1
|
Park J, Ban C. Development of a one-shot dual aptamer-based fluorescence nanosensor for rapid, sensitive, and label-free detection of periostin. Sci Rep 2023; 13:10224. [PMID: 37353600 PMCID: PMC10290134 DOI: 10.1038/s41598-023-37418-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/21/2023] [Indexed: 06/25/2023] Open
Abstract
Periostin is associated with several diseases, including cancers. Therefore, monitoring blood periostin levels is a powerful tool for diagnosing various diseases and identifying their severity. However, conventional detection methods pose several challenges, including high costs. To address these issues, we developed a novel one-shot dual aptamer-based fluorescence nanosensor for detecting periostin. The proposed nanosensor facilitates rapid, label-free, and sensitive detection of periostin using gold nanoprobes constructed by rhodamine-b isothiocyanate, PL2trunc aptamer, and gold nanoparticles and silver nanoprobes fabricated by the PL5trunc aptamer and silver nanoparticles. The two nanoprobes form a core-satellite structure by interacting with periostin, and the nanosensor detects periostin through the fluorescence regenerated by the increased proximity between them. The nanosensor successfully detected periostin with remarkable detection limits of 106.68 pM in buffer and 463.3 pM in serum-spiked conditions within 30 min without additional washing or signal amplification processes. Considering serum periostin levels in various diseases, the proposed nanosensor provides a suitable method for identifying patients with various diseases and determining disease severity. Moreover, the platform can be helpful as a practical method for on-site medical diagnosis because it can be adapted to detect other biomarkers simply by replacing the aptamer with other detection probes.
Collapse
Affiliation(s)
- Jonghoon Park
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea.
| |
Collapse
|
2
|
Mok J, Kim E, Kang M, Jeon J, Ban C. Development of an optical sandwich ELONA using a pair of DNA aptamers for yellow fever virus NS1. Talanta 2023; 253:123979. [PMID: 36208558 DOI: 10.1016/j.talanta.2022.123979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 12/13/2022]
Abstract
Here, we proposed an enzyme-linked oligonucleotide assay (ELONA) for yellow fever (YF) diagnosis that uses a pair of aptamers, YFns1-4 and YFns1-31. The aptamers were selected to specifically bind to nonstructural protein 1 (NS1), which is secreted at a high concentration after YF infection. We applied the aptamers which did not interfere with each other on binding to the NS1 in a sandwich ELONA. In the assay, the best detection sensitivity was obtained when the combination of YFns1-31 as a capture aptamer and YFns1-4 as a detect aptamer was used. The sensitivity could be attributed to the results of the direct ELONA with each YFns1-4 and YFns1-31; a great absorbance intensity and a broad detectable range of NS1, respectively. The sandwich ELONA achieved a low detection limit of 0.85 nM in buffer and was highly specific to the YFV-NS1 as its detection signals were significantly distinct from those of other flavivirus-derived NS1. In addition, the assay showed a desirable sensitivity in serum-spiked condition. Our developed sandwich ELONA can be a new practical and applicable serological diagnostics in YF endemic regions where other flaviviruses coexist and facilities for complex diagnostic tests are lacking.
Collapse
Affiliation(s)
- Jihyun Mok
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk, 790-784, Republic of Korea
| | - Eunseon Kim
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk, 790-784, Republic of Korea
| | - Minji Kang
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk, 790-784, Republic of Korea
| | - Jinseong Jeon
- POSTECH Biotech Center, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk, 790-784, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk, 790-784, Republic of Korea.
| |
Collapse
|
3
|
Jo J, Bae S, Jeon J, Youn H, Lee G, Ban C. Bifunctional G-Quadruplex Aptamer Targeting Nucleolin and Topoisomerase 1: Antiproliferative Activity and Synergistic Effect of Conjugated Drugs. Bioconjug Chem 2023; 34:238-247. [PMID: 36516871 DOI: 10.1021/acs.bioconjchem.2c00540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As a counterpart to antibody-drug conjugates (ADCs), aptamer-drug conjugates (ApDCs) have been considered a promising strategy for targeted therapy due to the various benefits of aptamers. However, an aptamer merely serves as a targeting ligand in ApDCs, whereas the antibody enables the unexpected therapeutic efficacy of ADCs through antibody-dependent cellular cytotoxicity (ADCC). In this study, we developed a tumor-specific aptamer with an effector function and used it to confirm the feasibility of more potent ApDCs. First, we designed a nucleolin (NCL)-binding G-quadruplex (GQ) library based on the ability of NCL to bind to telomeric sequences. We then identified a bifunctional GQ aptamer (BGA) inhibiting the catalytic activity of topoisomerase 1 (TOP1) by forming an irreversible cleavage complex. Our BGA specifically targeted NCL-positive MCF-7 cells, exhibiting antiproliferative activity, and this suggested that tumor-specific therapeutic aptamers can be developed by using a biased library to screen aptamer candidates for functional targets. Finally, we utilized DM1, which has a synergistic interaction with TOP1 inhibitors, as a conjugated drug. BGA-DM1 exerted an anticancer effect 20-fold stronger than free DM1 and even 10-fold stronger than AS1411 (NCL aptamer)-DM1, highlighting our approach to develop synergistic ApDCs. Therefore, we anticipate that our library might be utilized for the identification of aptamers with effector functions. Furthermore, by employing such aptamers and appropriate drugs, synergistic ApDCs can be developed for targeted cancer therapy in a manner distinct from how ADCs exhibit additional therapeutic efficacy.
Collapse
Affiliation(s)
- Jihoon Jo
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk790-784, Republic of Korea
| | - Sangmin Bae
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk790-784, Republic of Korea
| | - Jinseong Jeon
- POSTECH Biotech Center, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk790-784, Republic of Korea
| | - Hyungjun Youn
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk790-784, Republic of Korea
| | - Gyeongjin Lee
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk790-784, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk790-784, Republic of Korea
| |
Collapse
|
4
|
Mishra S, Jeon J, Kang JK, Song SH, Kim TY, Ban C, Choi H, Kim Y, Kim M, Park JW. Direct Detection of Low Abundance Genes of Single Point Mutation. Nano Lett 2021; 21:9061-9068. [PMID: 34672610 DOI: 10.1021/acs.nanolett.1c02728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell-free DNA (cfDNA) analysis, specifically circulating tumor DNA (ctDNA) analysis, provides enormous opportunities for noninvasive early assessment of cancers. To date, PCR-based methods have led this field. However, the limited sensitivity/specificity of PCR-based methods necessitates the search for new methods. Here, we describe a direct approach to detect KRAS G12D mutated genes in clinical ctDNA samples with the utmost LOD and sensitivity/specificity. In this study, MutS protein was immobilized on the tip of an atomic force microscope (AFM), and the protein sensed the mismatched sites of the duplex formed between the capture probe on the surface and mutated DNA. A noteworthy LOD (3 copies, 0.006% allele frequency) was achieved, along with superb sensitivity/specificity (100%/100%). These observations demonstrate that force-based AFM, in combination with the protein found in nature and properly designed capture probes/blockers, represents an exciting new avenue for ctDNA analysis.
Collapse
Affiliation(s)
- Sourav Mishra
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Jinseong Jeon
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Jun-Kyu Kang
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Sang-Hyun Song
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Tae-You Kim
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Yonggoo Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Myungshin Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| |
Collapse
|
5
|
Chung S, Gurudatt NG, Jeon J, Ban C, Shim YB. Fast Aptamer Generation Method Based on the Electrodynamic Microfluidic Channel and Evaluation of Aptamer Sensor Performance. Anal Chem 2020; 93:1416-1422. [PMID: 33369387 DOI: 10.1021/acs.analchem.0c03231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We demonstrate for the first time a fast aptamer generation method based on the screen-printed electrodynamic microfluidic channel device, where a specific aptamer selectively binds to a target protein on channel walls, following recovery and separation. A malaria protein as a model target, Plasmodium vivax lactate dehydrogenase (PvLDH) was covalently bonded to the conductive polymer layer formed on the carbon channel walls to react with the DNA library in a fluid. Then, the AC electric field was symmetrically applied on the channel walls for inducing the specific binding of the target protein to DNA library molecules. In this case, the partitioning efficiency between PvLDH and DNA library in the channel was attained to be 1.67 × 107 with the background of 5.56 × 10-6, which was confirmed using the quantitative polymerase chain reaction (qPCR). The selectively captured DNAs were isolated from the protein and separated in situ to give five aptamers with different sequences by one round cycle. The dissociation constants (Kd) of the selected aptamers were determined employing both electrochemical impedance spectroscopy (EIS) and the fluorescence method. The sensing performance of each aptamer was evaluated for the PvLDH detection after individual immobilization on the screen-printed array electrodes. The most sensitive aptamer revealed a detection limit of 7.8 ± 0.4 fM. The sensor reliability was evaluated by comparing it with other malaria sensors.
Collapse
Affiliation(s)
- Saeromi Chung
- Department of Chemistry and Institute of Biophysio Sensor Technology, Pusan National University, Busan 46241, Republic of Korea
| | - Nanjanagudu Ganesh Gurudatt
- Department of Chemistry and Institute of Biophysio Sensor Technology, Pusan National University, Busan 46241, Republic of Korea
| | - Jinsung Jeon
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Yoon-Bo Shim
- Department of Chemistry and Institute of Biophysio Sensor Technology, Pusan National University, Busan 46241, Republic of Korea
| |
Collapse
|
6
|
Lee H, Youn H, Hwang A, Lee H, Park JY, Kim W, Yoo Y, Ban C, Kang T, Kim B. Troponin Aptamer on an Atomically Flat Au Nanoplate Platform for Detection of Cardiac Troponin I. Nanomaterials (Basel) 2020; 10:nano10071402. [PMID: 32708486 PMCID: PMC7407982 DOI: 10.3390/nano10071402] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/14/2020] [Accepted: 07/14/2020] [Indexed: 01/14/2023]
Abstract
Well-ordered bioreceptors on atomically flat Au surfaces can be a high-performance biosensor. Cardiac troponin I proteins (cTnIs) have been regarded as a specific biomarker for acute myocardial infarction (AMI). Here, we report the accurate detection of cTnIs using an aptamer-immobilized Au nanoplate platform. The single-crystalline and atomically flat Au nanoplate was characterized by atomic force microscopy. For the precise detection of cTnI, we immobilized an aptamer that can strongly bind to cTnI onto an atomically flat Au nanoplate. Using the aptamer-immobilized Au nanoplate, cTnIs were successfully detected at a concentration of 100 aM (2.4 fg/mL) in buffer solution. Furthermore, cTnIs in serum could be identified at a concentration of 100 fM (2.4 pg/mL). The total assay time was ~7 h. Importantly, the aptamer-immobilized Au nanoplate enabled us to diagnose AMI patients accurately, suggesting the potential of the present method in the diagnosis of AMI.
