation at multiple levels for cancer therapy. To validate network-based [...] Read more.
Multiple proteins are involved in network regulation through the crosstalk of different signaling pathways in cancers. Here, we propose a novel strategy of genome therapy with branch-PCR-assembled gene nanovectors to perform network-based gene regulation at multiple levels for cancer therapy. To validate network-based multiplex-gene regulation for genome therapy, we chose to simultaneously target one tumor suppressor gene (TP53) and one oncogene (MYC) in two different signaling pathways. The results showed that, compared to gene nanovectors targeting single genes (NP-TP53 and NP-shMYC), branch-PCR-assembled gene nanovectors simultaneously expressing p53 proteins and MYC shRNA arrays (NP-TP53-shMYC) showed enhanced antitumor efficacy in both MDA-MB-231 cancer cells and an MDA-MB-231-tumor-bearing mouse model. These findings indicate the feasibility and effectiveness of genome therapy in cancer therapy. Full article
(This article belongs to the Special Issue Nucleic Acid Chemical Biology: An Honorary Issue for Professor Li-He Zhang on the Occasion of His 85th Birthday)
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16 pages, 7155 KiB  
Article
Development of a Highly Selective and Sensitive Fluorescent Probe for Imaging RNA Dynamics in Live Cells
by Lan Fang, Wen Shao, Shu-Tang Zeng, Gui-Xue Tang, Jia-Tong Yan, Shuo-Bin Chen, Zhi-Shu Huang, Jia-Heng Tan and Xiu-Cai Chen
Molecules 2022, 27(20), 6927; https://doi.org/10.3390/molecules27206927 - 15 Oct 2022
Cited by 5 | Viewed by 3063
Abstract
RNA imaging is of great importance for understanding its complex spatiotemporal dynamics and cellular functions. Considerable effort has been devoted to the development of small-molecule fluorescent probes for RNA imaging. However, most of the reported studies have mainly focused on improving the photostability, [...] Read more.
RNA imaging is of great importance for understanding its complex spatiotemporal dynamics and cellular functions. Considerable effort has been devoted to the development of small-molecule fluorescent probes for RNA imaging. However, most of the reported studies have mainly focused on improving the photostability, permeability, long emission wavelength, and compatibility with live-cell imaging of RNA probes. Less attention has been paid to the selectivity and detection limit of this class of probes. Highly selective and sensitive RNA probes are still rarely available. In this study, a new set of styryl probes were designed and synthesized, with the aim of upgrading the detection limit and maintaining the selectivity of a lead probe QUID−1 for RNA. Among these newly synthesized compounds, QUID−2 was the most promising candidate. The limit of detection (LOD) value of QUID−2 for the RNA was up to 1.8 ng/mL in solution. This property was significantly improved in comparison with that of QUID−1. Further spectroscopy and cell imaging studies demonstrated the advantages of QUID−2 over a commercially available RNA staining probe, SYTO RNASelect, for highly selective and sensitive RNA imaging. In addition, QUID−2 exhibited excellent photostability and low cytotoxicity. Using QUID−2, the global dynamics of RNA were revealed in live cells. More importantly, QUID−2 was found to be potentially applicable for detecting RNA granules in live cells. Collectively, our work provides an ideal probe for RNA imaging. We anticipate that this powerful tool may create new opportunities to investigate the underlying roles of RNA and RNA granules in live cells. Full article
(This article belongs to the Special Issue Nucleic Acid Chemical Biology: An Honorary Issue for Professor Li-He Zhang on the Occasion of His 85th Birthday)
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8 pages, 1525 KiB  
Article
Site-Specific Radioiodination of Oligonucleotides with a Phenolic Element in a Programmable Approach
by Haitao Zhao, Yu Qin, Dunfang Liu, Xinyao Geng, Cheng Wang, Ding Ding, Xuan Ding, Qian Xia, Jianjun Liu, Ruowen Wang and Weihong Tan
Molecules 2022, 27(19), 6257; https://doi.org/10.3390/molecules27196257 - 23 Sep 2022
Viewed by 2008
Abstract
Radioiodination of oligonucleotides provides an extra modality for nucleic acid-based theranostics with potential applications. Herein, we report the design and synthesis of a phosphoramidite embedded with a phenolic moiety and demonstrate that oligonucleotides can be readily functionalized with phenol as a precursor by [...] Read more.
