1
|
Mohsen M, Midy MK, Balaji A, Breaker RR. Engineered Branaplam Aptamers Exploit Structural Elements from Natural Riboswitches. ACS Chem Biol 2024; 19:1447-1452. [PMID: 38954594 PMCID: PMC11267568 DOI: 10.1021/acschembio.4c00358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 07/04/2024]
Abstract
Drug candidates that fail in clinical trials for efficacy reasons might still have favorable safety and bioavailability characteristics that could be exploited. A failed drug candidate could be repurposed if a receptor, such as an aptamer, were created that binds the compound with high specificity. Branaplam is a small molecule that was previously in development to treat spinal muscular atrophy and Huntington's disease. Here, we report the development of a small (48-nucleotide) RNA aptamer for branaplam with a dissociation constant of ∼150 nM. Starting with a combinatorial RNA pool integrating the secondary and tertiary structural scaffold of a Guanine-I riboswitch aptamer interspersed with regions of random sequence, in vitro selection yielded aptamer candidates for branaplam. Reselection and rational design were employed to improve binding of a representative branaplam aptamer candidate. A resulting variant retains the pseudoknot and two of the paired elements (P2 and P3) from the scaffold but lacks the enclosing paired element (P1) that is essential for the function of the natural Guanine-I riboswitch aptamer. A second combinatorial RNA pool based on the scaffold for TPP (thiamin pyrophosphate) riboswitches also yielded a candidate offering additional opportunities for branaplam aptamer development.
Collapse
Affiliation(s)
- Michael
G. Mohsen
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
- Howard
Hughes Medical Institute, Yale University, New Haven, Connecticut 06511, United States
| | - Matthew K. Midy
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Aparaajita Balaji
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
| | - Ronald R. Breaker
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
- Howard
Hughes Medical Institute, Yale University, New Haven, Connecticut 06511, United States
| |
Collapse
|
2
|
Domsicova M, Korcekova J, Poturnayova A, Breier A. New Insights into Aptamers: An Alternative to Antibodies in the Detection of Molecular Biomarkers. Int J Mol Sci 2024; 25:6833. [PMID: 38999943 PMCID: PMC11240909 DOI: 10.3390/ijms25136833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024] Open
Abstract
Aptamers are short oligonucleotides with single-stranded regions or peptides that recently started to transform the field of diagnostics. Their unique ability to bind to specific target molecules with high affinity and specificity is at least comparable to many traditional biorecognition elements. Aptamers are synthetically produced, with a compact size that facilitates deeper tissue penetration and improved cellular targeting. Furthermore, they can be easily modified with various labels or functional groups, tailoring them for diverse applications. Even more uniquely, aptamers can be regenerated after use, making aptasensors a cost-effective and sustainable alternative compared to disposable biosensors. This review delves into the inherent properties of aptamers that make them advantageous in established diagnostic methods. Furthermore, we will examine some of the limitations of aptamers, such as the need to engage in bioinformatics procedures in order to understand the relationship between the structure of the aptamer and its binding abilities. The objective is to develop a targeted design for specific targets. We analyse the process of aptamer selection and design by exploring the current landscape of aptamer utilisation across various industries. Here, we illuminate the potential advantages and applications of aptamers in a range of diagnostic techniques, with a specific focus on quartz crystal microbalance (QCM) aptasensors and their integration into the well-established ELISA method. This review serves as a comprehensive resource, summarising the latest knowledge and applications of aptamers, particularly highlighting their potential to revolutionise diagnostic approaches.
Collapse
Affiliation(s)
- Michaela Domsicova
- Centre of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.D.); (J.K.); (A.P.)
| | - Jana Korcekova
- Centre of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.D.); (J.K.); (A.P.)
| | - Alexandra Poturnayova
- Centre of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.D.); (J.K.); (A.P.)
| | - Albert Breier
- Centre of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.D.); (J.K.); (A.P.)
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 81237 Bratislava, Slovakia
| |
Collapse
|
3
|
Park SV, Kang B, Lee M, Yoo H, Jo H, Woo S, Oh SS. In vitro selection of a trans aptamer complex for target-responsive fluorescence activation. Anal Chim Acta 2024; 1301:342465. [PMID: 38553123 DOI: 10.1016/j.aca.2024.342465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/23/2024] [Accepted: 03/10/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Most biological molecular complexes consist of multiple functional domains, yet rationally constructing such multifunctional complexes is challenging. Aptamers, the nucleic acid-based functional molecules, can perform multiple tasks including target recognition, conformational changes, and enzymatic activities, while being chemically synthesizable and tunable, and thus provide a basis for engineering enhanced functionalities through combination of multiple units. However, the conventional approach of simply combining aptamer units in a serial manner is susceptible to undesired crosstalk or interference between the aptamer units and to false interactions with non-target molecules; besides, the approach would require additional mechanisms to separate the units if they are desired to function independently. It is clearly a challenge to develop multi-aptamer complexes that preserve independent functions of each unit while avoiding undesired interference and non-specific interactions. RESULTS By directly in vitro selecting a 'trans' aptamer complex, we demonstrate that one aptamer unit ('utility module') can remain hidden or 'inactive' until a target analyte triggers the other unit ('sensing module') and separates the two aptamers. Since the operation of the utility module occurs free from the sensing module, unnecessary crosstalk between the two units can be avoided. Because the utility module is kept inactive until separated from the complex, non-specific interactions of the hidden module with noncognate targets can be naturally prevented. In our demonstration, the sensing module was selected to detect serotonin, a clinically important neurotransmitter, and the target-binding-induced structure-switching of the sensing module reveals and activates the utility module that turns on a fluorescence signal. The aptamer complex exhibited a moderately high affinity and an excellent specificity for serotonin with ∼16-fold discrimination against common neurotransmitter molecules, and displayed strong robustness to perturbations in the design, disallowing nonspecific reactions against various challenges. SIGNIFICANCE This work represents the first example of a trans aptamer complex that was in vitro selected de novo. The trans aptamer complex selected by our strategy does not require chemical modifications or immediate optimization processes to function, because the complex is directly selected to perform desired functions. This strategy should be applicable to a wide range of functional nucleic acid moieties, which will open up diverse applications in biosensing and molecular therapeutics.
Collapse
Affiliation(s)
- Soyeon V Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Byunghwa Kang
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Minjong Lee
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Hyebin Yoo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Hyesung Jo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Sungwook Woo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea.
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea.
| |
Collapse
|
4
|
Abdeeva IA, Maloshenok LG, Pogorelko GV, Bruskin SA. Using an RNA Aptamer to Inhibit the Action of Effector Proteins of Plant Pathogens. Int J Mol Sci 2023; 24:16604. [PMID: 38068927 PMCID: PMC10705891 DOI: 10.3390/ijms242316604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/10/2023] [Accepted: 11/18/2023] [Indexed: 12/18/2023] Open
Abstract
In previous work, we experimentally demonstrated the possibility of using RNA aptamers to inhibit endogenous protein expression and their function within plant cells In the current work, we show that our proposed method is suitable for inhibiting the functions of exogenous, foreign proteins delivered into the plant via various mechanisms, including pathogen proteins. Stringent experimentation produced robust RNA aptamers that are able to bind to the recombinant HopU1 effector protein of P. syringae bacteria. This research uses genetic engineering methods to constitutively express/transcribe HopU1 RNA aptamers in transgenic A. thaliana. Our findings support the hypothesis that HopU1 aptamers can actively interfere with the function of the HopU1 protein and thereby increase resistance to phytopathogens of the genus P. syringae pv. tomato DC 3000.
Collapse
Affiliation(s)
- Inna A. Abdeeva
- N.I. Vavilov Institute of General Genetics Russian Academy of Sciences, Gubkina Str. 3, 119333 Moscow, Russia (S.A.B.)
| | - Liliya G. Maloshenok
- N.I. Vavilov Institute of General Genetics Russian Academy of Sciences, Gubkina Str. 3, 119333 Moscow, Russia (S.A.B.)
| | - Gennady V. Pogorelko
- N.I. Vavilov Institute of General Genetics Russian Academy of Sciences, Gubkina Str. 3, 119333 Moscow, Russia (S.A.B.)
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Sergey A. Bruskin
- N.I. Vavilov Institute of General Genetics Russian Academy of Sciences, Gubkina Str. 3, 119333 Moscow, Russia (S.A.B.)
| |
Collapse
|
5
|
Gibaut QR, Bush JA, Tong Y, Baisden JT, Taghavi A, Olafson H, Yao X, Childs-Disney JL, Wang ET, Disney MD. Transcriptome-Wide Studies of RNA-Targeted Small Molecules Provide a Simple and Selective r(CUG) exp Degrader in Myotonic Dystrophy. ACS CENTRAL SCIENCE 2023; 9:1342-1353. [PMID: 37521782 PMCID: PMC10375898 DOI: 10.1021/acscentsci.2c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Indexed: 08/01/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is caused by a highly structured RNA repeat expansion, r(CUG)exp, harbored in the 3' untranslated region (3' UTR) of dystrophia myotonica protein kinase (DMPK) mRNA and drives disease through a gain-of-function mechanism. A panel of low-molecular-weight fragments capable of reacting with RNA upon UV irradiation was studied for cross-linking to r(CUG)expin vitro, affording perimidin-2-amine diazirine (1) that bound to r(CUG)exp. The interactions between the small molecule and RNA were further studied by nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. Binding of 1 in DM1 myotubes was profiled transcriptome-wide, identifying 12 transcripts including DMPK that were bound by 1. Augmenting the functionality of 1 with cleaving capability created a chimeric degrader that specifically targets r(CUG)exp for elimination. The degrader broadly improved DM1-associated defects as assessed by RNA-seq, while having limited effects on healthy myotubes. This study (i) provides a platform to investigate molecular recognition of ligands directly in disease-affected cells; (ii) illustrates that RNA degraders can be more specific than the binders from which they are derived; and (iii) suggests that repeating transcripts can be selectively degraded due to the presence of multiple ligand binding sites.