Collapse
Affiliation(s)
- Hyoban Lee
- Department of Chemistry, KAIST, Daejeon 34141, Korea; (H.L.); (A.H.); (H.L.); (J.Y.P.)
| | - Hyungjun Youn
- Department of Chemistry, POSTECH, Pohang 37673, Korea;
| | - Ahreum Hwang
- Department of Chemistry, KAIST, Daejeon 34141, Korea; (H.L.); (A.H.); (H.L.); (J.Y.P.)
- Bionanotechnology Research Center, KRIBB, Daejeon 34141, Korea
| | - Hyunsoo Lee
- Department of Chemistry, KAIST, Daejeon 34141, Korea; (H.L.); (A.H.); (H.L.); (J.Y.P.)
- Center for Nanomaterials and Chemical Reactions, IBS, Daejeon 34141, Korea
| | - Jeong Young Park
- Department of Chemistry, KAIST, Daejeon 34141, Korea; (H.L.); (A.H.); (H.L.); (J.Y.P.)
- Center for Nanomaterials and Chemical Reactions, IBS, Daejeon 34141, Korea
| | - Weon Kim
- Division of Cardiology, Department of Internal Medicine, Kyung Hee University Hospital, Kyung Hee University, Seoul 02447, Korea;
| | - Youngdong Yoo
- Department of Chemistry, Ajou University, Suwon 16499, Korea;
| | - Changill Ban
- Department of Chemistry, POSTECH, Pohang 37673, Korea;
- Correspondence: (C.B.); (T.K.); (B.K.)
| | - Taejoon Kang
- Bionanotechnology Research Center, KRIBB, Daejeon 34141, Korea
- Correspondence: (C.B.); (T.K.); (B.K.)
| | - Bongsoo Kim
- Department of Chemistry, KAIST, Daejeon 34141, Korea; (H.L.); (A.H.); (H.L.); (J.Y.P.)
- Correspondence: (C.B.); (T.K.); (B.K.)
| |
Collapse
|
7
|
Huang J, Ban C, Liu L, Ye Y. Dynamics and risk indicators of intrasinus elevation height following transalveolar sinus floor elevation with immediate implant placement: a longitudinal cohort study. Int J Oral Maxillofac Surg 2020; 50:109-115. [PMID: 32507405 DOI: 10.1016/j.ijom.2020.04.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 02/19/2020] [Accepted: 04/30/2020] [Indexed: 12/11/2022]
Abstract
Successful intrasinus graft consolidation is essential for the treatment outcome of transalveolar sinus floor elevation (SFE). This study was performed to examine the dynamics and risk indicators related to the elevation height after transalveolar SFE with grafting material and simultaneous implant placement. Fifty-two patients with 55 sites undergoing transalveolar SFE with immediate implant placement were enrolled retrospectively. Cone beam computed tomography (CBCT) images were collected and saved in DICOM format, at the following time-points: pre-surgery (T0), immediately post-surgery (T1), and 6 months post-surgery (T2). Voxel-based CBCT superimposition was performed to measure the sinus width, residual alveolar height, implant protrusion length, total elevation height, and apical graft height. The change in total elevation height from T1 to T2 was defined as the study outcome. Clinical and linear variables were analysed using linear regression. From T1 to T2, the total elevation height showed an average reduction of 1.0±1.1mm, while 10.9% sites showed an increased elevation height. Univariate regression analysis showed no significant correlation between tested clinical or linear variables and the study outcome. The results suggest that the change in elevation height was not influenced by the alveolar or sinus dimensions, graft materials, implant diameter, implant protrusion length, or the total elevation height at T1.
Collapse
Affiliation(s)
- J Huang
- Department of Oral Implantology, School and Hospital of Stomatology, Tongji University; Shanghai Engineering Research Centre of Tooth Restoration and Regeneration, Shanghai, China
| | - C Ban
- Department of Oral Implantology, School and Hospital of Stomatology, Tongji University; Shanghai Engineering Research Centre of Tooth Restoration and Regeneration, Shanghai, China
| | - L Liu
- Department of Oral Implantology, School and Hospital of Stomatology, Tongji University; Shanghai Engineering Research Centre of Tooth Restoration and Regeneration, Shanghai, China
| | - Y Ye
- Department of Oral Implantology, School and Hospital of Stomatology, Tongji University; Shanghai Engineering Research Centre of Tooth Restoration and Regeneration, Shanghai, China.
| |
Collapse
|
8
|
Jeon J, Jo H, Her J, Youn H, Park J, Jo J, Lee J, Chang CL, Ban C. A Rapid Colorimetric Sensor for Soluble Interleukin-2 Receptor α, Based on Aptamer-Adsorbed AuNP. Chembiochem 2019; 20:2236-2240. [PMID: 31270926 DOI: 10.1002/cbic.201900109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/10/2019] [Indexed: 01/01/2023]
Abstract
The soluble interleukin-2 receptor α (sIL-2Rα) is a broad indicator of clinical disease activity in various inflammatory diseases. Here we have developed, for the first time, a rapid, washing-free colorimetric aptasensor based on a sIL-2Rα aptamer (Kd =1.33 nm). The aptasensor was fabricated with Au nanoparticles (AuNPs) adsorbing sIL-2Rα aptamers. On addition of sIL-2Rα, the aptamers become desorbed from the AuNPs, and this in turn weakens the absorption corresponding to AuNP-catalyzed oxidation of ortho-phenylenediamine (oPD) with H2 O2 . The aptasensor was characterized by TEM imaging, ζ potential measurements, dynamic light scattering (DLS) analysis, and UV/Vis spectrometry, followed by further optimization. The fabricated sensor exhibited great analytical performance, with a linear range of 1 to 100 nm and a detection limit of 1 nm both in buffer and in spiked human serum within 25 min. Other proteins, such as bovine serum albumin (BSA), IL-17Rα, IL-5Rα, IL-13Rα2 , and CD166, showed negligible effects on the aptasensor. Thanks to the great advantages of the aptamers and AuNPs, this aptasensor provides a rapid, simple, and inexpensive process that might offer insights into various diagnostic applications of sIL-2Rα.
Collapse
Affiliation(s)
- Jinseong Jeon
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37674, Republic of Korea
| | - Hunho Jo
- InnaMed, 3675 Market St Suite 200, Philadelphia, PA, 19104, USA
| | - Jin Her
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37674, Republic of Korea
| | - Hyungjun Youn
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37674, Republic of Korea
| | - Jonghoon Park
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37674, Republic of Korea
| | - Jihoon Jo
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37674, Republic of Korea
| | - Jiseon Lee
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37674, Republic of Korea
| | - Chulhun L Chang
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, 20 Geumo-ro, Mulgeum-eup, Yangsan-si, Gyeongsangnam-do, 50612, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37674, Republic of Korea
| |
Collapse
|
9
|
Tian XZ, Paengkoum P, Paengkoum S, Chumpawadee S, Ban C, Thongpea S. Short communication: Purple corn (Zea mays L.) stover silage with abundant anthocyanins transferring anthocyanin composition to the milk and increasing antioxidant status of lactating dairy goats. J Dairy Sci 2018; 102:413-418. [PMID: 30415857 DOI: 10.3168/jds.2018-15423] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 09/22/2018] [Indexed: 12/13/2022]
Abstract
The present study used 16 multiparous lactating Saanen dairy goats (body weight, 41.80 ± 2.92 kg; mean ± standard deviation) with healthy and symmetrical udders. Goats were divided into 2 blocks of 8 goats based on milk yield averaged from 75 d in milk in a randomized completed block design. The 2 study groups were the control (CSSS), in which goats were fed sticky corn stover silage, and the treatment (TPSS), in which goats were fed anthocyanin-rich purple corn (Zea mays L.) stover silage (PSS). The results indicated that the TPSS group led to an elevation in the content of milk lactose relative to the CSSS. The inclusion of anthocyanin-rich PSS had no effect on the level of 5 particular anthocyanins [i.e., cyanidin-3-glucoside, delphinidin, cyanidin, pelargonidin (Pel), as well as total anthocyanins in milk]. The pelargonidin-3-glucoside and malvidin were unable to be detected in both groups. However, the TPSS resulted in higher levels of peonidin (Peo) and malvidin-3-O-glucoside (M3G) compared with the control. Moreover, goats receiving TPSS exhibited a higher level of superoxide dismutase (SOD) in plasma and milk relative to the CSSS. Interestingly, some positive correlations were detected between the certain milk components [i.e., fat and total solids as well as fat and solids-not-fat (SNF); protein and SNF; and total solids and SNF]. In addition, the positive correlations were observed between individual anthocyanins (cyanidin-3-glucoside, delphinidin, Peo, M3G, cyanidin, and Pel) and total anthocyanins. Specifically, stronger positive correlations were noted between several antioxidant enzymes and anthocyanin composition in milk (total antioxidant capacity and Pel; SOD and Peo as well as SOD and M3G). Taken together, PSS with abundant anthocyanins can transfer anthocyanins to the milk and enhance the amount of antioxidants in lactating dairy goats.