Radioiodination of oligonucleotides provides an extra modality for nucleic acid-based theranostics with potential applications. Herein, we report the design and synthesis of a phosphoramidite embedded with a phenolic moiety and demonstrate that oligonucleotides can be readily functionalized with phenol as a precursor by general DNA synthesis. It was identified that the introduction of the precursor does not block the specificity of an aptamer, and the radioiodination is applicable to both DNA and RNA oligonucleotides in a site-specific approach with a commercial kit. Full article
(This article belongs to the Special Issue Nucleic Acid Chemical Biology: An Honorary Issue for Professor Li-He Zhang on the Occasion of His 85th Birthday)
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10 pages, 1906 KiB  
Article
A Label-Free Fluorescence Aptasensor Based on G-Quadruplex/Thioflavin T Complex for the Detection of Trypsin
by Pan Gu, Yangfan Lu, Shanni Li and Changbei Ma
Molecules 2022, 27(18), 6093; https://doi.org/10.3390/molecules27186093 - 18 Sep 2022
Cited by 4 | Viewed by 2146
Abstract
A novel, label-free fluorescent assay has been developed for the detection of trypsin by using thioflavin T as a fluorescent probe. A specific DNA aptamer can be combined by adding cytochrome c. Trypsin hydrolyzes the cytochrome c into small peptide fragments, exposing the [...] Read more.
A novel, label-free fluorescent assay has been developed for the detection of trypsin by using thioflavin T as a fluorescent probe. A specific DNA aptamer can be combined by adding cytochrome c. Trypsin hydrolyzes the cytochrome c into small peptide fragments, exposing the G-quadruplex part of DNA aptamer, which has a high affinity for thioflavin T, which then enhances the fluorescence intensity. In the absence of trypsin, the fluorescence intensity was inhibited as the combination of cytochrome c and the DNA aptamer impeded thioflavin T’s binding. Thus, the fluorescent biosensor showed a linear relationship from 0.2 to 60 μg/mL with a detection limit of 0.2 μg/mL. Furthermore, the proposed method was also successfully employed for determining trypsin in biological samples. This method is simple, rapid, cheap, and selective and possesses great potential for the detection of trypsin in bioanalytical and biological samples and medical diagnoses. Full article
(This article belongs to the Special Issue Nucleic Acid Chemical Biology: An Honorary Issue for Professor Li-He Zhang on the Occasion of His 85th Birthday)
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13 pages, 2302 KiB  
Article
21 Fluorescent Protein-Based DNA Staining Dyes
by Yurie Tehee Kim, Hyesoo Oh, Myung Jun Seo, Dong Hyeun Lee, Jieun Shin, Serang Bong, Sujeong Heo, Natalia Diyah Hapsari and Kyubong Jo
Molecules 2022, 27(16), 5248; https://doi.org/10.3390/molecules27165248 - 17 Aug 2022
Cited by 4 | Viewed by 3170
Abstract
Fluorescent protein–DNA-binding peptides or proteins (FP-DBP) are a powerful means to stain and visualize large DNA molecules on a fluorescence microscope. Here, we constructed 21 kinds of FP-DBPs using various colors of fluorescent proteins and two DNA-binding motifs. From the database of fluorescent [...] Read more.