Collapse
Affiliation(s)
- Quentin
M. R. Gibaut
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica A. Bush
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yuquan Tong
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jared T. Baisden
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Amirhossein Taghavi
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Hailey Olafson
- Center
for NeuroGenetics, University of Florida, Gainesville, Florida 32610, United States
- Department
of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Xiyuan Yao
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica L. Childs-Disney
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Eric T. Wang
- Center
for NeuroGenetics, University of Florida, Gainesville, Florida 32610, United States
- Department
of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Matthew D. Disney
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| |
Collapse
|
6
|
Yik EJ, Medina E, Paegel BM, Chaput JC. Highly Parallelized Screening of Functionally Enhanced XNA Aptamers in Uniform Hydrogel Particles. ACS Synth Biol 2023. [PMID: 37410977 DOI: 10.1021/acssynbio.3c00189] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Xeno-nucleic acid (XNA) aptamers based on evolvable non-natural genetic polymers hold enormous potential as future diagnostic and therapeutic agents. However, time-consuming and costly procedures requiring the purification of individual XNA sequences produced by large-scale polymerase-mediated primer extension reactions pose a major bottleneck to the discovery of highly active XNA motifs for biomedical applications. Here, we describe a straightforward approach for rapidly surveying the binding properties of XNA aptamers identified by in vitro selection. Our strategy involves preparing XNA aptamer particles in which many copies of the same aptamer sequence are distributed throughout the gel matrix of a polyacrylamide-encapsulated magnetic particle. Aptamer particles are then screened by flow cytometry to assess target binding affinity and deduce structure-activity relationships. This generalizable and highly parallel assay dramatically accelerates the pace of secondary screening by allowing a single researcher to evaluate 48-96 sequences per day.
Collapse
Affiliation(s)
- E J Yik
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697-3958, United States
| | - E Medina
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697-3958, United States
| | - B M Paegel
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697-3958, United States
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-3958, United States
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697-3958, United States
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-3958, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697-3958, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3958, United States
| |
Collapse
|
7
|
Ai L, Jiang X, Zhang K, Cui C, Liu B, Tan W. Tools and techniques for the discovery of therapeutic aptamers: recent advances. Expert Opin Drug Discov 2023; 18:1393-1411. [PMID: 37840268 DOI: 10.1080/17460441.2023.2264187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023]
Abstract
INTRODUCTION The pursuit of novel therapeutic agents for serious diseases such as cancer has been a global endeavor. Aptamers characteristic of high affinity, programmability, low immunogenicity, and rapid permeability hold great promise for the treatment of diseases. Yet obtaining the approval for therapeutic aptamers remains challenging. Consequently, researchers are increasingly devoted to exploring innovative strategies and technologies to advance the development of these therapeutic aptamers. AREAS COVERED The authors provide a comprehensive summary of the recent progress of the SELEX (Systematic Evolution of Ligands by EXponential enrichment) technique, and how the integration of modern tools has facilitated the identification of therapeutic aptamers. Additionally, the engineering of aptamers to enhance their functional attributes, such as inhibiting and targeting, is discussed, demonstrating the potential to broaden their scope of utility. EXPERT OPINION The grand potential of aptamers and the insufficient development of relevant drugs have spurred countless efforts for stimulating their discovery and application in the therapeutic field. While SELEX techniques have undergone significant developments with the aid of advanced analysis instruments and ingeniously updated aptameric engineering strategies, several challenges still impede their clinical translation. A key challenge lies in the insufficient understanding of binding conformation and susceptibility to degradation under physiological conditions. Despite the hurdles, our opinion is optimistic. With continued progress in overcoming these obstacles, the widespread utilization of aptamers for clinical therapy is envisioned to become a reality soon.
Collapse
Affiliation(s)
- Lili Ai
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
| | - Xinyi Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
| | - Kejing Zhang
- Department of Geriatrics and Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, The People's Republic of China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, The People's Republic of China
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
| | - Bo Liu
- Department of Geriatrics and Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, The People's Republic of China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, The People's Republic of China
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, The People's Republic of China
| |
Collapse
|
8
|
Su Y, Huang Y, Kou Q, Lu L, Jiang H, Li X, Gui R, Huang R, Huang X, Ma J, Li J, Nie X. Study on the Role of an Erythrocyte Membrane-Coated Nanotheranostic System in Targeted Immune Regulation of Alzheimer's Disease. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301361. [PMID: 37075744 PMCID: PMC10288270 DOI: 10.1002/advs.202301361] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/18/2023] [Indexed: 05/03/2023]
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative diseases in the elderly population. Despite significant advances in studies of the pathobiology on AD, there is still no effective treatment. Here, an erythrocyte membrane-camouflaged nanodrug delivery system (TR-ZRA) modified with transferrin receptor aptamers that can be targeted across the blood-brain barrier to ameliorate AD immune environment is established. Based on metal-organic framework (Zn-CA), TR-ZRA is loaded with CD22shRNA plasmid to silence the abnormally high expression molecule CD22 in aging microglia. Most importantly, TR-ZRA can enhance the ability of microglia to phagocytose Aβ and alleviate complement activation, which can promote neuronal activity and decrease inflammation level in the AD brain. Moreover, TR-ZRA is also loaded with Aβ aptamers, which allow rapid and low-cost monitoring of Aβ plaques in vitro. After treatment with TR-ZRA, learning, and memory abilities are enhanced in AD mice. In conclusion, the biomimetic delivery nanosystem TR-ZRA in this study provides a promising strategy and novel immune targets for AD therapy.
Collapse
Affiliation(s)
- Yanrong Su
- Department of Laboratory MedicineThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Yufen Huang
- Department of Laboratory MedicineThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Qinjie Kou
- Department of Laboratory MedicineThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Lu Lu
- Department of Blood TransfusionThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Haiye Jiang
- Department of Laboratory MedicineThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Xisheng Li
- Department of Laboratory MedicineThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Rong Gui
- Department of Blood TransfusionThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Rong Huang
- Department of Blood TransfusionThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Xueyuan Huang
- Department of Blood TransfusionThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Jinqi Ma
- Department of Blood TransfusionThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Jian Li
- Department of Blood TransfusionThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
| | - Xinmin Nie
- Department of Laboratory MedicineThe Third Xiangya HospitalCentral South UniversityNo.138,Tongzipo Road,Yuelu DistrictChangshaHunan410013China
- Hunan Engineering Technology Research Center of Optoelectronic Health DetectionChangshaHunan410000China
| |
Collapse
|
9
|
Lee SY, Jang DH, Kim H, Yun M. Removal and isolation of radioactive cobalt using DNA aptamers. RADIOCHIM ACTA 2023. [DOI: 10.1515/ract-2022-0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Abstract
Electricity generation using nuclear power has various advantages, such as carbon reduction, but the treatment of nuclear waste is emerging as a big issue in many countries. The development of technology that can selectively remove radionuclides from liquid radioactive waste is one of the ways to reduce nuclear waste. Here, we assessed a new way of removing radioactive cobalt from a liquid using an aptamer. Aptamers specifically binding cobalt ions were selected through systematic evolution of ligands by exponential enrichment (SELEX). Their binding strength and stability of their complexes with cobalt were analyzed through surface plasmon resonance assay and 2D program Mfold, respectively. The optimal aptamer/bead conjugate conditions for binding cobalt were established using an FA-C1 aptamer with the strongest binding to cobalt. Under these conditions, more than 80% of radioactive cobalt was removed, and more than 99.95% of removed cobalt was recovered. These results proved that radioactive cobalt removal using this aptamer can effectively reduce liquid radioactive waste. This means that the aptamer/bead complex can be utilized to remove various radioactive metal ions.
Collapse
Affiliation(s)
- Sun Young Lee
- Laboratory of Functional Aptamers, Department of Bioindustry and Bioresource Engineering , College of Life Sciences, Sejong University , Seoul , South Korea
- Resource Upcycling and Discovery Research Institute, Sejong University , Seoul , South Korea
| | - Dae Hyuk Jang
- Laboratory of Functional Aptamers, Department of Bioindustry and Bioresource Engineering , College of Life Sciences, Sejong University , Seoul , South Korea
- Resource Upcycling and Discovery Research Institute, Sejong University , Seoul , South Korea
| | - Hyuncheol Kim
- Environmental Radioactivity Assessment Team , Korea Atomic Energy Research Institute , Daejeon , South Korea
| | - Miyong Yun
- Laboratory of Functional Aptamers, Department of Bioindustry and Bioresource Engineering , College of Life Sciences, Sejong University , Seoul , South Korea
- Environmental Radioactivity Assessment Team , Korea Atomic Energy Research Institute , Daejeon , South Korea
| |
Collapse
|
10
|
Wang J, Sha CM, Dokholyan NV. Combining Experimental Restraints and RNA 3D Structure Prediction in RNA Nanotechnology. Methods Mol Biol 2023; 2709:51-64. [PMID: 37572272 PMCID: PMC10680996 DOI: 10.1007/978-1-0716-3417-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Precise RNA tertiary structure prediction can aid in the design of RNA nanoparticles. However, most existing RNA tertiary structure prediction methods are limited to small RNAs with relatively simple secondary structures. Large RNA molecules usually have complex secondary structures, including multibranched loops and pseudoknots, allowing for highly flexible RNA geometries and multiple stable states. Various experiments and bioinformatics analyses can often provide information about the distance between atoms (or residues) in RNA, which can be used to guide the prediction of RNA tertiary structure. In this chapter, we will introduce a platform, iFoldNMR, that can incorporate non-exchangeable imino protons resonance data from NMR as restraints for RNA 3D structure prediction. We also introduce an algorithm, DVASS, which optimizes distance restraints for better RNA 3D structure prediction.
Collapse
Affiliation(s)
- Jian Wang
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA
| | - Congzhou M Sha
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA
- Department of Engineering Science and Mechanics, Penn State University, State College, PA, USA
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA.
- Department of Engineering Science and Mechanics, Penn State University, State College, PA, USA.
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA.
- Department of Chemistry, Penn State University, State College, PA, USA.
- Department of Biomedical Engineering, Penn State University, State College, PA, USA.
| |
Collapse
|
11
|
Wu L, Zhang Y, Wang Z, Zhang Y, Zou J, Qiu L. Aptamer-Based Cancer Cell Analysis and Treatment. Chemistry 2022; 11:e202200141. [PMID: 36264016 PMCID: PMC9583543 DOI: 10.1002/open.202200141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/31/2022] [Indexed: 11/09/2022]
Abstract
Aptamers are a class of single-stranded DNA or RNA oligonucleotides that can exclusively bind to various targets with high affinity and selectivity. Regarded as "chemical antibodies", aptamers possess several intrinsic advantages, including easy synthesis, convenient modification, high programmability, and good biocompatibility. In recent decades, many studies have demonstrated the superiority of aptamers as molecular tools for various biological applications, particularly in the area of cancer theranostics. In this review, we focus on recent progress in developing aptamer-based strategies for the precise analysis and treatment of cancer cells.
