Chemical Biology and Biotechnology of Nucleosides, Nucleotides, and Nucleic Acids

A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: 30 June 2025 | Viewed by 1808

Special Issue Editors


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Guest Editor
1. College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
2. Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
Interests: Z-DNA; Z-RNA; metabolism of nucleic acids; nutrition of nucleic acids; structure of nucleic acids; nucleic acids detection; circular nucleic acids; nucleic acids (nas); nanomaterials; chitosan
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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

Special Issue Information

Dear Colleagues,

Recently, there has been a great development of science and technology for NASs (nucleic acid substances of nucleic acids, nucleotides, and nucleosides), especially highlighted by the success of mRNA vaccines. Many new functions have been discovered for nucleic acids, such as circular RNA, circular ssDNA, and lncRNA, as well as other NASs. For example, circular RNAs have been found to regulate gene expression with many interesting pathways, and some nucleosides and nucleotides have been found to encompass nutritional and healthcare functions. On the other hand, many novel understandings of the relationship between their structures and functions are proposed, especially for left-handed DNA or RNA, quadruplex, triplex, R-loop, as well as the complex between NASs and other molecules such as proteins and carbohydrates. For this Special Issue entitled “Chemical Biology and Biotechnology of Nucleosides, Nucleotides, and Nucleic Acids”, the wide scope of research on NASs of either natural or artificially synthesized ones is welcome. We hope that these high-level research results can deepen our understanding of biomolecules and even life.

Prof. Dr. Xingguo Liang
Prof. Dr. Xinjing Tang
Guest Editors

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Keywords

  • nucleosides
  • nucleotides
  • nanostructure
  • circular ssDNA
  • circular RNA
  • quadruplex
  • conjugate
  • lncRNA
  • DNAzyme
  • ribozyme

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Published Papers (1 paper)

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Research

11 pages, 2808 KiB  
Article
Facile Splint-Free Circularization of ssDNA with T4 DNA Ligase by Redesigning the Linear Substrate to Form an Intramolecular Dynamic Nick
by Wenhua Sun, Kunling Hu, Mengqin Liu, Jian Luo, Ran An and Xingguo Liang
Biomolecules 2024, 14(8), 1027; https://doi.org/10.3390/biom14081027 - 18 Aug 2024
Viewed by 1224
Abstract
The efficient preparation of single-stranded DNA (ssDNA) rings, as a macromolecular construction approach with topological features, has aroused much interest due to the ssDNA rings’ numerous applications in biotechnology and DNA nanotechnology. However, an extra splint is essential for enzymatic circularization, and by-products [...] Read more.
The efficient preparation of single-stranded DNA (ssDNA) rings, as a macromolecular construction approach with topological features, has aroused much interest due to the ssDNA rings’ numerous applications in biotechnology and DNA nanotechnology. However, an extra splint is essential for enzymatic circularization, and by-products of multimers are usually present at high concentrations. Here, we proposed a simple and robust strategy using permuted precursor (linear ssDNA) for circularization by forming an intramolecular dynamic nick using a part of the linear ssDNA substrate itself as the template. After the simulation of the secondary structure for desired circular ssDNA, the linear ssDNA substrate is designed to have its ends on the duplex part (≥5 bp). By using this permuted substrate with 5′-phosphate, the splint-free circularization is simply carried out by T4 DNA ligase. Very interestingly, formation of only several base pairs (2–4) flanking the nick is enough for ligation, although they form only instantaneously under ligation conditions. More significantly, the 5-bp intramolecular duplex part commonly exists in genomes or functional DNA, demonstrating the high generality of our approach. Our findings are also helpful for understanding the mechanism of enzymatic DNA ligation from the viewpoint of substrate binding. Full article
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