Fluorescent protein–DNA-binding peptides or proteins (FP-DBP) are a powerful means to stain and visualize large DNA molecules on a fluorescence microscope. Here, we constructed 21 kinds of FP-DBPs using various colors of fluorescent proteins and two DNA-binding motifs. From the database of fluorescent proteins (FPbase.org), we chose bright FPs, such as RRvT, tdTomato, mNeonGreen, mClover3, YPet, and mScarlet, which are four to eight times brighter than original wild-type GFP. Additionally, we chose other FPs, such as mOrange2, Emerald, mTurquoise2, mStrawberry, and mCherry, for variations in emitting wavelengths. For DNA-binding motifs, we used HMG (high mobility group) as an 11-mer peptide or a 36 kDa tTALE (truncated transcription activator-like effector). Using 21 FP-DBPs, we attempted to stain DNA molecules and then analyzed fluorescence intensities. Most FP-DBPs successfully visualized DNA molecules. Even with the same DNA-binding motif, the order of FP and DBP affected DNA staining in terms of brightness and DNA stretching. The DNA staining pattern by FP-DBPs was also affected by the FP types. The data from 21 FP-DBPs provided a guideline to develop novel DNA-binding fluorescent proteins. Full article
(This article belongs to the Special Issue Nucleic Acid Chemical Biology: An Honorary Issue for Professor Li-He Zhang on the Occasion of His 85th Birthday)
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9 pages, 2022 KiB  
Article
Tetrazine-Induced Bioorthogonal Activation of Vitamin E-Modified siRNA for Gene Silencing
by Xueli Zhang, Amu Gubu, Jianfei Xu, Ning Yan, Wenbo Su, Di Feng, Qian Wang and Xinjing Tang
Molecules 2022, 27(14), 4377; https://doi.org/10.3390/molecules27144377 - 8 Jul 2022
Cited by 5 | Viewed by 2333
Abstract
The temporal activation of siRNA provides a valuable strategy for the regulation of siRNA activity and conditional gene silencing. The bioorthogonal bond-cleavage reaction of benzonorbonadiene and tetrazine is a promising trigger in siRNA temporal activation. Here, we developed a new method for the [...] Read more.
The temporal activation of siRNA provides a valuable strategy for the regulation of siRNA activity and conditional gene silencing. The bioorthogonal bond-cleavage reaction of benzonorbonadiene and tetrazine is a promising trigger in siRNA temporal activation. Here, we developed a new method for the bio-orthogonal chemical activation of siRNA based on the tetrazine-induced bond-cleavage reaction. Small-molecule activatable caged siRNAs were developed with the 5′-vitamin E-benzonobonadiene-modified antisense strand targeting the green fluorescent protein (GFP) gene and the mitotic kinesin-5 (Eg5) gene. The addition of tetrazine triggered the reaction with benzonobonadiene linker and induced the linker cleavage to release the active siRNA. Additionally, the conditional gene silencing of both exogenous GFP and endogenous Eg5 genes was successfully achieved with 5′-vitamin E-benzonobonadiene-caged siRNAs, which provides a new uncaging strategy with small molecules. Full article
(This article belongs to the Special Issue Nucleic Acid Chemical Biology: An Honorary Issue for Professor Li-He Zhang on the Occasion of His 85th Birthday)
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Review

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22 pages, 7952 KiB  
Review
Recent Advances in Exosomal miRNA Biosensing for Liquid Biopsy
by Bingqian Lin, Jinting Jiang, Jingxuan Jia and Xiang Zhou
Molecules 2022, 27(21), 7145; https://doi.org/10.3390/molecules27217145 - 22 Oct 2022
Cited by 12 | Viewed by 3288
Abstract
As a noninvasive detection technique, liquid biopsy plays a valuable role in cancer diagnosis, disease monitoring, and prognostic assessment. In liquid biopsies, exosomes are considered among the potential biomarkers because they are important bioinformation carriers for intercellular communication. Exosomes transport miRNAs and, thus, [...] Read more.