Collapse
Affiliation(s)
- Limei Wu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan ProvinceHunan UniversityChangsha, Hunan410082P. R. China
| | - Yutong Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan ProvinceHunan UniversityChangsha, Hunan410082P. R. China
| | - Zhimin Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan ProvinceHunan UniversityChangsha, Hunan410082P. R. China
| | - Yue Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan ProvinceHunan UniversityChangsha, Hunan410082P. R. China
| | - Jianmei Zou
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and BioengineeringGuilin University of TechnologyGuilin, Guangxi541004P. R. China
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan ProvinceHunan UniversityChangsha, Hunan410082P. R. China
| |
Collapse
|
12
|
Onaş AM, Dascălu C, Raicopol MD, Pilan L. Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets. BIOSENSORS 2022; 12:816. [PMID: 36290952 PMCID: PMC9599214 DOI: 10.3390/bios12100816] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Nucleic-acid aptamers consisting in single-stranded DNA oligonucleotides emerged as very promising biorecognition elements for electrochemical biosensors applied in various fields such as medicine, environmental, and food safety. Despite their outstanding features, such as high-binding affinity for a broad range of targets, high stability, low cost and ease of modification, numerous challenges had to be overcome from the aptamer selection process on the design of functioning biosensing devices. Moreover, in the case of small molecules such as metabolites, toxins, drugs, etc., obtaining efficient binding aptamer sequences proved a challenging task given their small molecular surface and limited interactions between their functional groups and aptamer sequences. Thus, establishing consistent evaluation standards for aptamer affinity is crucial for the success of these aptamers in biosensing applications. In this context, this article will give an overview on the thermodynamic and structural aspects of the aptamer-target interaction, its specificity and selectivity, and will also highlight the current methods employed for determining the aptamer-binding affinity and the structural characterization of the aptamer-target complex. The critical aspects regarding the generation of aptamer-modified electrodes suitable for electrochemical sensing, such as appropriate bioreceptor immobilization strategy and experimental conditions which facilitate a convenient anchoring and stability of the aptamer, are also discussed. The review also summarizes some effective small molecule aptasensing platforms from the recent literature.
Collapse
Affiliation(s)
- Andra Mihaela Onaş
- Advanced Polymer Materials Group, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
| | - Constanţa Dascălu
- Faculty of Applied Sciences, University ‘Politehnica’ of Bucharest, 313 Splaiul Independenţei, District 6, 060042 Bucharest, Romania
| | - Matei D. Raicopol
- Faculty of Chemical Engineering and Biotechnologies, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
| | - Luisa Pilan
- Faculty of Chemical Engineering and Biotechnologies, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
| |
Collapse
|
13
|
Mukherjee M, Appaiah P, Sistla S, Bk B, Bhatt P. Bio-Layer Interferometry-Based SELEX and Label-Free Detection of Patulin Using Generated Aptamer. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6239-6246. [PMID: 35546052 DOI: 10.1021/acs.jafc.2c01591] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study reports a novel bio-layer interferometry (BLI)-based SELEX for generation of high affinity aptamers against patulin. Unlike conventional SELEX, the present method enabled real-time monitoring of increasing affinity of the oligonucleotides to the toxin. After seven rounds of selection cycles, the enriched pool of aptamers was characterized by cloning and sequencing and clustered into two families based on similarity. Two sequences, PAT C3 and PAT C4, each belonging to different clades, were further evaluated for their binding affinity. SPR studies determined the dissociation constants (KD) of 8.2 × 10-8 and 1.9 × 10-7 M for aptamer PAT C3 and PAT C4, respectively. The highest affinity PAT C3 aptamer was used to develop a patulin BLI aptasensor, which indicated a linear detection range from 0.045 to 100 ng/mL [limit of detection (LOD) = 0.173 ng/mL; limit of quantification (LOQ) = 0.526 ng/mL]. The aptasensor displayed no cross-reactivity with its structural analogue isopatulin or any of the other mycotoxin groups tested. Spiking studies in simulated apple juice samples showed recoveries in the range of 82.11 to 100.23%, indicating good sensor performance. The study is the first report of BLI-based SELEX for a non-protein toxin, which resulted in the generation of high affinity aptamers and development of an aptasensor which can have wide application in the food industry for high throughput screening of samples for patulin contamination within a short span of time.
Collapse
Affiliation(s)
- Monali Mukherjee
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysuru 570020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Prakruthi Appaiah
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysuru 570020, India
| | - Srinivas Sistla
- Department of Microbiology & Immunology, Stonybrook University, New York, New York 11794, United States
| | - Bettadaiah Bk
- Spices and Flavour Sciences Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysuru 570020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Praveena Bhatt
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysuru 570020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| |
Collapse
|
14
|
Non-immobilized GO-SELEX of aptamers for label-free detection of thiamethoxam in vegetables. Anal Chim Acta 2022; 1202:339677. [DOI: 10.1016/j.aca.2022.339677] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/26/2022] [Accepted: 03/02/2022] [Indexed: 12/19/2022]
|
15
|
Afosah DK, Ofori E, Mottamal M, Al-Horani RA. Factor IX(a) inhibitors: an updated patent review (2003-present). Expert Opin Ther Pat 2022; 32:381-400. [PMID: 34991418 DOI: 10.1080/13543776.2022.2026926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Anticoagulation with no bleeding complications is the current objective of drug discovery programs in the area of treating and/or preventing thromboembolism. Despite the promises of therapeutics targeting factors XI(a) and XII(a), none has been approved thus far. Clinically used thrombin- and/or factor Xa-based anticoagulants continue to be associated with a significant bleeding risk which limits their safe use in a broad range of thrombotic patients. Research findings in animals and humans indicate that it is possible to target factor IX(a) (FIX(a)) to achieve anticoagulation with a limited risk of bleeding. AREAS COVERED A review of patents literature has retrieved >35 patents on the development of molecules targeting FIX(a) since 2003. Small molecules, antibodies, and aptamers have been developed to target FIX(a) to potentially promote effective and safer anticoagulation. Most of these agents are in the pre-clinical development phase and few have been tested in clinical trials. EXPERT OPINION FIX(a) system is being considered to develop new anticoagulants with fewer bleeding complications. Our survey indicates that the number of FIX(a)-targeting agents is mediocre. The agents under development are diverse. Although additional development is essential, moving one or more of these agents to the clinic will facilitate achieving better clinical outcomes.
Collapse
Affiliation(s)
- Daniel K Afosah
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, VA, USA
| | - Edward Ofori
- Department of Pharmaceutical Sciences, College of Pharmacy, Chicago State University, Chicago, IL, USA
| | - Madhusoodanan Mottamal
- Department of Chemistry, College of Arts and Sciences, Xavier University of Louisiana, New Orleans, LA, USA
| | - Rami A Al-Horani
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, Louisiana, USA
| |
Collapse
|
16
|
Wang Y, Liu X, Wu L, Ding L, Effah CY, Wu Y, Xiong Y, He L. Construction and bioapplications of aptamer-based dual recognition strategy. Biosens Bioelectron 2022; 195:113661. [PMID: 34592501 DOI: 10.1016/j.bios.2021.113661] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 02/08/2023]
Abstract
Aptamer-based dual recognition strategy, using dual aptamers or the cooperation of aptamers with other recognition elements, can better utilize the advantages of each recognition molecule and increase the design flexibility to effectively overcome the limitations of a single molecule recognition strategy, thereby improving the sensitivity and selectivity and facilitating the regulation of biological process. Hence, this review systematically tracks the construction and application of dual aptamers recognition strategy in the versatile detection of protein biomarkers, pathogenic microorganisms, cancer cells, and the treatment of some diseases and, more importantly, in functional regulation and imaging of cell-surface protein receptors. Then, the cooperation of aptamers with other recognition elements are briefly introduced. Potential challenges facing this field have been highlighted, aiming to expand bioanalytical applications of aptamer-based dual or multiple recognition strategies and meet the growing demand for precision medicine.
Collapse
Affiliation(s)
- Ya Wang
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Xinlian Liu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Longjie Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Lihua Ding
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Clement Yaw Effah
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yamin Xiong
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Leiliang He
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China.
| |
Collapse
|
17
|
Kim HR, Kim M, Kim BC. Specific detection of Cronobacter sakazakii in powdered infant formula using ssDNA aptamer. Analyst 2021; 146:3534-3542. [PMID: 33884389 DOI: 10.1039/d1an00118c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cronobacter sakazakii (C. sakazakii) is a foodborne pathogen associated with bacterial meningitis, sepsis, and necrotizing enterocolitis in premature and immuno-compromised infants. C. sakazakii is typically acquired by ingesting contaminated powdered infant formula (PIF). The growing demand for a safe food supply requires rapid detection of foodborne pathogens for delivering safe-to-consume food to consumers. In the present study, we isolated C. sakazakii-specific aptamers using a centrifugation-based partitioning method (CBPM) instead of systematic evolution of ligands by exponential enrichment (SELEX) process. Unlike SELEX, the CBPM reduces the evolution-loop time to obtain enriched probes, allowing the isolation of target-specific aptamers in a shorter time. The two aptamers (SC25 and SC45) isolated using the CBPM showed high affinity and specificity for C. sakazakii (Kd: 34 and 66 nM). Among the two aptamers, SC25 aptamer detected efficiently C. sakazakii in PIF with less cross-reactivity. Our results indicate that the isolated aptamers could be used for detecting C. sakazakii in PIF and reducing the overall testing time compared with the conventional C. sakazakii detection method.
Collapse
Affiliation(s)
- Hye Ri Kim
- Center for Environment, Health and Welfare Research, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. and Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Myunghee Kim
- Department of Food Science and Technology, Yeungnam University, 280 Daehak-ro, Gyeongsan-si, Gyeongsangbuk-do 38541, Republic of Korea
| | - Byoung Chan Kim
- Center for Environment, Health and Welfare Research, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. and Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| |
Collapse
|
18
|
Zhou L, Ding D, Szostak JW. The virtual circular genome model for primordial RNA replication. RNA (NEW YORK, N.Y.) 2021; 27:1-11. [PMID: 33028653 PMCID: PMC7749632 DOI: 10.1261/rna.077693.120] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/02/2020] [Indexed: 05/13/2023]
Abstract
We propose a model for the replication of primordial protocell genomes that builds upon recent advances in the nonenzymatic copying of RNA. We suggest that the original genomes consisted of collections of oligonucleotides beginning and ending at all possible positions on both strands of one or more virtual circular sequences. Replication is driven by feeding with activated monomers and by the activation of monomers and oligonucleotides in situ. A fraction of the annealed configurations of the protocellular oligonucleotides would allow for template-directed oligonucleotide growth by primer extension or ligation. Rearrangements of these annealed configurations, driven either by environmental fluctuations or occurring spontaneously, would allow for continued oligonucleotide elongation. Assuming that shorter oligonucleotides were more abundant than longer ones, replication of the entire genome could occur by the growth of all oligonucleotides by as little as one nucleotide on average. We consider possible scenarios that could have given rise to such protocell genomes, as well as potential routes to the emergence of catalytically active ribozymes and thus the more complex cells of the RNA World.