Collapse
Affiliation(s)
- X Z Tian
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Muang, Nakhon Ratchasima 30000, Thailand
| | - P Paengkoum
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Muang, Nakhon Ratchasima 30000, Thailand.
| | - S Paengkoum
- Program in Agriculture, Faculty of Science and Technology, Nakhon Ratchasima Rajabhat University, Muang, Nakhon Ratchasima 30000, Thailand
| | - S Chumpawadee
- Department of Agricultural Technology, Faculty of Technology, Mahasarakham University, Bangkok 44150, Thailand
| | - C Ban
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Muang, Nakhon Ratchasima 30000, Thailand
| | - S Thongpea
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Muang, Nakhon Ratchasima 30000, Thailand
| |
Collapse
|
10
|
Youn H, Her J, Mok J, Kil B, Kim E, Park H, Ban C. A Novel Eosinophilia Diagnostics Using Label-free Impedimetric Aptasensor for Soluble Interleukin-5 Receptor Alpha. ELECTROANAL 2018. [DOI: 10.1002/elan.201800453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hyungjun Youn
- Department of Chemistry; Pohang University of Science and Technology, 77; Cheongam-Ro Nam-Gu, Pohang, Gyeongbuk 37673 South Korea
| | - Jin Her
- Department of Chemistry; Pohang University of Science and Technology, 77; Cheongam-Ro Nam-Gu, Pohang, Gyeongbuk 37673 South Korea
| | - Jihyun Mok
- Department of Chemistry; Pohang University of Science and Technology, 77; Cheongam-Ro Nam-Gu, Pohang, Gyeongbuk 37673 South Korea
| | - Bareum Kil
- Department of Chemistry; Pohang University of Science and Technology, 77; Cheongam-Ro Nam-Gu, Pohang, Gyeongbuk 37673 South Korea
| | - Eunseon Kim
- Department of Chemistry; Pohang University of Science and Technology, 77; Cheongam-Ro Nam-Gu, Pohang, Gyeongbuk 37673 South Korea
| | - Haesim Park
- Department of Allergy and Clinical Immunology; Ajou University School of Medicine; San-5, Woncheon-dong, Yeongtong-gu Suwon 16499 South Korea
| | - Changill Ban
- Department of Chemistry; Pohang University of Science and Technology, 77; Cheongam-Ro Nam-Gu, Pohang, Gyeongbuk 37673 South Korea
| |
Collapse
|
11
|
Cho H, Cho HS, Nam H, Jo H, Yoon J, Park C, Dang TVT, Kim E, Jeong J, Park S, Wallner ES, Youn H, Park J, Jeon J, Ryu H, Greb T, Choi K, Lee Y, Jang SK, Ban C, Hwang I. Translational control of phloem development by RNA G-quadruplex-JULGI determines plant sink strength. Nat Plants 2018; 4:376-390. [PMID: 29808026 DOI: 10.1038/s41477-018-0157-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/19/2018] [Indexed: 05/24/2023]
Abstract
The emergence of a plant vascular system was a prerequisite for the colonization of land; however, it is unclear how the photosynthate transporting system was established during plant evolution. Here, we identify a novel translational regulatory module for phloem development involving the zinc-finger protein JULGI (JUL) and its targets, the 5' untranslated regions (UTRs) of the SUPPRESSOR OF MAX2 1-LIKE4/5 (SMXL4/5) mRNAs, which is exclusively conserved in vascular plants. JUL directly binds and induces an RNA G-quadruplex in the 5' UTR of SMXL4/5, which are key promoters of phloem differentiation. We show that RNA G-quadruplex formation suppresses SMXL4/5 translation and restricts phloem differentiation. In turn, JUL deficiency promotes phloem formation and strikingly increases sink strength per seed. We propose that the translational regulation by the JUL/5' UTR G-quadruplex module is a major determinant of phloem establishment, thereby determining carbon allocation to sink tissues, and that this mechanism was a key invention during the emergence of vascular plants.
Collapse
Affiliation(s)
- Hyunwoo Cho
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Hyun Seob Cho
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Hoyoung Nam
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
| | - Joonseon Yoon
- Crop Seed Development Team, Seed Business Division, FarmHannong Co. Ltd., Daejeon, Korea
| | - Chanyoung Park
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Tuong Vi T Dang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Eunah Kim
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Jongmin Jeong
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Soyoung Park
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Eva-Sophie Wallner
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Hyungjun Youn
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
| | - Jongmin Park
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Jinseong Jeon
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, Korea
| | - Thomas Greb
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Kyuha Choi
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Yoontae Lee
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Sung Key Jang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
| | - Ildoo Hwang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea.
| |
Collapse
|
12
|
Jeon J, Park SC, Her J, Lee JW, Han JK, Kim YK, Kim KP, Ban C. Comparative lipidomic profiling of the human commensal bacterium Propionibacterium acnes and its extracellular vesicles. RSC Adv 2018; 8:15241-15247. [PMID: 35541326 PMCID: PMC9080044 DOI: 10.1039/c7ra13769a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 04/05/2018] [Indexed: 12/27/2022] Open
Abstract
Propionibacterium acnes is a lipophilic commensal bacterium mainly found on the skin and in the gastrointestinal tract. Pathophysiological effects of P. acnes have recently been reported not only in acne progression but in various diseases. As an emerging mode of bacterial communication, extracellular vesicles (EVs) have been demonstrated to conduct critical pathophysiological functions. To provide information on P. acnes lipid composition for the first time, we conducted a comparative lipidomic analysis of P. acnes and P. acnes EVs and identified 214 lipids with high confidence using triplicated liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) analyses. P. acnes EVs contained substantially more PCs, DGs, PAs, PEs, LPAs, LPCs, and MGs than P. acnes, and contained fewer PSs, SO1Ps, SA1Ps, LPGs, LPIs, and LPSs. Distinctively, P. acnes EVs possessed a markedly reduced amount of TG. These findings will provide useful clues for understanding the biological and pathophysiological mechanisms of P. acnes and for clinical applications such as vaccine development, diagnostics and therapeutics.
Collapse
Affiliation(s)
- Jinseong Jeon
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH) 77, Cheongam-Ro, Nam-Gu Pohang Gyeongbuk 37673 Republic of Korea
| | - Seung Cheol Park
- Department of Applied Chemistry, College of Applied Science, Kyung Hee University Yongin 17104 Republic of Korea
| | - Jin Her
- Department of Chemistry, Pohang University of Science and Technology (POSTECH) 77, Cheongam-Ro, Nam-Gu Pohang Gyeongbuk 37673 Republic of Korea
| | - Jae Won Lee
- Department of Applied Chemistry, College of Applied Science, Kyung Hee University Yongin 17104 Republic of Korea
| | - Jin-Kwan Han
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH) 77, Cheongam-Ro, Nam-Gu Pohang Gyeongbuk 37673 Republic of Korea
| | - Yoon-Keun Kim
- Myeongdong Medical Woori Technology Building, World Cup buk-ro 56-gil 9, Mapo-gu Seoul 03923 Republic of Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, College of Applied Science, Kyung Hee University Yongin 17104 Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology (POSTECH) 77, Cheongam-Ro, Nam-Gu Pohang Gyeongbuk 37673 Republic of Korea
| |
Collapse
|
13
|
Kim JS, Jang Y, Kim JH, Park YH, Hwang SA, Kim J, Lee SR, Xu Z, Ban C, Ahn K, Chun KJ. Cardioprotective Effect of the SDF-1α/CXCR4 Axis in Ischemic Postconditioning in Isolated Rat Hearts. Korean Circ J 2017; 47:949-959. [PMID: 29035436 PMCID: PMC5711687 DOI: 10.4070/kcj.2016.0353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/29/2016] [Accepted: 08/06/2017] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Information about the role of the stromal cell-derived factor-1α (SDF-1α)/chemokine receptor type 4 (CXCR4) axis in ischemic postconditioning (IPOC) is currently limited. We hypothesized that the SDF-1α/CXCR4 signaling pathway is directly involved in the cardioprotective effect of IPOC. METHODS Isolated rat hearts were divided into four groups. The control group was subjected to 30-min of regional ischemia and 2-hour of reperfusion (n=12). The IPOC group was induced with 6 cycles of 10-second reperfusion and 10-second global ischemia (n=8) in each cycle. The CXCR4 antagonist, AMD3100, was applied before reperfusion in the IPOC group (AMD+IPOC group, n=11) and control group (AMD group, n=9). Hemodynamic changes with electrocardiography were monitored and infarct size was measured. The SDF-1α, lactate dehydrogenase (LDH) and creatine kinase (CK) concentrations in perfusate were measured. We also analyzed extracellular signal-regulated kinase 1/2 (ERK1/2) and Akt phosphorylation state expression. RESULTS IPOC significantly reduced infarct size, but AMD3100 attenuated the infarct reducing effect of IPOC. IPOC significantly decreased LDH and CK, but these effects were reversed by AMD3100. ERK1/2 and Akt phosphorylation increased with IPOC and these effects were blocked by AMD3100. CONCLUSION Based on the results of this study, SDF-1α/CXCR4 signaling may be involved in IPOC cardioprotection and this signaling pathway couples to the ERK1/2 and Akt pathways.
Collapse
Affiliation(s)
- Jeong Su Kim
- Cardiovascular Research Institute, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Youngho Jang
- Cardiovascular Research Institute, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - June Hong Kim
- Cardiovascular Research Institute, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Yong Hyun Park
- Cardiovascular Research Institute, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Sun Ae Hwang
- Cardiovascular Research Institute, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Jun Kim
- Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sung Ryul Lee
- National Research Laboratory for Mitochondrial Signaling, Department of Physiology, Inje University College of Medicine, Busan, Korea
| | - Zhelong Xu
- Department of Anesthesiology, University of North Carolina, Chapel Hill, NC, USA
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
| | - Kyohan Ahn
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
| | - Kook Jin Chun
- Cardiovascular Research Institute, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea.
| |
Collapse
|
14
|
Jo H, Her J, Lee H, Shim YB, Ban C. Highly sensitive amperometric detection of cardiac troponin I using sandwich aptamers and screen-printed carbon electrodes. Talanta 2016; 165:442-448. [PMID: 28153281 DOI: 10.1016/j.talanta.2016.12.091] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/30/2016] [Accepted: 12/30/2016] [Indexed: 02/07/2023]
Abstract
In this study, we developed a sandwich aptamer-based screen-printed carbon electrode (SPCE) using chronoamperometry for the detection of cardiac troponin I (cTnI), one of the promising biomarkers for acute myocardial infarction (AMI). Disposable three-electrode SPCEs were manufactured using a screen printer, and various modifications such as electrodeposition of gold nanoparticles and electropolymerization of conductive polymers were performed. From the bare electrode to the aptamer-immobilized SPCE, all processes were monitored and analyzed via various techniques such as cyclic voltammetry, electrochemical impedance spectroscopy, and X-ray photoelectron spectroscopy. The quantification of cTnI was conducted based on amperometric signals from the catalytic reaction between hydrazine and H2O2. The fabricated aptasensor in a buffer, as well as in a serum-added solution, exhibited great analytical performance with a dynamic range of 1-100 pM (0.024-2.4ng/mL) and a detection limit of 1.0 pM (24pg/mL), which is lower than the existing cutoff values (40-700pg/mL). Furthermore, the developed sensor showed high sensitivity to cTnI over other proteins. It is anticipated that this potable SPCE aptasensor for cTnI will become an innovative diagnostic tool for AMI.