As a noninvasive detection technique, liquid biopsy plays a valuable role in cancer diagnosis, disease monitoring, and prognostic assessment. In liquid biopsies, exosomes are considered among the potential biomarkers because they are important bioinformation carriers for intercellular communication. Exosomes transport miRNAs and, thus, play an important role in the regulation of cell growth and function; therefore, detection of cancer cell-derived exosomal miRNAs (exo-miRNAs) gives effective information in liquid biopsy. The development of sensitive, convenient, and reliable exo-miRNA assays will provide new perspectives for medical diagnosis. This review presents different designs and detection strategies of recent exo-miRNA assays in terms of signal transduction and amplification, as well as signal detection. In addition, this review outlines the current attempts at bioassay methods in liquid biopsies. Lastly, the challenges and prospects of exosome bioassays are also considered. Full article
(This article belongs to the Special Issue Nucleic Acid Chemical Biology: An Honorary Issue for Professor Li-He Zhang on the Occasion of His 85th Birthday)
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17 pages, 1601 KiB  
Review
Noncoding RNAs Emerging as Drugs or Drug Targets: Their Chemical Modification, Bio-Conjugation and Intracellular Regulation
by Jin Wang, Tian Tian, Xin Li and Yan Zhang
Molecules 2022, 27(19), 6717; https://doi.org/10.3390/molecules27196717 - 9 Oct 2022
Cited by 10 | Viewed by 3070
Abstract
With the increasing understanding of various disease-related noncoding RNAs, ncRNAs are emerging as novel drugs and drug targets. Nucleic acid drugs based on different types of noncoding RNAs have been designed and tested. Chemical modification has been applied to noncoding RNAs such as [...] Read more.
With the increasing understanding of various disease-related noncoding RNAs, ncRNAs are emerging as novel drugs and drug targets. Nucleic acid drugs based on different types of noncoding RNAs have been designed and tested. Chemical modification has been applied to noncoding RNAs such as siRNA or miRNA to increase the resistance to degradation with minimum influence on their biological function. Chemical biological methods have also been developed to regulate relevant noncoding RNAs in the occurrence of various diseases. New strategies such as designing ribonuclease targeting chimeras to degrade endogenous noncoding RNAs are emerging as promising approaches to regulate gene expressions, serving as next-generation drugs. This review summarized the current state of noncoding RNA-based theranostics, major chemical modifications of noncoding RNAs to develop nucleic acid drugs, conjugation of RNA with different functional biomolecules as well as design and screening of potential molecules to regulate the expression or activity of endogenous noncoding RNAs for drug development. Finally, strategies of improving the delivery of noncoding RNAs are discussed. Full article
(This article belongs to the Special Issue Nucleic Acid Chemical Biology: An Honorary Issue for Professor Li-He Zhang on the Occasion of His 85th Birthday)
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Other

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12 pages, 3662 KiB  
Perspective
Tellurium-Modified Nucleosides, Nucleotides, and Nucleic Acids with Potential Applications
by Cen Chen and Zhen Huang
Molecules 2022, 27(23), 8379; https://doi.org/10.3390/molecules27238379 - 1 Dec 2022
Cited by 3 | Viewed by 1842
Abstract
Tellurium was successfully incorporated into proteins and applied to protein structure determination through X-ray crystallography. However, studies on tellurium modification of DNA and RNA are limited. This review highlights the recent development of Te-modified nucleosides, nucleotides, and nucleic acids, and summarizes the main [...] Read more.
Tellurium was successfully incorporated into proteins and applied to protein structure determination through X-ray crystallography. However, studies on tellurium modification of DNA and RNA are limited. This review highlights the recent development of Te-modified nucleosides, nucleotides, and nucleic acids, and summarizes the main synthetic approaches for the preparation of 5-PhTe, 2′-MeTe, and 2′-PhTe modifications. Those modifications are compatible with solid-phase synthesis and stable during Te-oligonucleotide purification. Moreover, the ideal electronic and atomic properties of tellurium for generating clear isomorphous signals give Te-modified DNA and RNA great potential applications in 3D crystal structure determination through X-ray diffraction. STM study also shows that Te-modified DNA has strong topographic and current peaks, which immediately suggests potential applications in nucleic acid direct imaging, nanomaterials, molecular electronics, and diagnostics. Theoretical studies indicate the potential application of Te-modified nucleosides in cancer therapy. Full article
(This article belongs to the Special Issue Nucleic Acid Chemical Biology: An Honorary Issue for Professor Li-He Zhang on the Occasion of His 85th Birthday)
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