Collapse
Affiliation(s)
- Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dian Ding
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| |
Collapse
|
19
|
|
20
|
Rituximab-specific DNA aptamers are able to selectively recognize heat-treated antibodies. PLoS One 2020; 15:e0241560. [PMID: 33151990 PMCID: PMC7644011 DOI: 10.1371/journal.pone.0241560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/18/2020] [Indexed: 01/01/2023] Open
Abstract
The monoclonal anti-CD20 IgG1 antibody rituximab is used as a first-line treatment for B cell lymphoma. Like all therapeutic antibodies, it is a complex protein for which both safety and efficacy heavily depend on the integrity of its three-dimensional structure. Aptamers, short oligonucleotides with a distinct fold, can be used to detect minor modifications or structural variations of a molecule or protein. To detect antibody molecules in a fold state occurring prior to protein precipitation, we generated DNA aptamers that were selected for extensively heat-treated rituximab. Using the magnetic bead-based systematic evolution of ligands by exponential enrichment (SELEX), we obtained six DNA aptamer sequences (40-mers) specific for 80°C heat-treated rituximab. In silico fold prediction and circular dichroism analysis revealed a G-quadruplex structure for one aptamer, while all others exhibited a B-DNA helix. Binding affinities ranging from 8.8–86.7 nM were determined by an enzyme-linked apta-sorbent assay (ELASA). Aptamers additionally detected structural changes in rituximab treated for 5 min at 70°C, although with lower binding activity. Notably, none of the aptamers recognized rituximab in its native state nor did they detect the antibody after it was exposed to lower temperatures or different physical stressors. Aptamers also reacted with the therapeutic antibody adalimumab incubated at 80°C suggesting similar aptamer binding motifs located on extensively heat-treated IgG1 antibodies. Within this work, we obtained the first aptamer panel, which is specific for an antibody fold state specifically present prior to protein aggregation. This study demonstrates the potential of aptamer selection for specific stress-based protein variants, which has potential impact for quality control of biopharmaceuticals.
Collapse
|
21
|
Novel aptasensor-based assay of sonic hedgehog ligand for detection of portal vein invasion of hepatocellular carcinoma. Biosens Bioelectron 2020; 174:112738. [PMID: 33257185 DOI: 10.1016/j.bios.2020.112738] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/13/2022]
Abstract
The high expression of sonic hedgehog ligand (SHh) is closely correlated to the metastasis, drug resistance and poor prognosis of hepatocellular carcinoma (HCC). Therefore, sensitive, specific and efficient detection methods for SHh are needed for the early diagnosis and assessment of prognosis. Herein, an aptamer, AP32 that specifically binds to SHh (KD = 25.7 ± 4.1 nM) was obtained by SELEX technology with further optimization. In vivo experiments confirmed that AP32 has the potential to be an imaging probe for Huh-7 cell-derived xenograft. The interaction mode in 3-dimensional configuration between the aptamer and SHh was established by molecular simulation and confirmed by mutations at key sites of the aptamer. An aptasensor-based assay was successfully developed by conjugating Texas-Red-labeled AP32 to microbeads, and was used to analyze SHh content in hepatoma cell lysates, serum and HCC specimens. The method exhibited a broad detection range from 0.07 to 62.5 nM with a low detection limit of 69 pM, and a recovery rate of 104.6 ± 3.9% in serum. When the assay was used to measure SHh content in tissue lysates, the results demonstrated that it possessed 57.1% positivity, 100% specificity in distinguishing 28 HCC specimens from normal tissues, and was compensatory for detection of HCC in AFP-negative cases. Moreover, elevated SHh levels are indicative of portal vein invasion at 77.8% positive rate. This novel aptasensor-based SHh assay may offer a reliable means in predicting early metastasis and poor prognosis in hepatocellular carcinoma.
Collapse
|
22
|
Navien TN, Thevendran R, Hamdani HY, Tang TH, Citartan M. In silico molecular docking in DNA aptamer development. Biochimie 2020; 180:54-67. [PMID: 33086095 DOI: 10.1016/j.biochi.2020.10.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/23/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022]
Abstract
Aptamers are single-stranded DNA or RNA oligonucleotides generated by SELEX that exhibit binding affinity and specificity against a wide variety of target molecules. Compared to RNA aptamers, DNA aptamers are much more stable and therefore are widely adopted in a number of applications especially in diagnostics. The tediousness and rigor associated with certain steps of the SELEX intensify the efforts to adopt in silico molecular docking approaches together with in vitro SELEX procedures in developing DNA aptamers. Inspired by these endeavors, we carry out an overview of the in silico molecular docking approaches in DNA aptamer generation, by detailing the stepwise procedures as well as shedding some light on the various softwares used. The in silico maturation strategy and the limitations of the in silico approaches are also underscored.
Collapse
Affiliation(s)
- Tholasi Nadhan Navien
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Ramesh Thevendran
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Hazrina Yusof Hamdani
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| |
Collapse
|
23
|
Eilers A, Witt S, Walter J. Aptamer-Modified Nanoparticles in Medical Applications. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 174:161-193. [PMID: 32157319 DOI: 10.1007/10_2020_124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Since aptamers have been selected against a broad range of target structures of medical interest and nanoparticles are available with diverse properties, aptamer-modified nanoparticles can be used in various diagnostic and therapeutic applications. While the aptamer is responsible for specificity and affinity of the conjugate, the nanoparticles' function varies from signal generation in diagnostic approaches to drug loading in drug delivery systems. Within this chapter different medical applications of aptamer-modified nanoparticles will be summarized and underlying principles will be described.
Collapse
Affiliation(s)
- Alina Eilers
- Institut für Technische Chemie, Hannover, Germany
| | - Sandra Witt
- Institut für Technische Chemie, Hannover, Germany
| | | |
Collapse
|
24
|
Piccolo KA, McNeil B, Crouse J, Lim SJ, Bickers SC, Hopkins WS, Dieckmann T. Ligand specificity and affinity in the sulforhodamine B binding RNA aptamer. Biochem Biophys Res Commun 2020; 529:666-671. [PMID: 32736690 DOI: 10.1016/j.bbrc.2020.06.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 06/12/2020] [Indexed: 10/23/2022]
Abstract
Binding affinity and selectivity are critical properties of aptamers that must be optimized for any application. The sulforhodamine B binding RNA aptamer (SRB-2) is a somewhat promiscuous aptamer that can bind ligands that vary markedly in shape, size and charge. Here we categorize potential ligands based on their binding mode and structural characteristics required for high affinity and selectivity. Several known and potential ligands of SRB-2 were screened for binding affinity using LSPR, ITC and NMR spectroscopy. The study shows that rhodamine B has the ideal structural and electrostatic properties for selective and high-affinity binding of the SRB-2 aptamer.
Collapse
Affiliation(s)
- Kyle A Piccolo
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Brooke McNeil
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Jeff Crouse
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada; Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Su Ji Lim
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada; Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Sarah C Bickers
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada; Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Thorsten Dieckmann
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
| |
Collapse
|
25
|
Singh V. Ultrasensitive quantum dot-coupled-surface plasmon microfluidic aptasensor array for serum insulin detection. Talanta 2020; 219:121314. [PMID: 32887054 DOI: 10.1016/j.talanta.2020.121314] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/22/2022]
Abstract
Monitoring insulin levels in complex clinical matrices such as serum, holds immense importance in diagnosing type of diabetes. The present study reports the development of surface plasmon resonance aptamer based insulin sensor array in a four-channel microfluidic format which utilizes antibody attached to magnetic nanoparticles for capturing insulin from diabetic patient serum samples and surface immobilized plasmon enhancing quantum dots for signal amplification. The aptasensor gives minimal non-specific binding due to the immobilization of high molecular weight dendrimers on a cysteamine monolayer. The aptamer-insulin-antibody sandwich microarray monitors insulin levels in two-fold diluted serum and offers a detection limit 800 fM with a linear dynamic range 0.8-250 pM. Its clinical applicability on measuring serum insulin levels in 24 diabetic patient samples and correlation with ELISA is demonstrated.
Collapse
Affiliation(s)
- Vini Singh
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA.
| |
Collapse
|
26
|
Aptamer Selection for Detecting Molecular Target Using Cell-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) Technology. Methods Mol Biol 2020; 2054:223-241. [PMID: 31482459 DOI: 10.1007/978-1-4939-9769-5_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cell-SELEX is a live cell-based in vitro selection method that generates functional oligonucleotides, or aptamers. Often referenced as the chemist's antibody, aptamers bind to select targets with high affinity and can be utilized in a number of applications, including biomedicine, bioimaging, and biosensing. Here we describe the cell-SELEX technique and discuss this methodology's unique merit(s)-namely the ability to isolate highly selective aptamer panels with no prior knowledge of cellular signatures. This strategy thus presents as a technology that has the potential to enhance the precision of molecular medicine and targeted therapeutics.
Collapse
|
27
|
Panda PK, Saraf S, Tiwari A, Verma A, Raikwar S, Jain A, Jain SK. Novel Strategies for Targeting Prostate Cancer. Curr Drug Deliv 2020; 16:712-727. [PMID: 31433757 DOI: 10.2174/1567201816666190821143805] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/24/2019] [Accepted: 08/06/2019] [Indexed: 12/15/2022]
Abstract
Prostate cancer (PCa) is a worldwide issue, with a rapid increase in its occurrence and mortality. Over the years, various strategies have been implemented to overcome the hurdles that exist in the treatment of PCa. Consistently, there is a change in opinion about the methodologies in clinical trial that have engrossed towards the treatment of PCa. Currently, there is a need to resolve these newly recognized challenges by developing newer rational targeting systems. The ongoing clinical protocol for the therapy using different targeting systems is undertaken followed by local targeting to cancer site. A number of new drug targeting systems like liposomes, nanoemulsions, magnetic nanoparticles (MNPs), solid lipid nanoparticles, drug-peptide conjugate systems, drug-antibody conjugate systems, epigenetic and gene therapy approaches, and therapeutic aptamers are being developed to suit this protocol. Recent advancements in the treatment of PCa with various nanocarriers have been reported with respect to newly identified biological barriers and intended to solve the contexts. This review encompasses the input of nanotechnology in particular targeting of PCa which might escape the lifethreatening side effects and potentially contribute to bring fruitful clinical outcomes.