Collapse
Affiliation(s)
- Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| | - Jin Her
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| | - Heehyun Lee
- Department of Life Science, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| | - Yoon-Bo Shim
- Department of Chemistry, Pusan National University, Keumjeong-Ku, Busan 609-735, South Korea.
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| |
Collapse
|
15
|
Gurudatt N, Naveen MH, Ban C, Shim YB. Enhanced electrochemical sensing of leukemia cells using drug/lipid co-immobilized on the conducting polymer layer. Biosens Bioelectron 2016; 86:33-40. [DOI: 10.1016/j.bios.2016.06.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 12/28/2022]
|
16
|
Choi SJ, Ban C. Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition. Sci Rep 2016; 6:34998. [PMID: 27725738 PMCID: PMC5057103 DOI: 10.1038/srep34998] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/22/2016] [Indexed: 02/07/2023] Open
Abstract
Structural elements are key elements for understanding single-stranded nucleic acid folding. Although various RNA structural elements have been documented, structural elements of single-stranded DNA (ssDNA) have rarely been reported. Herein, we determined a crystal structure of PvLDH in complex with a DNA aptamer called pL1. This aptamer folds into a hairpin-bulge contact by adopting three novel structural elements, viz, DNA T-loop-like motif, base-phosphate zipper, and DNA G·G metal ion zipper. Moreover, the pL1:PvLDH complex shows unique properties compared with other protein:nucleic acid complexes. Generally, extensive intermolecular hydrogen bonds occur between unpaired nucleotides and proteins for specific recognitions. Although most protein-interacting nucleotides of pL1 are unpaired nucleotides, pL1 recognizes PvLDH by predominant shape complementarity with many bridging water molecules owing to the combination of three novel structural elements making protein-binding unpaired nucleotides stable. Moreover, the additional set of Plasmodium LDH residues which were shown to form extensive hydrogen bonds with unpaired nucleotides of 2008s does not participate in the recognition of pL1. Superimposition of the pL1:PvLDH complex with hLDH reveals steric clashes between pL1 and hLDH in contrast with no steric clashes between 2008s and hLDH. Therefore, specific protein recognition mode of pL1 is totally different from that of 2008s.
Collapse
Affiliation(s)
- Sung-Jin Choi
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, South Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, South Korea
| |
Collapse
|
17
|
Abstract
Correct diagnosis and successful therapy are extremely important to enjoy a healthy life when suffering from a disease. To achieve these aims, various cutting-edge technologies have been designed and fabricated to diagnose and treat specific diseases. Among these technologies, aptamer-nanomaterial hybrids have received considerable attention from scientists and doctors because they have numerous advantages over other methods, such as good biocompatibility, low immunogenicity and controllable selectivity. In particular, aptamers, oligonucleic acids or peptides that bind to a specific target molecule, are regarded as outstanding biomolecules. In this review, several screening techniques for aptamers, also called systematic evolution of ligands by exponential enrichment (SELEX) methods, are introduced, and diagnostic and therapeutic aptamer applications are also presented. Furthermore, we describe diverse aptamer-nanomaterial conjugate designs and their applications for diagnosis and therapy.
Collapse
Affiliation(s)
- Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea
| |
Collapse
|
18
|
Oh E, Kim JY, Cho Y, An H, Lee N, Jo H, Ban C, Seo JH. Overexpression of angiotensin II type 1 receptor in breast cancer cells induces epithelial-mesenchymal transition and promotes tumor growth and angiogenesis. Biochim Biophys Acta 2016; 1863:1071-81. [PMID: 26975580 DOI: 10.1016/j.bbamcr.2016.03.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/15/2016] [Accepted: 03/10/2016] [Indexed: 01/10/2023]
Abstract
The angiotensin II type I receptor (AGTR1) has been implicated in diverse aspects of human disease, from the regulation of blood pressure and cardiovascular homeostasis to cancer progression. We sought to investigate the role of AGTR1 in cell proliferation, epithelial-mesenchymal transition (EMT), migration, invasion, angiogenesis and tumor growth in the breast cancer cell line MCF7. Stable overexpression of AGTR1 was associated with accelerated cell proliferation, concomitant with increased expression of survival factors including poly(ADP-ribose) polymerase (PARP) and X-linked inhibitor of apoptosis (XIAP), as well as extracellular signal-regulated kinase (ERK) activation. AGTR1-overexpressing MCF7 cells were more aggressive than their parent line, with significantly increased activity in migration and invasion assays. These observations were associated with changes in EMT markers, including reduced E-cadherin expression and increased p-Smad3, Smad4 and Snail levels. Treatment with the AGTR1 antagonist losartan attenuated these effects. AGTR1 overexpression also accelerated tumor growth and increased Ki-67 expression in a xenograft model. This was associated with increased tumor angiogenesis, as evidenced by a significant increase in microvessels in the intratumoral and peritumoral areas, and enhanced tumor invasion, with the latter response associated with increased EMT marker expression and matrix metallopeptidase 9 (MMP-9) upregulation. In vivo administration of losartan significantly reduced both tumor growth and angiogenesis. Our findings suggest that AGTR1 plays a significant role in tumor aggressiveness, and its inhibition may have therapeutic implications.
Collapse
MESH Headings
- Angiotensin II Type 1 Receptor Blockers/pharmacology
- Animals
- Blotting, Western
- Breast Neoplasms/blood supply
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Cadherins/genetics
- Cadherins/metabolism
- Cell Proliferation/drug effects
- Cell Proliferation/genetics
- Epithelial-Mesenchymal Transition/genetics
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Expression Regulation, Neoplastic/genetics
- Humans
- Losartan/pharmacology
- MCF-7 Cells
- Matrix Metalloproteinase 9/genetics
- Matrix Metalloproteinase 9/metabolism
- Mice, Inbred BALB C
- Mice, Nude
- Microscopy, Confocal
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/metabolism
- Neovascularization, Pathologic/prevention & control
- Poly(ADP-ribose) Polymerases/genetics
- Poly(ADP-ribose) Polymerases/metabolism
- Receptor, Angiotensin, Type 1/genetics
- Receptor, Angiotensin, Type 1/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Smad4 Protein/genetics
- Smad4 Protein/metabolism
- Transplantation, Heterologous
- Tumor Burden/drug effects
- Tumor Burden/genetics
Collapse
Affiliation(s)
- Eunhye Oh
- Division of Medical Oncology, Department of Internal Medicine, Korea University College of Medicine, Korea University, Seoul 136-705, Republic of Korea; Brain Korea 21 Program for Biomedical Science, Korea University College of Medicine, Korea University, Seoul 152-703, Republic of Korea
| | - Ji Young Kim
- Division of Medical Oncology, Department of Internal Medicine, Korea University College of Medicine, Korea University, Seoul 136-705, Republic of Korea; Brain Korea 21 Program for Biomedical Science, Korea University College of Medicine, Korea University, Seoul 152-703, Republic of Korea
| | - Youngkwan Cho
- Division of Medical Oncology, Department of Internal Medicine, Korea University College of Medicine, Korea University, Seoul 136-705, Republic of Korea; Brain Korea 21 Program for Biomedical Science, Korea University College of Medicine, Korea University, Seoul 152-703, Republic of Korea
| | - Hyunsook An
- Division of Medical Oncology, Department of Internal Medicine, Korea University College of Medicine, Korea University, Seoul 136-705, Republic of Korea; Brain Korea 21 Program for Biomedical Science, Korea University College of Medicine, Korea University, Seoul 152-703, Republic of Korea
| | - Nahyun Lee
- Division of Medical Oncology, Department of Internal Medicine, Korea University College of Medicine, Korea University, Seoul 136-705, Republic of Korea; Brain Korea 21 Program for Biomedical Science, Korea University College of Medicine, Korea University, Seoul 152-703, Republic of Korea
| | - Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, Republic of Korea
| | - Jae Hong Seo
- Division of Medical Oncology, Department of Internal Medicine, Korea University College of Medicine, Korea University, Seoul 136-705, Republic of Korea; Brain Korea 21 Program for Biomedical Science, Korea University College of Medicine, Korea University, Seoul 152-703, Republic of Korea.
| |
Collapse
|
19
|
Jo H, Kim SK, Youn H, Lee H, Lee K, Jeong J, Mok J, Kim SH, Park HS, Ban C. A highly sensitive and selective impedimetric aptasensor for interleukin-17 receptor A. Biosens Bioelectron 2016; 81:80-86. [PMID: 26921556 DOI: 10.1016/j.bios.2016.02.050] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 01/10/2023]
Abstract
Interleukin-17 receptor A (IL-17RA) has been recognized as a valuable biomarker for diverse diseases, including autoimmune diseases. In this work, an electrochemical biosensor with great sensitivity and selectivity toward IL-17RA was fabricated using an IL-17RA aptamer (Kd=14.00nM) for the first time. The aptasensor was manufactured using electrodeposition of gold nanoparticles, and then quantitative detection of IL-17RA was performed based on impedimetry. The developed sensor exhibited a superior analytical performance for IL-17RA with a wide dynamic range of 10-10,000pg/mL in buffer and a detection limit of 2.13pg/mL, which is lower than that of commercially available ELISA kits. In addition, we validated the high specificity of the designed aptasensor to only IL-17RA, which showed good sensitivity even in human serum solution. Furthermore, the detection of the differentiated HL-60 cells expressing IL-17RA was successfully performed. Clinical applicability of the sensor was also demonstrated utilizing neutrophils separated from asthma patients. It is expected that the fabricated aptasensor will become an excellent diagnostic platform for IL-17RA-mediated diseases.
