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Kumagai K, Okubo H, Amano R, Kozu T, Ochiai M, Horiuchi M, Sakamoto T. Selection of aptamers using β-1,3-glucan recognition protein-tagged proteins and curdlan beads. J Biochem 2023; 174:433-440. [PMID: 37500079 DOI: 10.1093/jb/mvad059] [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: 04/27/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023] Open
Abstract
RNA aptamersare nucleic acids that are obtained using the systematic evolution of ligands by exponential enrichment (SELEX) method. When using conventional selection methods to immobilize target proteins on matrix beads using protein tags, sequences are obtained that bind not only to the target proteins but also to the protein tags and matrix beads. In this study, we performed SELEX using β-1,3-glucan recognition protein (GRP)-tags and curdlan beads to immobilize the acute myeloid leukaemia 1 (AML1) Runt domain (RD) and analysed the enrichment of aptamers using high-throughput sequencing. Comparison of aptamer enrichment using the GRP-tag and His-tag suggested that aptamers were enriched using the GRP-tag as well as using the His-tag. Furthermore, surface plasmon resonance analysis revealed that the aptamer did not bind to the GRP-tag and that the conjugation of the GRP-tag to RD weakened the interaction between the aptamer and RD. The GRP-tag could have acted as a competitor to reduce weakly bound RNAs. Therefore, the affinity system of the GRP-tagged proteins and curdlan beads is suitable for obtaining specific aptamers using SELEX.
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Key Words
- SELEX.Abbreviations:
AML1, acute myeloid leukaemia 1; βGRP, β-1,3-glucan recognition protein; GST, glutathione S-transferase; His-tag, poly histidine tag; HTS, high-throughput sequencing; MBP, maltose-binding protein; RD, Runt domain; RUNX1, RUNX family transcription factor 1; SELEX, systematic evolution of ligands by exponential enrichment; SPR, surface plasmon resonance
- aptamer
- curdlan
- βGRP
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Affiliation(s)
- Kazuyuki Kumagai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Hiroki Okubo
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Ryo Amano
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology, Saitama Cancer Center, 780 Komuro, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Masanori Ochiai
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Masataka Horiuchi
- Faculty of Pharmaceutical Science, Health Sciences University of Hokkaido, 1757 Kanazawa, Toubetsu, Ishikari, Hokkaido 061-0293, Japan
| | - Taiichi Sakamoto
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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Chen X, Yang L, Tang J, Wen X, Zheng X, Chen L, Li J, Xie Y, Le T. An AuNPs-Based Fluorescent Sensor with Truncated Aptamer for Detection of Sulfaquinoxaline in Water. BIOSENSORS 2022; 12:bios12070513. [PMID: 35884316 PMCID: PMC9312917 DOI: 10.3390/bios12070513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/07/2022] [Accepted: 07/09/2022] [Indexed: 11/28/2022]
Abstract
Herein, we developed a novel truncation technique for aptamer sequences to fabricate highly sensitive aptasensors based on molecular docking and molecular dynamics simulations. The binding mechanism and energy composition of the aptamer/sulfaquinoxaline (SQX) complexes were investigated. We successfully obtained a new SQX-specific aptamer (SBA28-1: CCCTAGGGG) with high affinity (Kd = 27.36 nM) and high specificity determined using graphene oxide. This aptamer has a unique stem-loop structure that can bind to SQX. Then, we fabricated a fluorescence aptasensor based on SBA28-1, gold nanoparticles (AuNPs), and rhodamine B (RhoB) that presented a good linear range of 1.25–160 ng/mL and a limit of detection of 1.04 ng/mL. When used to analyze water samples, the aptasensor presented acceptable recovery rates of 93.1–100.1% and coefficients of variation (CVs) of 2.2–10.2%. In conclusion, the fluorescence aptasensor can accurately and sensitively detect SQX in water samples and has good application prospects.
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Affiliation(s)
- Xingyue Chen
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.C.); (L.Y.); (J.T.); (X.W.); (X.Z.); (L.C.); (J.L.)
| | - Lulan Yang
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.C.); (L.Y.); (J.T.); (X.W.); (X.Z.); (L.C.); (J.L.)
| | - Jiaming Tang
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.C.); (L.Y.); (J.T.); (X.W.); (X.Z.); (L.C.); (J.L.)
| | - Xu Wen
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.C.); (L.Y.); (J.T.); (X.W.); (X.Z.); (L.C.); (J.L.)
| | - Xiaoling Zheng
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.C.); (L.Y.); (J.T.); (X.W.); (X.Z.); (L.C.); (J.L.)
| | - Lingling Chen
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.C.); (L.Y.); (J.T.); (X.W.); (X.Z.); (L.C.); (J.L.)
| | - Jiaqi Li
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.C.); (L.Y.); (J.T.); (X.W.); (X.Z.); (L.C.); (J.L.)
| | - Yong Xie
- Bioassay 3D Reconstruction Laboratory, Chongqing College of Electronic Engineering, Chongqing 401331, China
- Correspondence: (Y.X.); (T.L.)
| | - Tao Le
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (X.C.); (L.Y.); (J.T.); (X.W.); (X.Z.); (L.C.); (J.L.)
- Correspondence: (Y.X.); (T.L.)
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