Collapse
Affiliation(s)
- Pritish Kumar Panda
- Pharmaceutics Research Projects Laboratory, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Central University, Sagar (M.P.), 470 003, India
| | - Shivani Saraf
- Pharmaceutics Research Projects Laboratory, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Central University, Sagar (M.P.), 470 003, India
| | - Ankita Tiwari
- Pharmaceutics Research Projects Laboratory, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Central University, Sagar (M.P.), 470 003, India
| | - Amit Verma
- Pharmaceutics Research Projects Laboratory, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Central University, Sagar (M.P.), 470 003, India
| | - Sarjana Raikwar
- Pharmaceutics Research Projects Laboratory, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Central University, Sagar (M.P.), 470 003, India
| | - Ankit Jain
- Institute of Pharmaceutical Research, GLA University, NH-2, Mathura-Delhi Road, Mathura (U.P.), 281 406, India
| | - Sanjay K Jain
- Pharmaceutics Research Projects Laboratory, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Central University, Sagar (M.P.), 470 003, India
| |
Collapse
|
28
|
Grau FC, Jaeger J, Groher F, Suess B, Muller YA. The complex formed between a synthetic RNA aptamer and the transcription repressor TetR is a structural and functional twin of the operator DNA-TetR regulator complex. Nucleic Acids Res 2020; 48:3366-3378. [PMID: 32052019 PMCID: PMC7102968 DOI: 10.1093/nar/gkaa083] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/22/2020] [Accepted: 02/11/2020] [Indexed: 02/06/2023] Open
Abstract
RNAs play major roles in the regulation of gene expression. Hence, designer RNA molecules are increasingly explored as regulatory switches in synthetic biology. Among these, the TetR-binding RNA aptamer was selected by its ability to compete with operator DNA for binding to the bacterial repressor TetR. A fortuitous finding was that induction of TetR by tetracycline abolishes both RNA aptamer and operator DNA binding in TetR. This enabled numerous applications exploiting both the specificity of the RNA aptamer and the efficient gene repressor properties of TetR. Here, we present the crystal structure of the TetR-RNA aptamer complex at 2.7 Å resolution together with a comprehensive characterization of the TetR–RNA aptamer versus TetR–operator DNA interaction using site-directed mutagenesis, size exclusion chromatography, electrophoretic mobility shift assays and isothermal titration calorimetry. The fold of the RNA aptamer bears no resemblance to regular B-DNA, and neither does the thermodynamic characterization of the complex formation reaction. Nevertheless, the functional aptamer-binding epitope of TetR is fully contained within its DNA-binding epitope. In the RNA aptamer complex, TetR adopts the well-characterized DNA-binding-competent conformation of TetR, thus revealing how the synthetic TetR-binding aptamer strikes the chords of the bimodal allosteric behaviour of TetR to function as a synthetic regulator.
Collapse
Affiliation(s)
- Florian C Grau
- Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestr. 91, D-91052 Erlangen, Germany
| | - Jeannine Jaeger
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany
| | - Florian Groher
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt
| | - Yves A Muller
- Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestr. 91, D-91052 Erlangen, Germany
| |
Collapse
|
29
|
Shi J, Shi Z, Dong Y, Wu F, Liu D. Responsive DNA-Based Supramolecular Hydrogels. ACS APPLIED BIO MATERIALS 2020; 3:2827-2837. [DOI: 10.1021/acsabm.0c00081] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jiezhong Shi
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ziwei Shi
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yuanchen Dong
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Fen Wu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
| |
Collapse
|
30
|
Liu J, Guo B. RNA-based therapeutics for colorectal cancer: Updates and future directions. Pharmacol Res 2019; 152:104550. [PMID: 31866285 DOI: 10.1016/j.phrs.2019.104550] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/12/2019] [Accepted: 11/16/2019] [Indexed: 01/20/2023]
Abstract
Colorectal cancer (CRC) is one of the most common causes of cancer death worldwide. While standard chemotherapy and new targeted therapy have been improved recently, problems such as multidrug resistance (MDR) and severe side effects remain unresolved. RNAs are essential to all biological processes including cell proliferation and differentiation, cell cycle, apoptosis, activation of tumor suppressor genes, suppression of oncogenes. Therefore, there are various potential approaches to address genetic disease like CRC at the RNA level. In contrast to conventional treatments, RNA-based therapeutics such as RNA interference, antisense oligonucleotides, RNA aptamer, ribozymes, have the advantages of high specificity, high potency and low toxicity. It has gained more and more attention due to the flexibility in modulating a wide range of targets. Here, we highlight recent advances and clinical studies involving RNA-based therapeutics and CRC. We also discuss their advantages and limitations that remain to be overcome for the treatment of human CRC.
Collapse
Affiliation(s)
- Jingwen Liu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77030, United States.
| | - Bin Guo
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77030, United States.
| |
Collapse
|
31
|
Hu B, Zhou R, Li Z, Ouyang S, Li Z, Hu W, Wang L, Jiao B. Study of the binding mechanism of aptamer to palytoxin by docking and molecular simulation. Sci Rep 2019; 9:15494. [PMID: 31664144 PMCID: PMC6820544 DOI: 10.1038/s41598-019-52066-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/13/2019] [Indexed: 12/11/2022] Open
Abstract
This paper provides a feasible model for molecular structure analysis and interaction mechanism of aptamer and micromolecule. In this study, modeling and dynamic simulation of ssDNA aptamer (P-18S2) and target (Palytoxin, PTX) were performed separately. Then, the complex structure between DNA and PTX was predicted, and docking results showed that PTX could combine steadily at the groove’s top of DNA model by strong hydrogen-bonds and electrostatic interaction. Thus, we truncated and optimized P-18S2 by simulating. At the same time, we also confirmed the reliability of simulation results by experiments. With the experimental and computational results, the study provided a more reasonable interpretation for the high affinity and specific binding of P-18S2 and PTX, which laid the foundation for further optimization and development of aptamers in molecular diagnostics and therapeutic applications.
Collapse
Affiliation(s)
- Bo Hu
- Department of Biochemistry and Molecular Biology, College of Basic Medical, Second Military Medical University, Shanghai, 200433, China.,Marine Biological Institute, College of Marine Military Medicine, Second Military Medical University, Shanghai, 200433, China
| | - Rong Zhou
- Department of Biochemistry and Molecular Biology, College of Basic Medical, Second Military Medical University, Shanghai, 200433, China.,Marine Biological Institute, College of Marine Military Medicine, Second Military Medical University, Shanghai, 200433, China
| | - Zhengang Li
- Department of Biochemistry and Molecular Biology, College of Basic Medical, Second Military Medical University, Shanghai, 200433, China.,Marine Biological Institute, College of Marine Military Medicine, Second Military Medical University, Shanghai, 200433, China
| | - Shengqun Ouyang
- Department of Biochemistry and Molecular Biology, College of Basic Medical, Second Military Medical University, Shanghai, 200433, China
| | - Zhen Li
- Department of Biochemistry and Molecular Biology, College of Basic Medical, Second Military Medical University, Shanghai, 200433, China
| | - Wei Hu
- Chengdu FenDi Technology Co., Ltd, Chengdu, 610041, China
| | - Lianghua Wang
- Department of Biochemistry and Molecular Biology, College of Basic Medical, Second Military Medical University, Shanghai, 200433, China.
| | - Binghua Jiao
- Department of Biochemistry and Molecular Biology, College of Basic Medical, Second Military Medical University, Shanghai, 200433, China. .,Marine Biological Institute, College of Marine Military Medicine, Second Military Medical University, Shanghai, 200433, China.
| |
Collapse
|
32
|
Roueinfar M, Abraham KM, Hong KL. In-Solution Molecular Recognition Comparison of Aptamers against the Herbicide Atrazine. ACS OMEGA 2019; 4:16201-16208. [PMID: 31592487 PMCID: PMC6777074 DOI: 10.1021/acsomega.9b02414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/13/2019] [Indexed: 06/10/2023]
Abstract
Atrazine is a common herbicide that is widely used to control weed growth in both agricultural and residential settings. It has been shown to act as an endocrine disruptor that affects aquatic organisms. Rapid and low-cost monitoring methods for atrazine is the first step to mitigate its widespread persistency. Aptamers are small synthetic oligonucleotides that can assume a 3D structure to act as the molecular recognition element for a specific target of interest. Two different atrazine binding aptamers (R12.23 Trunc. and R12.45 Trunc.) have been identified from the same library design but with fundamentally different in vitro selection methodologies. While the R12.23 Trunc. has been utilized in immobilized biosensing platforms, it is unclear if in-solution-based applications would be suitable for both atrazine binding aptamers. This study provides the first insight of comparative in-solution binding profiles of the two atrazine binding aptamers. Based on our results, this information will be useful for future biosensing platform development utilizing the two aptamers.
Collapse
Affiliation(s)
- Mina Roueinfar
- Department
of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Department of Biology,
College of Science and Engineering, and Department of Physics, College of
Science and Engineering, Wilkes University, 84 W. South Street, Wilkes-Barre, Pennsylvania 18766, United States
| | - Kevin M. Abraham
- Department
of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Department of Biology,
College of Science and Engineering, and Department of Physics, College of
Science and Engineering, Wilkes University, 84 W. South Street, Wilkes-Barre, Pennsylvania 18766, United States
| | - Ka Lok Hong
- Department
of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Department of Biology,
College of Science and Engineering, and Department of Physics, College of
Science and Engineering, Wilkes University, 84 W. South Street, Wilkes-Barre, Pennsylvania 18766, United States
| |
Collapse
|
33
|
Sharma S, Zajac M, Krishnan Y. A DNA Aptamer for Cyclic Adenosine Monophosphate that Shows Adaptive Recognition. Chembiochem 2019; 21:157-162. [PMID: 31099939 DOI: 10.1002/cbic.201900259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Indexed: 12/12/2022]
Abstract
As a ubiquitous second messenger, cyclic adenosine monophosphate (cAMP) mediates diverse biological processes such as cell growth, inflammation, and metabolism. The ability to probe these pathways would be significantly enhanced if we had a DNA-based sensor for cAMP. Herein, we describe a new, 31-base long single-stranded DNA aptamer for cAMP, denoted caDNApt-1, that was isolated by in vitro selection using systemic evolution of ligands after exponential enrichment (SELEX). caDNApt-1 has an approximately threefold higher affinity for cAMP than ATP, ADP, and AMP. Using non-denaturing gel electrophoresis and fluorescence spectroscopy, we characterized the structural changes caDNApt-1 undergoes upon binding to cAMP and revealed its potential as a cAMP sensor.