Collapse
Affiliation(s)
- Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| | - Seong-Kyeong Kim
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| | - Hyungjun Youn
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| | - Heehyun Lee
- Department of Life Sciences, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| | - Kwanghyun Lee
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| | - Jian Jeong
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| | - Jihyun Mok
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| | - Seung-Hyun Kim
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, San-5, Woncheon-dong, Yeongtong-gu, Suwon 442-749, South Korea.
| | - Hae-Sim Park
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, San-5, Woncheon-dong, Yeongtong-gu, Suwon 442-749, South Korea.
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| |
Collapse
|
20
|
Jo H, Gu H, Jeon W, Youn H, Her J, Kim SK, Lee J, Shin JH, Ban C. Electrochemical aptasensor of cardiac troponin I for the early diagnosis of acute myocardial infarction. Anal Chem 2015; 87:9869-75. [PMID: 26352249 DOI: 10.1021/acs.analchem.5b02312] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cardiac troponin I (cTnI) is well-known as a promising biomarker for the early diagnosis of acute myocardial infarction (AMI). In this work, single-stranded DNA aptamers against cTnI were identified by the Systematic Evolution of Ligands by Exponential enrichment (SELEX) method. The aptamer candidates exhibited a high selectivity and sensitivity toward both cTnI and the cardiac Troponin complex. The binding affinities of each aptamer were evaluated based on their dissociation constants (Kd) by surface plasma resonance. The Tro4 aptamer that had the highest binding capacity to cTnI showed a very low Kd value (270 pM) compared with that of a cTnI antibody (20.8 nM). Furthermore, we designed a new electrochemical aptasensor based on square wave voltammetry using ferrocene-modified silica nanoparticles. The developed aptasensor demonstrated an excellent analytical performance for cTnI with a wide linear range of 1-10 000 pM in a buffer and a detection limit of 1.0 pM (24 pg/mL; S/N = 3), which was noticeably lower than the cutoff values (70-400 pg/mL). The specificity of the aptamers was also examined using nontarget proteins, demonstrating that the proposed sensor responded to only cTnI. In addition, cTnI was successfully detected in a human serum albumin solution. On the basis of the calibration curve that was constructed, the concentrations of cTnI in a solution supplemented with human serum were effectively measured. The calculated values correlated well with the actual concentrations of cTnI. It is anticipated that the highly sensitive and selective aptasensor for cTnI could be readily applicable for the accurate diagnosis of AMI.
Collapse
Affiliation(s)
- Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology , 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea
| | - Hyunwoo Gu
- Department of Chemistry, Kwangwoon University , Wolgye-Dong, Nowon-Gu, Seoul 139-701, South Korea
| | - Weejeong Jeon
- Department of Chemistry, Pohang University of Science and Technology , 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea
| | - Hyungjun Youn
- Department of Chemistry, Pohang University of Science and Technology , 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea
| | - Jin Her
- Department of Chemistry, Pohang University of Science and Technology , 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea
| | - Seong-Kyeong Kim
- Department of Chemistry, Pohang University of Science and Technology , 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea
| | - Jeongbong Lee
- Department of Chemistry, Kwangwoon University , Wolgye-Dong, Nowon-Gu, Seoul 139-701, South Korea
| | - Jae Ho Shin
- Department of Chemistry, Kwangwoon University , Wolgye-Dong, Nowon-Gu, Seoul 139-701, South Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology , 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea
| |
Collapse
|
21
|
Jo H, Her J, Ban C. Dual aptamer-functionalized silica nanoparticles for the highly sensitive detection of breast cancer. Biosens Bioelectron 2015; 71:129-136. [PMID: 25897882 DOI: 10.1016/j.bios.2015.04.030] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/26/2015] [Accepted: 04/12/2015] [Indexed: 02/07/2023]
Abstract
In this study, we synthesized dual aptamer-modified silica nanoparticles that simultaneously target two types of breast cancer cells: the mucin 1 (MUC1)(+) and human epidermal growth factor receptor 2 (HER2)(+) cell lines. Dual aptamer system enables a broad diagnosis for breast cancer in comparison with the single aptamer system. The dye-doped silica nanoparticles offer great stability with respect to photobleaching and enable the accurate quantification of breast cancer cells. The morphological and spectroscopic characteristics of the designed Dual-SiNPs were demonstrated via diverse methods such as DLS, zeta potential measurements, UV-vis spectroscopy, and fluorescence spectroscopy. Negatively charged Dual-SiNPs with a homogeneous size distribution showed robust and strong fluorescence. In addition, Dual-SiNPs did not affect cell viability, implying that this probe might be readily available for use in an in vivo system. Through ratio optimization of the MUC1 and HER2 aptamers, the binding capacities of the Dual-SiNPs to both cell lines were maximized. Based on Dual-SiNPs, a highly sensitive quantification of breast cancer cells was performed, resulting in a detection limit of 1 cell/100 μL, which is significantly lower compared with those reported in other studies. Moreover, the developed detection platform displayed high selectivity for only the MUC1(+) and HER2(+) cell lines. It is expected that this valuable diagnostic probe will be a noteworthy platform for the diagnosis and prognosis of breast cancer.
Collapse
Affiliation(s)
- Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| | - Jin Her
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| |
Collapse
|
22
|
Lee S, Jo H, Her J, Lee HY, Ban C. Ultrasensitive electrochemical detection of engrailed-2 based on homeodomain-specific DNA probe recognition for the diagnosis of prostate cancer. Biosens Bioelectron 2015; 66:32-8. [DOI: 10.1016/j.bios.2014.11.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/01/2014] [Accepted: 11/03/2014] [Indexed: 12/13/2022]
|
23
|
Teng W, Ban C, Hahn JH. Formation of lipid bilayer membrane in a poly(dimethylsiloxane) microchip integrated with a stacked polycarbonate membrane support and an on-site nanoinjector. Biomicrofluidics 2015; 9:024120. [PMID: 26015832 PMCID: PMC4409621 DOI: 10.1063/1.4919066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/14/2015] [Indexed: 06/04/2023]
Abstract
This paper describes a new and facile approach for the formation of pore-spanning bilayer lipid membranes (BLMs) within a poly(dimethylsiloxane) (PDMS) microfluidic device. Commercially, readily available polycarbonate (PC) membranes are employed for the support of BLMs. PC sheets with 5 μm, 2 μm, and 0.4 μm pore diameters, respectively, are thermally bonded into a multilayer-stack, reducing the pore density of 0.4 μm-pore PC by a factor of 200. The BLMs on this support are considerably stable (a mean lifetime: 17 h). This multilayer-stack PC (MSPC) membrane is integrated into the PDMS chip by an epoxy bonding method developed to secure durable bonding under the use of organic solvents. The microchip has a special channel for guiding a micropipette in the proximity of the MSPC support. With this on-site injection technique, tens to hundreds of nanoliters of solutions can be directly dispensed to the support. Incorporating gramicidin ion channels into BLMs on the MSPC support has confirmed the formation of single BLMs, which is based on the observation from current signals of 20 pS conductance that is typical to single channel opening. Based on the bilayer capacitance (1.4 pF), about 15% of through pores across the MSPC membrane are estimated to be covered with BLMs.
Collapse
Affiliation(s)
- Wei Teng
- Department of Chemistry, BioNanotechnology Center, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, 790-784 Pohang, South Korea
| | - Changill Ban
- Department of Chemistry, BioNanotechnology Center, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, 790-784 Pohang, South Korea
| | - Jong Hoon Hahn
- Department of Chemistry, BioNanotechnology Center, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, 790-784 Pohang, South Korea
| |
Collapse
|
24
|
Jo H, Jeong EY, Jeon J, Ban C. Structural insights into Escherichia coli polymyxin B resistance protein D with X-ray crystallography and small-angle X-ray scattering. BMC Struct Biol 2014; 14:24. [PMID: 25480013 PMCID: PMC4263063 DOI: 10.1186/s12900-014-0024-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/24/2014] [Indexed: 01/08/2023]
Abstract
BACKGROUND Polymyxin B resistance protein D (PmrD) plays a key role in the polymyxin B-resistance pathway, as it is the signaling protein that can act as a specific connecter between PmrA/PmrB and PhoP/PhoQ. We conducted structural analysis to characterize Escherichia coli (E. coli) PmrD, which exhibits different features compared with PmrD in other bacteria. RESULTS The X-ray crystal structure of E. coli PmrD was determined at a 2.00 Å resolution, revealing novel information such as the unambiguous secondary structures of the protein and the presence of a disulfide bond. Furthermore, various assays such as native gel electrophoresis, surface plasmon resonance (SPR), size-exclusion chromatography, dynamic light scattering (DLS), and small-angle X-ray scattering (SAXS) measurements, were performed to elucidate the structural and functional role of the internal disulfide bond in E. coli PmrD. CONCLUSIONS The structural characteristics of E. coli PmrD were clearly identified via diverse techniques. The findings help explain the different protective mechanism of E. coli compared to other Gram-negative bacteria.
Collapse
Affiliation(s)
- Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 790-784, South Korea.
| | - Eui Young Jeong
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 790-784, South Korea.
| | - Jinseong Jeon
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 790-784, South Korea.
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 790-784, South Korea.
| |
Collapse
|
25
|
Lee S, Manjunatha DH, Jeon W, Ban C. Cationic surfactant-based colorimetric detection of Plasmodium lactate dehydrogenase, a biomarker for malaria, using the specific DNA aptamer. PLoS One 2014; 9:e100847. [PMID: 24992632 PMCID: PMC4081113 DOI: 10.1371/journal.pone.0100847] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 05/30/2014] [Indexed: 02/07/2023] Open
Abstract
A simple, sensitive, and selective colorimetric biosensor for the detection of the malarial biomarkers Plasmodium vivax lactate dehydrogenase (PvLDH) and Plasmodium falciparum LDH (PfLDH) was demonstrated using the pL1 aptamer as the recognition element and gold nanoparticles (AuNPs) as probes. The proposed method is based on the aggregation of AuNPs using hexadecyltrimethylammonium bromide (CTAB). The AuNPs exhibited a sensitive color change from red to blue, which could be seen directly with the naked eye and was monitored using UV-visible absorption spectroscopy and transmission electron microscopy (TEM). The reaction conditions were optimized to obtain the maximum color intensity. PvLDH and PfLDH were discernible with a detection limit of 1.25 pM and 2.94 pM, respectively. The applicability of the proposed biosensor was also examined in commercially available human serum.
