دورية أكاديمية
أعرض في EDS

Facile Splint-Free Circularization of ssDNA with T4 DNA Ligase by Redesigning the Linear Substrate to Form an Intramolecular Dynamic Nick.

التفاصيل البيبلوغرافية
العنوان: Facile Splint-Free Circularization of ssDNA with T4 DNA Ligase by Redesigning the Linear Substrate to Form an Intramolecular Dynamic Nick.
المؤلفون: Sun W; State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao 266404, China., Hu K; State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao 266404, China., Liu M; State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao 266404, China., Luo J; State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao 266404, China., An R; State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao 266404, China.; Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, No. 1 Wenhai Road, Qingdao 266237, China., Liang X; State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao 266404, China.; Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, No. 1 Wenhai Road, Qingdao 266237, China.
المصدر: Biomolecules [Biomolecules] 2024 Aug 18; Vol. 14 (8). Date of Electronic Publication: 2024 Aug 18.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101596414 Publication Model: Electronic Cited Medium: Internet ISSN: 2218-273X (Electronic) Linking ISSN: 2218273X NLM ISO Abbreviation: Biomolecules Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Basel, Switzerland : MDPI, 2011-
مواضيع طبية MeSH: DNA, Single-Stranded*/metabolism , DNA, Single-Stranded*/chemistry , DNA Ligases*/metabolism , DNA Ligases*/chemistry , DNA, Circular*/chemistry , DNA, Circular*/metabolism, Nucleic Acid Conformation
مستخلص: 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.
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معلومات مُعتمدة: SKL202308 Open Foundation of State Key Laboratory of Marine Food Processing & Safety Control; 32102064 the National Natural Science Foundation of China; 2019YFD0901701 the National Key R&D Program of China; 2023KJ040 Youth Innovation Team Program of Universities in Shandong Province
فهرسة مساهمة: Keywords: T4 DNA ligase; permuted sequence; splint-free ligation; ssDNA circularization
المشرفين على المادة: 0 (DNA, Single-Stranded)
EC 6.5.1.- (DNA Ligases)
0 (DNA, Circular)
تواريخ الأحداث: Date Created: 20240829 Date Completed: 20240829 Latest Revision: 20240903
رمز التحديث: 20240903
مُعرف محوري في PubMed: PMC11352879
DOI: 10.3390/biom14081027
PMID: 39199414
قاعدة البيانات: MEDLINE
الوصف
تدمد:2218-273X
DOI:10.3390/biom14081027