Collapse
Affiliation(s)
- Suruchi Sharma
- Tata Institute of Fundamental Research, GKVK, National Centre for Biological Sciences, Bellary Road, Bengaluru, 560065, India
| | - Matthew Zajac
- Present address: Department of Chemistry, The University of Chicago, GCIS E305A, 929E, 57th Street, ., Chicago, IL, 60637, USA
| | - Yamuna Krishnan
- Tata Institute of Fundamental Research, GKVK, National Centre for Biological Sciences, Bellary Road, Bengaluru, 560065, India.,Present address: Department of Chemistry, The University of Chicago, GCIS E305A, 929E, 57th Street, ., Chicago, IL, 60637, USA.,Grossman Institute of Neuroscience, Quantitative Biology and, Human Behavior, University of Chicago, Chicago, IL, 60637, USA
| |
Collapse
|
34
|
Nucleic acid-based fluorescent methods for the determination of DNA repair enzyme activities: A review. Anal Chim Acta 2019; 1060:30-44. [DOI: 10.1016/j.aca.2018.12.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/09/2018] [Accepted: 12/18/2018] [Indexed: 12/13/2022]
|
35
|
Sengupta RN, Herschlag D. Enhancement of RNA/Ligand Association Kinetics via an Electrostatic Anchor. Biochemistry 2019; 58:2760-2768. [PMID: 31117387 PMCID: PMC6586055 DOI: 10.1021/acs.biochem.9b00231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
The diverse biological
processes mediated by RNA rest upon its
recognition of various ligands, including small molecules and nucleic
acids. Nevertheless, a recent literature survey suggests that RNA
molecular recognition of these ligands is slow, with association rate
constants orders of magnitude below the diffusional limit. Thus, we
were prompted to consider strategies for increasing RNA association
kinetics. Proteins can accelerate ligand association via electrostatic
forces, and here, using the Tetrahymena group I ribozyme,
we provide evidence that electrostatic forces can accelerate RNA/ligand
association. This RNA enzyme (E) catalyzes cleavage of an oligonucleotide
substrate (S) by an exogenous guanosine (G) cofactor. The G 2′-
and 3′-OH groups interact with an active site metal ion, termed
MC, within E·S·G, and we perturbed each of these
contacts via −NH3+ substitution. New
and prior data indicate that G(2′NH3+) and G(3′NH3+) bind as strongly as
G, suggesting that the −NH3+ substituents
of these analogues avoid repulsive interactions with MC and make alternative interactions. Unexpectedly, removal of the
adjacent −OH via −H substitution to give G(2′H,3′NH3+) and G(2′NH3+,3′H) enhanced binding, in stark contrast to the deleterious
effect of these substitutions on G binding. Pulse–chase experiments
indicate that the −NH3+ moiety of G(2′H,3′NH3+) increases the rate of G association. These results
suggest that the positively charged −NH3+ group can act as a molecular “anchor” to increase
the residence time of the encounter complex and thereby enhance productive
binding. Electrostatic anchors may provide a broadly applicable strategy
for the development of fast binding RNA ligands and RNA-targeted therapeutics.
Collapse
Affiliation(s)
- Raghuvir N Sengupta
- Department of Biochemistry , Stanford University , Stanford , California 94305 , United States
| | - Daniel Herschlag
- Department of Biochemistry , Stanford University , Stanford , California 94305 , United States.,Departments of Chemical Engineering and Chemistry , Stanford University , Stanford , California 94305 , United States.,Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health) , Stanford University , Stanford , California 94305 , United States
| |
Collapse
|
36
|
Wang WW, Han X, Chu LQ. Polyadenine-mediated Immobilization of Aptamers on a Gold Substrate for the Direct Detection of Bacterial Pathogens. ANAL SCI 2019; 35:967-972. [PMID: 31080198 DOI: 10.2116/analsci.19p110] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Nucleic acid aptamers have been widely used as synthetic probes for bioanalytical applications. Herein, we carried out a detailed study on the immobilization of a series of aptamers ranging from 37 to 88 bases, which are specific to either Escherichia coli (E. coli) or Staphylococcus aureus (S. aureus), on a planar gold substrate via a polyadenine-mediated immobilization method. The resultant surfaces were characterized by both surface plasmon resonance spectroscopy (SPR) and X-ray photoelectron spectroscopy. The results clearly show that the aptamer solution at a lower ionic strength gives rise to a higher lateral density of the aptamer when compared to that at a higher ionic strength. The SPR aptasensors are then employed for detecting their corresponding bacteria (i.e., E. coli and S. aureus, respectively). The data indicate that the SPR aptasensor with a higher density of aptamer exhibits a better capture of target bacteria.
Collapse
Affiliation(s)
- Wen-Wen Wang
- College of Chemical Engineering and Materials Science, Tianjin University of Science & Technology
| | - Xiao Han
- College of Chemical Engineering and Materials Science, Tianjin University of Science & Technology
| | - Li-Qiang Chu
- College of Chemical Engineering and Materials Science, Tianjin University of Science & Technology
| |
Collapse
|
37
|
Munzar JD, Ng A, Juncker D. Duplexed aptamers: history, design, theory, and application to biosensing. Chem Soc Rev 2019; 48:1390-1419. [PMID: 30707214 DOI: 10.1039/c8cs00880a] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.
Collapse
Affiliation(s)
- Jeffrey D Munzar
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | | | | |
Collapse
|
38
|
Wales DJ, Disney MD, Yildirim I. Computational Investigation of RNA A-Bulges Related to the Microtubule-Associated Protein Tau Causing Frontotemporal Dementia and Parkinsonism. J Phys Chem B 2019; 123:57-65. [PMID: 30517788 PMCID: PMC6465094 DOI: 10.1021/acs.jpcb.8b09139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mutations in the human tau gene result in alternative splicing of the tau protein, which causes frontotemporal dementia and Parkinsonism. One disease mechanism is linked to the stability of a hairpin within the microtubule-associated protein tau (MAPT) mRNA, which contains an A-bulge. Here we employ computational methods to investigate the structural and thermodynamic properties of several A-bulge RNAs with different closing base-pairs. We find that the current amber RNA force field has a preference to overstabilize base-triple over stacked states, even though some of the A-bulges are known to prefer stacked states according to NMR studies. We further determined that if the neighboring base-pairs of A-bulges are AU, this situation can lead to base slippage. However, when the 3'-side of the A-bulge has an UA base-pair, the stacked state is stabilized by an extra interaction that is not observed in the other sequences. We suggest that these A-bulge RNA systems could be used as benchmarks to improve the current RNA force fields.
Collapse
Affiliation(s)
- David J. Wales
- Department of Chemistry, University of Cambridge, Cambridge, Cambridgeshire CB2 1EW, U.K
| | - Matthew D. Disney
- Department of Chemistry, Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Ilyas Yildirim
- Department of Chemistry, Scripps Research Institute, Jupiter, Florida 33458, United States
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States
| |
Collapse
|
39
|
Abstract
Our current knowledge on the unique roles of RNA in cells makes it vital to investigate the properties of RNA systems using computational methods because of the potential pharmaceutical applications. With the continuous advancement of computer technology, it is now possible to study RNA folding. Molecular mechanics calculations are useful in discovering the structural and thermodynamic properties of RNA systems. Yet, the predictions depend on the quality of the RNA force field, which is a set of parameters describing the potential energy of the system. Torsional parameters are one of the terms in a force field that can be revised using physics-based approaches. This chapter focuses on improvements provided by revisions of torsional parameters of the AMBER (Assisted Model Building with Energy Refinement) RNA force field. The theory behind torsional revisions and re-parameterization of several RNA torsions is briefly described. Applications of the revised torsional parameters to study RNA nucleosides, single-stranded RNA tetramers, and RNA repeat expansions are described in detail. It is concluded that RNA force fields require constant revisions and should be benchmarked against diverse RNA systems such as single strands and internal loops in order to test their qualities.
Collapse
|
40
|
Chen X, Liu Y, Fang X, Li Z, Pu H, Chang J, Chen J, Mao S. Ultratrace antibiotic sensing using aptamer/graphene-based field-effect transistors. Biosens Bioelectron 2018; 126:664-671. [PMID: 30530212 DOI: 10.1016/j.bios.2018.11.034] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 12/11/2022]
Abstract
Antibiotic residue, as emerging pollution resulting from antibiotic abuse, poses a serious threat on ecosystem and human health. Conventional methods for antibiotic detection, e.g., liquid/gas chromatography, are based on complicated instruments and time-consuming; therefore, efforts have been made to realize in situ and real-time monitoring of antibiotics. Here, a miniaturized and integratable electronic antibiotic sensor based on field-effect transistor (FET) is reported. The reduced graphene oxide (rGO) nanosheet is used as the channel material and the aptamer RNA for tobramycin is modified onto rGO as the probe. A novel sensor design with 6-mercapto-1-hexanol (MCH)/1-pyrenebutanol (PBA) blocking layer (BL) for structure optimization is applied to enhance the sensor reliability and specificity. This rGO/aptamer/BL sensor shows an ultra-sensitivity to tobramycin with a lower detection limit of 0.3 nM and a quick response within 5 s, as well as a high specificity over other antibiotics such as kanamycin, streptomycin, ciprofloxacin, and tetracycline. The sensing mechanism based on the deformation of the charged aptamer probe is proposed via an in-depth analysis of the interactions between aptamer, tobramycin and rGO. In addition, sensing test performed under controlled microfluidic flow conditions demonstrates a great potential of the sensors in practical applications.