Collapse
Affiliation(s)
- Seonghwan Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - D H Manjunatha
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Weejeong Jeon
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
- * E-mail:
| |
Collapse
|
26
|
Jo H, Youn H, Lee S, Ban C. Ultra-effective photothermal therapy for prostate cancer cells using dual aptamer-modified gold nanostars. J Mater Chem B 2014; 2:4862-4867. [PMID: 32261777 DOI: 10.1039/c4tb00643g] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although various studies related to nanoparticles-based photothermal therapy have been actively performed, an epoch-making photothermolysis therapy exhibiting both high selectivity and efficiency has yet not been discovered. For the first time, we have developed novel valuable therapeutic complexes, namely, dual aptamer-modified gold nanostars, for the targeting of prostate cancers, including PSMA(+) and PSMA(-) cells. The synthesized probes were characterized through several techniques, including UV-VIS spectral analysis, DLS analysis, zeta potential measurements, and TEM imaging, and were subsequently subjected to cytotoxicity tests, cell uptake confirmation, and in vitro photothermal therapy. The homogeneously well-fabricated nanostars presented high selectivity to prostate cancer cells and extremely high efficiency for therapy using an 808 nm laser under an irradiance of 0.3 W cm-2, which is lower than the permitted value for skin exposure (0.329 W cm-2). It is anticipated that this novel photothermal agent will become the general platform for targeted therapy.
Collapse
Affiliation(s)
- Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, Korea.
| | | | | | | |
Collapse
|
27
|
Lee SJC, Lee JW, Choi TS, Jin KS, Lee S, Ban C, Kim HI. Probing Conformational Change of Intrinsically Disordered α-Synuclein to Helical Structures by Distinctive Regional Interactions with Lipid Membranes. Anal Chem 2014; 86:1909-16. [DOI: 10.1021/ac404132g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Shin Jung C. Lee
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Jong Wha Lee
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Tae Su Choi
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Kyeong Sik Jin
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Seonghwan Lee
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Changill Ban
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Hugh I. Kim
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| |
Collapse
|
28
|
Cho WK, Jeong C, Kim D, Chang M, Song KM, Hanne J, Ban C, Fishel R, Lee JB. ATP alters the diffusion mechanics of MutS on mismatched DNA. Structure 2012; 20:1264-1274. [PMID: 22682745 DOI: 10.1016/j.str.2012.04.017] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 04/20/2012] [Accepted: 04/23/2012] [Indexed: 11/18/2022]
Abstract
The mismatch repair (MMR) initiation protein MutS forms at least two types of sliding clamps on DNA: a transient mismatch searching clamp (∼1 s) and an unusually stable (∼600 s) ATP-bound clamp that recruits downstream MMR components. Remarkably, direct visualization of single MutS particles on mismatched DNA has not been reported. We have combined real-time particle tracking with fluorescence resonance energy transfer (FRET) to image MutS diffusion dynamics on DNA containing a single mismatch. We show searching MutS rotates during diffusion independent of ionic strength or flow rate, suggesting continuous contact with the DNA backbone. In contrast, ATP-bound MutS clamps that are visually and successively released from the mismatch spin freely around the DNA, and their diffusion is affected by ionic strength and flow rate. These observations show that ATP binding alters the MutS diffusion mechanics on DNA, which has a number of implications for the mechanism of MMR.
Collapse
Affiliation(s)
- Won-Ki Cho
- Department of Physics, Bioengineering Pohang University of Science and Technology (POSTECH), Pohang, 790-784, Korea
| | - Cherlhyun Jeong
- Department of Physics, Bioengineering Pohang University of Science and Technology (POSTECH), Pohang, 790-784, Korea
| | - Daehyung Kim
- Department of Physics, Bioengineering Pohang University of Science and Technology (POSTECH), Pohang, 790-784, Korea
| | - Minhyeok Chang
- Department of Physics, Bioengineering Pohang University of Science and Technology (POSTECH), Pohang, 790-784, Korea
| | - Kyung-Mi Song
- Department of Chemistry, Bioengineering Pohang University of Science and Technology (POSTECH), Pohang, 790-784, Korea
| | - Jeungphill Hanne
- Department of Molecular Virology, Immunology and Medical Genetics The Ohio State University, Columbus, OH 43210, USA
| | - Changill Ban
- Department of Chemistry, Bioengineering Pohang University of Science and Technology (POSTECH), Pohang, 790-784, Korea
| | - Richard Fishel
- Department of Molecular Virology, Immunology and Medical Genetics The Ohio State University, Columbus, OH 43210, USA
- Physics Department, The Ohio State University, Columbus, OH 43210, USA
| | - Jong-Bong Lee
- Department of Physics, Bioengineering Pohang University of Science and Technology (POSTECH), Pohang, 790-784, Korea
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology (POSTECH), Pohang, 790-784, Korea
| |
Collapse
|
29
|
Jeong E, Jo H, Kim TG, Ban C. Characterization of multi-functional properties and conformational analysis of MutS2 from Thermotoga maritima MSB8. PLoS One 2012; 7:e34529. [PMID: 22545085 PMCID: PMC3335848 DOI: 10.1371/journal.pone.0034529] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 03/01/2012] [Indexed: 11/18/2022] Open
Abstract
The MutS2 homologues have received attention because of their unusual activities that differ from those of MutS. In this work, we report on the functional characteristics and conformational diversities of Thermotoga maritima MutS2 (TmMutS2). Various biochemical features of the protein were demonstrated via diverse techniques such as scanning probe microscopy (SPM), ATPase assays, analytical ultracentrifugation, DNA binding assays, size chromatography, and limited proteolytic analysis. Dimeric TmMutS2 showed the temperature-dependent ATPase activity. The non-specific nicking endonuclease activities of TmMutS2 were inactivated in the presence of nonhydrolytic ATP (ADPnP) and enhanced by the addition of TmMutL. In addition, TmMutS2 suppressed the TmRecA-mediated DNA strand exchange reaction in a TmMutL-dependent manner. We also demonstrated that small-angle X-ray scattering (SAXS) analysis of dimeric TmMutS2 exhibited nucleotide- and DNA-dependent conformational transitions. Particularly, TmMutS2-ADPnP showed the most compressed form rather than apo-TmMutS2 and the TmMutS2-ADP complex, in accordance with the results of biochemical assays. In the case of the DNA-binding complexes, the stretched conformation appeared in the TmMutS2-four-way junction (FWJ)-DNA complex. Convergences of biochemical- and SAXS analysis provided abundant information for TmMutS2 and clarified ambiguous experimental results.
Collapse
Affiliation(s)
- Euiyoung Jeong
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk, South Korea
| | - Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk, South Korea
| | - Tae Gyun Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk, South Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk, South Korea
- * E-mail:
| |
Collapse
|
30
|
Zhu Y, Chandra P, Song KM, Ban C, Shim YB. Label-free detection of kanamycin based on the aptamer-functionalized conducting polymer/gold nanocomposite. Biosens Bioelectron 2012; 36:29-34. [PMID: 22542925 DOI: 10.1016/j.bios.2012.03.034] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 03/19/2012] [Accepted: 03/21/2012] [Indexed: 11/24/2022]
Abstract
Highly sensitive label-free detection of kanamycin is achieved with an aptamer sensor based on a conducting polymer/gold self-assembled nanocomposite. The sensor probe is fabricated by covalently immobilizing an in vitro selected DNA aptamer for kanamycin onto gold nanoparticle (AuNP)-comprised conducting polymer, poly-[2, 5-di-(2-thienyl)-1H-pyrrole-1-(p-benzoic acid)] (poly-DPB). The self-assembling of DPB on AuNP is investigated by TEM and UV-vis spectroscopy and the modification of the aptamer sensor is characterized using XPS and electrochemical impedance spectroscopy. The probe is applied to detect kanamycin by using voltammetric techniques. The sensor shows a pair of redox peaks around 0.26/ 0.08 V (vs. Ag/AgCl) for kanamycin captured by the aptamer-immobilized probe. The parameters that can affect the response, such as aptamer concentration, incubation time, temperature, and pH are optimized. The calibration plot shows a linear range from 0.05 μM to 9.0 μM kanamycin with a detection limit of 9.4±0.4 nM. The proposed aptamer sensor is examined with a real sample.
Collapse
Affiliation(s)
- Ye Zhu
- Department of Chemistry, Pusan National University, Busan 609-735, South Korea
| | | | | | | | | |
Collapse
|
31
|
|
32
|
Lee S, Song KM, Jeon W, Jo H, Shim YB, Ban C. A highly sensitive aptasensor towards Plasmodium lactate dehydrogenase for the diagnosis of malaria. Biosens Bioelectron 2012; 35:291-296. [PMID: 22459583 DOI: 10.1016/j.bios.2012.03.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/28/2012] [Accepted: 03/02/2012] [Indexed: 11/24/2022]
Abstract
Finding a highly sensitive diagnostic technique for malaria has challenged scientists for the last century. In the present study, we identified versatile single-strand DNA aptamers for Plasmodium lactate dehydrogenase (pLDH), a biomarker for malaria, via the Systematic Evolution of Ligands by EXponential enrichment (SELEX). The pLDH aptamers selectively bound to the target proteins with high sensitivity (K(d)=16.8-49.6 nM). The selected aptamers were characterized using an electrophoretic mobility shift assay, a quartz crystal microbalance, a fluorescence assay, and circular dichroism spectroscopy. We also designed a simple aptasensor using electrochemical impedance spectroscopy; both Plasmodium vivax LDH and Plasmodium falciparum LDH were selectively detected with a detection limit of 1 pM. Furthermore, the pLDH aptasensor clearly distinguished between malaria-positive blood samples of two major species (P. vivax and P. falciparum) and a negative control, indicating that it may be a useful tool for the diagnosis, monitoring, and surveillance of malaria.