Collapse
Affiliation(s)
- Xiaoyan Chen
- State Key Laboratory of Pollution Control and Resource Reuse, International Joint Research Center for Sustainable Urban Water System, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Ying Liu
- State Key Laboratory of Pollution Control and Resource Reuse, International Joint Research Center for Sustainable Urban Water System, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Xian Fang
- State Key Laboratory of Pollution Control and Resource Reuse, International Joint Research Center for Sustainable Urban Water System, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Zhuo Li
- State Key Laboratory of Pollution Control and Resource Reuse, International Joint Research Center for Sustainable Urban Water System, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Haihui Pu
- Department of Mechanical Engineering, University of Wisconsin-Milwaukee, 3200 N. Cramer Street, Milwaukee, WI 53211, USA
| | - Jingbo Chang
- Department of Mechanical Engineering, University of Wisconsin-Milwaukee, 3200 N. Cramer Street, Milwaukee, WI 53211, USA
| | - Junhong Chen
- Department of Mechanical Engineering, University of Wisconsin-Milwaukee, 3200 N. Cramer Street, Milwaukee, WI 53211, USA
| | - Shun Mao
- State Key Laboratory of Pollution Control and Resource Reuse, International Joint Research Center for Sustainable Urban Water System, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| |
Collapse
|
41
|
Abraham K, Roueinfar M, Ponce AT, Lussier ME, Benson DB, Hong KL. In Vitro Selection and Characterization of a Single-Stranded DNA Aptamer Against the Herbicide Atrazine. ACS OMEGA 2018; 3:13576-13583. [PMID: 30411044 PMCID: PMC6217647 DOI: 10.1021/acsomega.8b01859] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/08/2018] [Indexed: 05/14/2023]
Abstract
Atrazine is an herbicide that is widely used in crop production at about 70 million pounds per year in the United States. Its widespread use has led to contamination of groundwater and other aquatic systems. It has resulted in many serious environmental and human health issues. This study focuses on the identification and characterization of a single-stranded DNA (ssDNA) aptamer that binds to atrazine. In this study, a variation of the systematic evolution of ligands by exponential enrichment (SELEX) process was used to identify an aptamer, which binds to atrazine with high affinity and specificity. This SELEX focused on inducing the aptamer's ability to change conformation upon binding to atrazine, and stringent negative target selections. After 12 rounds of in vitro selection, the ssDNA aptamer candidate R12.45 was chosen and truncated to obtain a 46-base sequence. The binding affinity, specificity, and structural characteristics of this truncated candidate was investigated by using isothermal titration calorimetry, circular dichroism (CD) analysis, SYBR Green I (SG) fluorescence displacement assays, and gold nanoparticles (AuNPs) colorimetric assays. The truncated R12.45 candidate aptamer bound to atrazine with high affinity (K d = 3.7 nM) and displayed low cross-binding activities on structurally related herbicides. In addition, CD analysis data indicated a target induced structural stabilization. Finally, SG assays and AuNPs assays showed nonconventional binding activities between the truncated R12.45 aptamer candidate and atrazine, which warrants future studies.
Collapse
Affiliation(s)
- Kevin
M. Abraham
- Department
of Pharmaceutical Sciences, Nesbitt School of Pharmacy, and Department of
Biology, College of Science and Engineering, Wilkes University, 84
W. South Street, Wilkes-Barre, Pennsylvania 18766, United States
| | - Mina Roueinfar
- Department
of Pharmaceutical Sciences, Nesbitt School of Pharmacy, and Department of
Biology, College of Science and Engineering, Wilkes University, 84
W. South Street, Wilkes-Barre, Pennsylvania 18766, United States
| | - Alex T. Ponce
- Department
of Pharmaceutical Sciences, Nesbitt School of Pharmacy, and Department of
Biology, College of Science and Engineering, Wilkes University, 84
W. South Street, Wilkes-Barre, Pennsylvania 18766, United States
| | - Mia E. Lussier
- Department
of Pharmaceutical Sciences, Nesbitt School of Pharmacy, and Department of
Biology, College of Science and Engineering, Wilkes University, 84
W. South Street, Wilkes-Barre, Pennsylvania 18766, United States
| | - Danica B. Benson
- Department
of Pharmaceutical Sciences, Nesbitt School of Pharmacy, and Department of
Biology, College of Science and Engineering, Wilkes University, 84
W. South Street, Wilkes-Barre, Pennsylvania 18766, United States
| | - Ka Lok Hong
- Department
of Pharmaceutical Sciences, Nesbitt School of Pharmacy, and Department of
Biology, College of Science and Engineering, Wilkes University, 84
W. South Street, Wilkes-Barre, Pennsylvania 18766, United States
- E-mail: . Phone: +1-570-408-4296. Fax: +1-570-408-4299
| |
Collapse
|
42
|
Kizer M, Li P, Cress BF, Lin L, Jing TT, Zhang X, Xia K, Linhardt RJ, Wang X. RNA Aptamers with Specificity for Heparosan and Chondroitin Glycosaminoglycans. ACS OMEGA 2018; 3:13667-13675. [PMID: 30411046 PMCID: PMC6210061 DOI: 10.1021/acsomega.8b01853] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/10/2018] [Indexed: 06/08/2023]
Abstract
In this study, two respective groups of RNA aptamers have been selected against two main classes of glycosaminoglycans (GAGs), heparosan, and chondroitin, as they have proven difficult to specifically detect in biological samples. GAGs are linear, anionic, polydisperse polysaccharides found ubiquitously in nature, yet their detection remains problematic. GAGs comprised repeating disaccharide units, consisting of uronic acid and hexosamine residues that are often also sulfated at various positions. Monoclonal antibodies are frequently used in biology and medicine to recognize various biological analytes with high affinity and specificity. However, GAGs are conserved across the whole animal phylogenic tree and are nonimmunogenic in hosts traditionally used for natural antibody generation. Thus, it has been challenging to obtain high affinity, selective antibodies that recognize various GAGs. In the absence of anti-GAG antibodies, glycobiologists have relied on the use of specific enzymes to convert GAGs to oligosaccharides for analysis by mass spectrometry. Unfortunately, while these methods are sensitive, they can be labor-intensive and cannot be used for in situ detection of intact GAGs in cells and tissues. Aptamers are single-stranded oligonucleotide (DNA or RNA) ligands capable of high selectivity and high affinity detection of biological analytes. Aptamers can be developed in vitro by the systematic evolution of ligands by exponential enrichment (SELEX) to recognize nonimmunogenic targets, including neutral carbohydrates. This study utilizes the SELEX method to generate RNA aptamers, which specifically bind to the unmodified GAGs, heparosan, and chondroitin. Binding confirmation and cross-screening with other GAGs were performed using confocal microscopy to afford three specific GAGs to each target. Affinity constant of each RNA aptamer was obtained by fluorescent output after interaction with the respective GAG target immobilized on plates; the K D values were determined to be 0.71-1.0 μM for all aptamers. Upon the success of chemical modification (to stabilize RNA aptamers in actual biological systems) and fluorescent tagging (to only visualize RNA aptamers) of these aptamers, they would be able to serve as a specific detection reagent of these important GAGs in biological samples.
Collapse
Affiliation(s)
- Megan Kizer
- Department
of Chemistry and Chemical Biology, Department of Biology, Department of Chemical
and Biological Engineering, Department of Biomedical Engineering, and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer
Polytechnic Institute, 110 8th Avenue, Troy, New
York 12180, United
States
| | - Peiqin Li
- Department
of Chemistry and Chemical Biology, Department of Biology, Department of Chemical
and Biological Engineering, Department of Biomedical Engineering, and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer
Polytechnic Institute, 110 8th Avenue, Troy, New
York 12180, United
States
- Department
of Forest Pathology, College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Brady F. Cress
- Department
of Chemistry and Chemical Biology, Department of Biology, Department of Chemical
and Biological Engineering, Department of Biomedical Engineering, and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer
Polytechnic Institute, 110 8th Avenue, Troy, New
York 12180, United
States
| | - Lei Lin
- Department
of Chemistry and Chemical Biology, Department of Biology, Department of Chemical
and Biological Engineering, Department of Biomedical Engineering, and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer
Polytechnic Institute, 110 8th Avenue, Troy, New
York 12180, United
States
| | - Tom T. Jing
- Department
of Chemistry and Chemical Biology, Department of Biology, Department of Chemical
and Biological Engineering, Department of Biomedical Engineering, and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer
Polytechnic Institute, 110 8th Avenue, Troy, New
York 12180, United
States
| | - Xing Zhang
- Department
of Chemistry and Chemical Biology, Department of Biology, Department of Chemical
and Biological Engineering, Department of Biomedical Engineering, and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer
Polytechnic Institute, 110 8th Avenue, Troy, New
York 12180, United
States
| | - Ke Xia
- Department
of Chemistry and Chemical Biology, Department of Biology, Department of Chemical
and Biological Engineering, Department of Biomedical Engineering, and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer
Polytechnic Institute, 110 8th Avenue, Troy, New
York 12180, United
States
| | - Robert J. Linhardt
- Department
of Chemistry and Chemical Biology, Department of Biology, Department of Chemical
and Biological Engineering, Department of Biomedical Engineering, and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer
Polytechnic Institute, 110 8th Avenue, Troy, New
York 12180, United
States
| | - Xing Wang
- Department
of Chemistry and Chemical Biology, Department of Biology, Department of Chemical
and Biological Engineering, Department of Biomedical Engineering, and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer
Polytechnic Institute, 110 8th Avenue, Troy, New
York 12180, United
States
| |
Collapse
|
43
|
Gao R, Zhong Z, Gao X, Jia L. Graphene Oxide Quantum Dots Assisted Construction of Fluorescent Aptasensor for Rapid Detection of Pseudomonas aeruginosa in Food Samples. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:10898-10905. [PMID: 30247907 DOI: 10.1021/acs.jafc.8b02164] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We engineered an ingenious fluorescent aptasensor for detection of Pseudomonas aeruginosa ( P. aeruginosa) according to the DNA hybridization and fluorescence resonance energy transfer. In the absence of target bacteria, 5-carboxyfluorescein-labeled complementary DNA (FAM-cDNA) hybridizes with the partial sequences of aptamer and the fluorescence of FAM can be quenched by graphene oxide quantum dots (GOQDs). Upon the addition of target bacteria, the aptamer as a biorecognition element is bound with P. aeruginosa specifically. FAM-cDNA prefers to hybridize with the aptamer, resulting in the desorption of FAM-cDNA from GOQDs, thus recovering the fluorescence of FAM. The aptasensor shows a wide linear response to P. aeruginosa in the concentration range of 1.28 × 103-2.00 × 107 cfu/mL with acceptable selectivity. The detection limit is 100 cfu/mL. The whole process can be finished in 2 h. Moreover, the platform is successfully applied to detect P. aeruginosa in drinking water, orange juice, and popsicle samples.