Collapse
Affiliation(s)
- Seonghwan Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Kyung-Mi Song
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Weejeong Jeon
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Yoon-Bo Shim
- Department of Chemistry, Pusan National University, Busan, 609-735, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, 790-784, Republic of Korea.
| |
Collapse
|
33
|
Abstract
An acedan derivative containing Zn(II)-DPA has been developed as a two-photon probe for nucleoside phosphates, which shows enhanced fluorescence toward ATP and ADP at physiological pH 7.4 among other competing anions including AMP; the probe is permeable to cell membranes and thus can be directly used for two-photon imaging of ATP and ADP in live cells.
Collapse
Affiliation(s)
- Alla Sreenivasa Rao
- Department of Chemistry and the Center for Electro-Photo Behaviors in Advanced Molecular Systems, POSTECH, San 31, Hyoja-dong, Pohang, 790-784, Republic of Korea
| | | | | | | | | | | | | |
Collapse
|
34
|
Song KM, Jeong E, Jeon W, Cho M, Ban C. Aptasensor for ampicillin using gold nanoparticle based dual fluorescence-colorimetric methods. Anal Bioanal Chem 2012; 402:2153-61. [PMID: 22222912 DOI: 10.1007/s00216-011-5662-3] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 10/23/2011] [Accepted: 12/13/2011] [Indexed: 01/02/2023]
Abstract
A gold nanoparticle based dual fluorescence-colorimetric method was developed as an aptasensor to detect ampicillin using its single-stranded DNA (ssDNA) aptamer, which was discovered by a magnetic bead-based SELEX technique. The selected aptamers, AMP4 (5'-CACGGCATGGTGGGCGTCGTG-3'), AMP17 (5'-GCGGGCGGTTGTATAGCGG-3'), and AMP18 (5'-TTAGTTGGGGTTCAGTTGG-3'), were confirmed to have high sensitivity and specificity to ampicillin (K(d), AMP7 = 9.4 nM, AMP17 = 13.4 nM, and AMP18 = 9.8 nM, respectively). The 5'-fluorescein amidite (FAM)-modified aptamer was used as a dual probe for observing fluorescence differences and color changes simultaneously. The lower limits of detection for this dual method were a 2 ng/mL by fluorescence and a 10 ng/mL by colorimetry for ampicillin in the milk as well as in distilled water. Because these detection limits were below the maximum residue limit of ampicillin, this aptasensor was sensitive enough to detect antibiotics in food products, such as milk and animal tissues. In addition, this dual aptasensor will be a more accurate method for antibiotics in food products as it concurrently uses two detection methods: fluorescence and colorimetry.
Collapse
Affiliation(s)
- Kyung-Mi Song
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk, South Korea
| | | | | | | | | |
Collapse
|
35
|
Jeong EY, Kim TG, Ban C. Modulated nicking endonuclease function by the N-terminal extended region of the smr domain in human Bcl-3 binding protein. Proteins 2011; 80:327-32. [DOI: 10.1002/prot.23211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/09/2011] [Accepted: 09/22/2011] [Indexed: 11/07/2022]
|
36
|
Jang YH, Kim JH, Ban C, Ahn K, Cheong JH, Kim HH, Kim JS, Park YH, Kim J, Chun KJ, Lee GH, Kim M, Kim C, Xu Z. Stromal cell derived factor-1 (SDF-1) targeting reperfusion reduces myocardial infarction in isolated rat hearts. Cardiovasc Ther 2011; 30:264-72. [PMID: 22958220 DOI: 10.1111/j.1755-5922.2011.00301.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Recent studies have shown that stromal cell derived factor-1 (SDF-1), first known as a cytokine involved in recruiting stem cells into injured organs, confers myocardial protection in myocardial infarction, which is not dependent on stem cell recruitment but related with modulation of ischemia-reperfusion (I/R) injury. However, the effect of SDF has been studied only in a preischemic exposure model, which is not clinically relevant if SDF is to be used as a therapeutic agent. Our study was aimed at evaluating whether or not SDF-1 confers cardioprotection during the reperfusion period. Hearts from SD rats were isolated and perfused with the Langendorff system. Proximal left coronary artery ligation, reperfusion, and SDF perfusion in KH buffer was done according to study protocol. Area of necrosis (AN) relative to area at risk (AR) was the primary endpoint of the study. Significant reduction of AN/AR by SDF in an almost dose-dependent manner was noted during both the preischemic exposure and reperfusion periods. In particular, infusion of a high concentration of SDF (25 nM/L) resulted in a dramatic reduction of infarct size, which was greater than that achieved with ischemic pre- or postconditioning. SDF perfusion during reperfusion was associated with a similar significant reduction of infarct size as preischemic SDF exposure. Further studies are warranted to assess the potential of SDF as a therapeutic agent for reducing I/R injury in clinical practice.
Collapse
Affiliation(s)
- Young-Ho Jang
- Cardiovascular Research Institute, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan-city, Gyungsangnam-do, Republic of Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Song KM, Cho M, Jo H, Min K, Jeon SH, Kim T, Han MS, Ku JK, Ban C. Gold nanoparticle-based colorimetric detection of kanamycin using a DNA aptamer. Anal Biochem 2011; 415:175-81. [PMID: 21530479 DOI: 10.1016/j.ab.2011.04.007] [Citation(s) in RCA: 280] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 03/30/2011] [Accepted: 04/04/2011] [Indexed: 02/07/2023]
Abstract
A selective kanamycin-binding single-strand DNA (ssDNA) aptamer (TGGGGGTTGAGGCTAAGCCGA) was discovered through in vitro selection using affinity chromatography with kanamycin-immobilized sepharose beads. The selected aptamer has a high affinity for kanamycin and also for kanamycin derivatives such as kanamycin B and tobramycin. The dissociation constants (K(d) [kanamycin]=78.8 nM, K(d) [kanamycin B]=84.5 nM, and K(d) [tobramycin]=103 nM) of the new aptamer were determined by fluorescence intensity analysis using 5'-fluorescein amidite (FAM) modification. Using this aptamer, kanamycin was detected down to 25 nM by the gold nanoparticle-based colorimetric method. Because the designed colorimetric method is simple, easy, and visible to the naked eye, it has advantages that make it useful for the detection of kanamycin. Furthermore, the selected new aptamer has many potential applications as a bioprobe for the detection of kanamycin, kanamycin B, and tobramycin in pharmaceutical preparations and food products.
Collapse
Affiliation(s)
- Kyung-Mi Song
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk 790-784, South Korea
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Lee JB, Jeong C, Cho WK, Ban C, Fishel R. Distinct Conformational Changes of MutS during DNA Mismatch Repair. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.1527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
39
|
Jeong C, Cho WK, Song KM, Cook C, Yoon TY, Ban C, Fishel R, Lee JB. MutS switches between two fundamentally distinct clamps during mismatch repair. Nat Struct Mol Biol 2011; 18:379-85. [PMID: 21278758 PMCID: PMC3060787 DOI: 10.1038/nsmb.2009] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 11/19/2010] [Indexed: 12/19/2022]
Abstract
Single molecule trajectory analysis has suggested DNA repair proteins may perform a 1–dimensional (1D) search on naked DNA encompassing >10,000 nucleotides. Organized cellular DNA (chromatin) presents substantial barriers to such lengthy searches. Using dynamic single molecule fluorescence resonance energy transfer (smFRET) we determined that the mismatch repair (MMR) initiation protein MutS forms a transient clamp that scans duplex DNA for mismatched nucleotides by 1D diffusion for 1 sec (~700 bp) while in continuous rotational contact with the DNA. Mismatch identification provokes ATP binding (3 s) that induces distinctly different MutS sliding clamps with unusual stability on DNA (~600 s), which may be released by adjacent single–stranded DNA (ssDNA). These observations suggest that ATP transforms short–lived MutS lesion scanning clamps into highly stable MMR signaling clamps capable of competing with chromatin and recruiting MMR machinery, yet are recycled by ssDNA excision tracts.
Collapse
Affiliation(s)
- Cherlhyun Jeong
- Department of Physics, Pohang University of Science and Technology, Pohang, Korea
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Park J, Jeon Y, In D, Fishel R, Ban C, Lee JB. Single-molecule analysis reveals the kinetics and physiological relevance of MutL-ssDNA binding. PLoS One 2010; 5:e15496. [PMID: 21103398 PMCID: PMC2980497 DOI: 10.1371/journal.pone.0015496] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 10/02/2010] [Indexed: 01/30/2023] Open
Abstract
DNA binding by MutL homologs (MLH/PMS) during mismatch repair (MMR) has been considered based on biochemical and genetic studies. Bulk studies with MutL and its yeast homologs Mlh1-Pms1 have suggested an integral role for a single-stranded DNA (ssDNA) binding activity during MMR. We have developed single-molecule Förster resonance energy transfer (smFRET) and a single-molecule DNA flow-extension assays to examine MutL interaction with ssDNA in real time. The smFRET assay allowed us to observe MutL-ssDNA association and dissociation. We determined that MutL-ssDNA binding required ATP and was the greatest at ionic strength below 25 mM (K(D) = 29 nM) while it dramatically decreases above 100 mM (K(D)>2 µM). Single-molecule DNA flow-extension analysis suggests that multiple MutL proteins may bind ssDNA at low ionic strength but this activity does not enhance stability at elevated ionic strengths. These studies are consistent with the conclusion that a stable MutL-ssDNA interaction is unlikely to occur at physiological salt eliminating a number of MMR models. However, the activity may infer some related dynamic DNA transaction process during MMR.
Collapse
Affiliation(s)
- Jonghyun Park
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Kyungbuk, Republic of Korea
| | - Yongmoon Jeon
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Kyungbuk, Republic of Korea
| | - Daekil In
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Kyungbuk, Republic of Korea
| | - Richard Fishel
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, Ohio, United States of America
- Physics Department, The Ohio State University, Columbus, Ohio, United States of America
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Kyungbuk, Republic of Korea
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Kyungbuk, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Kyungbuk, Republic of Korea
| |
Collapse
|
41
|
Min K, Song KM, Cho M, Chun YS, Shim YB, Ku JK, Ban C. Simultaneous electrochemical detection of both PSMA (+) and PSMA (-) prostate cancer cells using an RNA/peptide dual-aptamer probe. Chem Commun (Camb) 2010; 46:5566-8. [PMID: 20407731 DOI: 10.1039/c002524k] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using an RNA/peptide dual-aptamer probe, both PSMA (+) and PSMA (-) prostate cancer cells were simultaneously detected by electrochemical impedance spectroscopy. This approach can be applied as a general tool for early diagnosis of prostate cancer.
Collapse
Affiliation(s)
- Kyoungin Min
- Department of Chemistry, Pohang University of Science and Technology, San31, Hyoja-dong, Pohang, Gyungbuk, 790-784, South Korea
| | | | | | | | | | | | | |
Collapse
|
42
|
Kim DM, Rahman MA, Do MH, Ban C, Shim YB. An amperometric chloramphenicol immunosensor based on cadmium sulfide nanoparticles modified-dendrimer bonded conducting polymer. Biosens Bioelectron 2010; 25:1781-8. [DOI: 10.1016/j.bios.2009.12.024] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2009] [Revised: 12/19/2009] [Accepted: 12/21/2009] [Indexed: 11/30/2022]
|
43
|
Park J, Jeon YM, In D, Heo SD, Ban C, Lee JB. Single-Molecule Studies of the ssDNA Binding Activity of E. Coli MutL. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
|
44
|
Kim S, Kim TG, Byon HR, Shin HJ, Ban C, Choi HC. Recognition of single mismatched DNA using MutS-immobilized carbon nanotube field effect transistor devices. J Phys Chem B 2009; 113:12164-8. [PMID: 19685907 DOI: 10.1021/jp9063559] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Label-free and real-time detections of mismatched dsDNAs are demonstrated using MutS-protein-immobilized, single-walled carbon nanotube field effect transistor (SWNT-FET) devices. The E. coli MutS proteins specifically recognizing mismatched dsDNAs are immobilized on SWNT-FET devices that have been fabricated for high sensitivity using a shadow mask lithographic technique to obtain a thin and wide Schottky contact region. The MutS-immobilized SWNT-FETs have successfully detected 40 base pair dsDNAs having single G-T mismatches at the 20th base pair positions by displaying significant electrical conductance drops at as low as 100 pM concentration. Systematic control experiments have revealed that the signal changes indeed originated from specific recognitions of mismatched DNAs by the immobilized MutS proteins.
Collapse
|
45
|
Heo SD, Ku JK, Ban C. Effect of E. coli MutL on the steady-state ATPase activity of MutS in the presence of short blocked end DNAs. Biochem Biophys Res Commun 2009; 385:225-9. [DOI: 10.1016/j.bbrc.2009.05.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 05/11/2009] [Indexed: 10/20/2022]
|
46
|
Chang CI, Kang HS, Ban C, Kim S, Lee DK. Dual-target gene silencing by using long, synthetic siRNA duplexes without triggering antiviral responses. Mol Cells 2009; 27:689-95. [PMID: 19533030 DOI: 10.1007/s10059-009-0093-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 05/20/2009] [Accepted: 05/20/2009] [Indexed: 12/18/2022] Open
Abstract
Chemically synthesized small interfering RNAs (siRNAs) can specifically knock-down expression of target genes via RNA interference (RNAi) pathway. To date, the length of synthetic siRNA duplex has been strictly maintained less than 30 bp, because an early study suggested that double-stranded RNAs (dsRNAs) longer than 30 bp could not trigger specific gene silencing due to the induction of nonspecific antiviral interferon responses. Contrary to the current belief, here we show that synthetic dsRNA as long as 38 bp can result in specific target gene silencing without nonspecific antiviral responses. Using this longer duplex structure, we have generated dsRNAs, which can simultaneously knock-down expression of two target genes (termed as dual-target siRNAs or dsiRNAs). Our results thus demonstrate the structural flexibility of gene silencing siRNAs, and provide a starting point to construct multifunctional RNA structures. The dsiRNAs could be utilized to develop a novel therapeutic gene silencing strategy against diseases with multiple gene alternations such as viral infection and cancer.
Collapse
Affiliation(s)
- Chan Il Chang
- Global Research Laboratory for RNAi Medicine, Department of Chemistry and Brain Korea 21 School of Chemical Materials Science, Sungkyunkwan University, Suwon 440-746, Korea
| | | | | | | | | |
Collapse
|
47
|
Abstract
The methyl-directed mismatch repair (MMR) mechanism has been extensively studied in vitro and in vivo, but one of the difficulties in determining the biological relationships between the MMR-related proteins is the tendency of MutL to self-aggregate. The properties of a stable MutL homologue were investigated using a thermostable MutL (TmL) from Thermotoga maritima MSB8 and whose size exclusion chromatographic and crosslinking analyses were compatible with a dimeric form of TmL. TmL underwent conformational changes in the presence of nucleotides and single-stranded DNA (ssDNA) with ATP binding not requiring ssDNA binding activity of TmL, while ADPnP-stimulated TmL showed a high ssDNA binding affinity. Finally, TmL interacted with the T. maritima MutS (TmS), increasing the affinity of TmS to mismatched DNA base pairs and suggesting that the role of TmL in the formation of a mismatched DNA-TmS complex may be a pivotal observation for the study of the initial MMR system. [BMB reports 2009; 42(1): 53-58].
Collapse
Affiliation(s)
- Tae Gyun Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784, Korea
| | | | | | | |
Collapse
|
48
|
Kim TG, Kwon TH, Min K, Dong MS, Park YI, Ban C. Crystal structures of substrate and inhibitor complexes of ribose 5-phosphate isomerase A from Vibrio vulnificus YJ016. Mol Cells 2009; 27:99-103. [PMID: 19214439 DOI: 10.1007/s10059-009-0010-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 10/28/2008] [Indexed: 11/27/2022] Open
Abstract
Ribose-5-phosphate isomerase A (RpiA) plays an important role in interconverting between ribose-5-phosphate (R5P) and ribulose-5-phosphate in the pentose phosphate pathway and the Calvin cycle. We have determined the crystal structures of the open form RpiA from Vibrio vulnificus YJ106 (VvRpiA) in complex with the R5P and the closed form with arabinose-5-phosphate (A5P) in parallel with the apo VvRpiA at 2.0 A resolution. VvRpiA is highly similar to Eschericihia coliRpiA, and the VvRpiA-R5P complex strongly resembles the E. coli RpiA-A5P complex. Interestingly, unlike the E. coli RpiA-A5P complex, the position of A5P in the VvRpiA-A5P complex reveals a different position than the R5P binding mode. VvRpiA-A5P has a sugar ring inside the binding pocket and a phosphate group outside the binding pocket: By contrast, the sugar ring of A5P interacts with the Asp4, Lys7, Ser30, Asp118, and Lys121 residues; the phosphate group of A5P interacts with two water molecules, W51 and W82.
Collapse
Affiliation(s)
- Tae Gyun Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | | | | | | | | | | |
Collapse
|
49
|
Chang CI, Yoo JW, Hong SW, Lee SE, Kang HS, Sun X, Rogoff HA, Ban C, Kim S, Li CJ, Lee DK. Asymmetric shorter-duplex siRNA structures trigger efficient gene silencing with reduced nonspecific effects. Mol Ther 2009; 17:725-32. [PMID: 19156133 DOI: 10.1038/mt.2008.298] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Small interfering RNAs (siRNAs) are short, double-stranded RNAs that mediate efficient gene silencing in a sequence-specific manner by utilizing the endogenous RNA interference (RNAi) pathway. The current standard synthetic siRNA structure harbors a 19-base-pair duplex region with 3' overhangs of 2 nucleotides (the so-called 19+2 form). However, the synthetic 19+2 siRNA structure exhibits several sequence-independent, nonspecific effects, which has posed challenges to the development of RNAi therapeutics and specific silencing of genes in research. In this study, we report on the identification of truncated siRNA backbone structures with duplex regions shorter than 19 bp (referred to as asymmetric shorter-duplex siRNAs or asiRNAs) that can efficiently trigger gene silencing in human cell lines. Importantly, this asiRNA structure significantly reduces nonspecific effects triggered by conventional 19+2 siRNA scaffold, such as sense-strand-mediated off-target gene silencing and saturation of the cellular RNAi machinery. Our results suggest that this asiRNA structure is an important alternative to conventional siRNAs for both functional genomics studies and therapeutic applications.
Collapse
Affiliation(s)
- Chan Il Chang
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Kim TG, Cha HJ, Lee HJ, Heo SD, Choi KY, Ku JK, Ban C. Structural insights of the nucleotide-dependent conformational changes of Thermotoga maritima MutL using small-angle X-ray scattering analysis. J Biochem 2008; 145:199-206. [PMID: 19029144 DOI: 10.1093/jb/mvn157] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MutL is required to assist the mismatch repair protein MutS during initiation of the methyl-directed mismatch repair (MMR) response in various organisms ranging from prokaryotes to eukaryotes. Despite this necessity, the inherent propensity of MutL to aggregate has led to significant difficulties in determining its biological relationship with other MMR-related proteins. Here, we perform analysis on the thermostable MutL protein found in Thermotoga maritima MSB8 (TmL). Size exclusion chromatographic analysis indicates the lack of aggregated forms with the exception of a dimeric TmL. Small-angle X-ray scattering (SAXS) analysis reveals that the solution structures of the full-length TmL and its corresponding complexes with nucleotides and ssDNA undergo conformational changes. The elucidated TmL SAXS model is superimposed to the crystal structure of the C-terminal domain of Escherichia coli MutL. In addition, the N-terminal SAXS model of TmL exists as monomeric form, indicating that TmL has a structurally flexible N-terminal domain. TmL SAXS analysis can suggest a considerable possibility on a new 3D view of the previously unresolved full-length MutL molecule.
Collapse
Affiliation(s)
- Tae Gyun Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk 790-784, Korea
| | | | | | | | | | | | | |
Collapse
|