Collapse
Affiliation(s)
- Ran Gao
- Ministry of Education Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics , South China Normal University , Guangzhou 510631 , China
| | - Zitao Zhong
- Ministry of Education Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics , South China Normal University , Guangzhou 510631 , China
| | - Xiaomei Gao
- Ministry of Education Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics , South China Normal University , Guangzhou 510631 , China
| | - Li Jia
- Ministry of Education Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics , South China Normal University , Guangzhou 510631 , China
| |
Collapse
|
44
|
Park KS. Nucleic acid aptamer-based methods for diagnosis of infections. Biosens Bioelectron 2018; 102:179-188. [PMID: 29136589 PMCID: PMC7125563 DOI: 10.1016/j.bios.2017.11.028] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 02/07/2023]
Abstract
Infectious diseases are a serious global problem, which not only take an enormous human toll but also incur tremendous economic losses. In combating infectious diseases, rapid and accurate diagnostic tests are required for pathogen identification at the point of care (POC). In this review, investigations of diagnostic strategies for infectious diseases that are based on aptamers, especially nucleic acid aptamers, oligonucleotides that have high affinities and specificities toward their targets, are described. Owing to their unique features including low cost of production, easy chemical modification, high chemical stability, reproducibility, and low levels of immunogenicity and toxicity, aptamers have been widely utilized as bio-recognition elements (bio-receptors) for the development of infection diagnostic systems. We discuss nucleic acid aptamer-based methods that have been developed for diagnosis of infections using a format that organizes discussion according to the target pathogenic analytes including toxins or proteins, whole cells and nucleic acids. Also included is, a summary of recent advances made in the sensitive detection of pathogenic bacteria utilizing the isothermal nucleic acid amplification method. Lastly, a nucleic acid aptamer-based POC system is described and future directions of studies in this area are discussed.
Collapse
Affiliation(s)
- Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea.
| |
Collapse
|
45
|
Blanco C, Bayas M, Yan F, Chen IA. Analysis of Evolutionarily Independent Protein-RNA Complexes Yields a Criterion to Evaluate the Relevance of Prebiotic Scenarios. Curr Biol 2018; 28:526-537.e5. [PMID: 29398222 DOI: 10.1016/j.cub.2018.01.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/04/2017] [Accepted: 01/03/2018] [Indexed: 12/30/2022]
Abstract
A central difficulty facing study of the origin of life on Earth is evaluating the relevance of different proposed prebiotic scenarios. Perhaps the most established feature of the origin of life was the progression through an RNA World, a prebiotic stage dominated by functional RNA. We use the appearance of proteins in the RNA World to understand the prebiotic milieu and develop a criterion to evaluate proposed synthetic scenarios. Current consensus suggests that the earliest amino acids of the genetic code were anionic or small hydrophobic or polar amino acids. However, the ability to interact with the RNA World would have been a crucial feature of early proteins. To determine which amino acids would be important for the RNA World, we analyze non-biological protein-aptamer complexes in which the RNA or DNA is the result of in vitro evolution. This approach avoids confounding effects of biological context and evolutionary history. We use bioinformatic analysis and molecular dynamics simulations to characterize these complexes. We find that positively charged and aromatic amino acids are over-represented whereas small hydrophobic amino acids are under-represented. Binding enthalpy is found to be primarily electrostatic, with positively charged amino acids contributing cooperatively to binding enthalpy. Arginine dominates all modes of interaction at the interface. These results suggest that proposed prebiotic syntheses must be compatible with cationic amino acids, particularly arginine or a biophysically similar amino acid, in order to be relevant to the invention of protein by the RNA World.
Collapse
Affiliation(s)
- Celia Blanco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106-9510, USA
| | - Marco Bayas
- Departamento de Fisica, Escuela Politécnica Nacional, Quito, Ladron de Guevara E11-253, Ecuador
| | - Fu Yan
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106-9510, USA
| | - Irene A Chen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106-9510, USA; Program in Biomolecular Sciences and Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106-9510, USA.
| |
Collapse
|
46
|
Williams B, Zhao B, Tandon A, Ding F, Weeks KM, Zhang Q, Dokholyan NV. Structure modeling of RNA using sparse NMR constraints. Nucleic Acids Res 2018; 45:12638-12647. [PMID: 29165648 PMCID: PMC5728392 DOI: 10.1093/nar/gkx1058] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 10/18/2017] [Indexed: 01/04/2023] Open
Abstract
RNAs fold into distinct molecular conformations that are often essential for their functions. Accurate structure modeling of complex RNA motifs, including ubiquitous non-canonical base pairs and pseudoknots, remains a challenge. Here, we present an NMR-guided all-atom discrete molecular dynamics (DMD) platform, iFoldNMR, for rapid and accurate structure modeling of complex RNAs. We show that sparse distance constraints from imino resonances, which can be readily obtained from routine NMR experiments and easier to compile than laborious assignments of non-solvent-exchangeable protons, are sufficient to direct a DMD search for low-energy RNA conformers. Benchmarking on a set of RNAs with complex folds spanning up to 56 nucleotides in length yields structural models that recapitulate experimentally determined structures with all-heavy-atom RMSDs ranging from 2.4 to 6.5 Å. This platform represents an efficient approach for high-throughput RNA structure modeling and will facilitate analysis of diverse, newly discovered functional RNAs.
Collapse
Affiliation(s)
- Benfeard Williams
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Molecular and Cellular Biophysics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bo Zhao
- Molecular and Cellular Biophysics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Arpit Tandon
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Molecular and Cellular Biophysics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Molecular and Cellular Biophysics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Molecular and Cellular Biophysics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
47
|
DU YL, MO LT, YI YS, QIU LP, TAN WH. Aptamers from Cell-based Selection for Bioanalysis and Bioimaging. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61052-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
48
|
Wales DJ, Yildirim I. Improving Computational Predictions of Single-Stranded RNA Tetramers with Revised α/γ Torsional Parameters for the Amber Force Field. J Phys Chem B 2017; 121:2989-2999. [PMID: 28319659 DOI: 10.1021/acs.jpcb.7b00819] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With current advancements in RNA based therapeutics, it is becoming crucial to utilize theoretical and computational methods to describe properly the physical properties of RNA molecules. NMR and X-ray crystallography are two powerful techniques for investigating structural properties. However, if the RNA molecules are complex or dynamic, these methods might not be adequate. For computational approaches, the quality of the force field will determine accuracy of our predictions. In this contribution, we revise the α/γ torsional parameters of RNA for amber force field using a model system representing an RNA dimer backbone. Combined with revised χ torsional parameters, previously shown to improve computational predictions, we benchmarked the revised force field on five single-stranded RNA (ssRNA) tetramers, three RNA dodecamer duplexes, and an RNA hairpin. A total of 60 μs of molecular dynamics (MD) simulations were run. We also employ the discrete path sampling (DPS) approach to compare the predictions for the revised amber force field with those for amber10. Our results indicate that the unphysical states observed with amber10 in ssRNA MD simulations are suppressed for the revised amber force field. In line with NMR experimental observations, incorporation of the revised α/γ and χ torsional parameters leads to A-form-like conformational states as the most favorable ssRNA tetramer conformations. Furthermore, the revised force field maintains the A-form geometry in regular RNA duplexes. Our revised amber force field for RNA should therefore improve structural and thermodynamic predictions for challenging RNA systems.
Collapse
Affiliation(s)
- David J Wales
- Department of Chemistry, University of Cambridge , Cambridge, Cambridgeshire CB2 1EW, United Kingdom
| | - Ilyas Yildirim
- Department of Chemistry and Biochemistry, Florida Atlantic University , Jupiter, Florida 33458, United States.,Scripps Research Institute , Jupiter, Florida 33458, United States
| |
Collapse
|
49
|
Munzar JD, Ng A, Corrado M, Juncker D. Complementary oligonucleotides regulate induced fit ligand binding in duplexed aptamers. Chem Sci 2017; 8:2251-2256. [PMID: 28507681 PMCID: PMC5408566 DOI: 10.1039/c6sc03993f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/07/2016] [Indexed: 12/20/2022] Open
Abstract
Duplexed aptamers (DAs) are engineered by hybridizing an aptamer-complementary element (ACE, e.g. a DNA oligonucleotide) to an aptamer; to date, ACEs have been presumed to sequester the aptamer into a non-binding duplex state, in line with a conformational selection-based model of ligand binding. Here, we uncover that DAs can actively bind a ligand from the duplex state through an ACE-regulated induced fit mechanism. Using a widely-studied ATP DNA aptamer and a solution-based equilibrium assay, DAs were found to exhibit affinities up to 1 000 000-fold higher than predicted by conformational selection alone, with different ACEs regulating the level of induced fit binding, as well as the cooperative allostery of the DA (Hill slope of 1.8 to 0.7). To validate these unexpected findings, we developed a non-equilibrium surface-based assay that only signals induced fit binding, and corroborated the results from the solution-based assay. Our findings indicate that ACEs regulate ATP DA ligand binding dynamics, opening new avenues for the study and design of ligand-responsive nucleic acids.
Collapse
Affiliation(s)
- Jeffrey D Munzar
- McGill University and Genome Quebec Innovation Centre , 740 Dr. Penfield Avenue , Montreal , Quebec H3A 0G1 , Canada .
- Department of Biomedical Engineering , McGill University , 3775 Rue University , Montreal , Quebec H3A 2B4 , Canada
| | - Andy Ng
- McGill University and Genome Quebec Innovation Centre , 740 Dr. Penfield Avenue , Montreal , Quebec H3A 0G1 , Canada .
- Department of Biomedical Engineering , McGill University , 3775 Rue University , Montreal , Quebec H3A 2B4 , Canada
| | - Mario Corrado
- McGill University and Genome Quebec Innovation Centre , 740 Dr. Penfield Avenue , Montreal , Quebec H3A 0G1 , Canada .
- Department of Biomedical Engineering , McGill University , 3775 Rue University , Montreal , Quebec H3A 2B4 , Canada
| | - David Juncker
- McGill University and Genome Quebec Innovation Centre , 740 Dr. Penfield Avenue , Montreal , Quebec H3A 0G1 , Canada .
- Department of Biomedical Engineering , McGill University , 3775 Rue University , Montreal , Quebec H3A 2B4 , Canada
- Department of Neurology and Neurosurgery , McGill University , 3801 Rue University , Montreal , Quebec H3A 2B4 , Canada
| |
Collapse
|
50
|
Urmann K, Modrejewski J, Scheper T, Walter JG. Aptamer-modified nanomaterials: principles and applications. ACTA ACUST UNITED AC 2017. [DOI: 10.1515/bnm-2016-0012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractAptamers are promising alternative binders that can substitute antibodies in various applications. Due to the advantages of aptamers, namely their high affinity, specificity and stability, along with the benefits originating from the chemical synthesis of aptamers, they have attracted attention in various applications including their use on nanostructured material. This necessitates the immobilization of aptamers on a solid support. Since aptamer immobilization may interfere with its binding properties, the immobilization of aptamers has to be investigated and optimized. Within this review, we give general insights into the principles and factors controlling the binding affinity of immobilized aptamers. Specific features of aptamer immobilization on nanostructured surfaces and nanoparticles are highlighted and a brief overview of applications of aptamer-modified nanostructured materials is given.
Collapse
|