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Robledo SM, Pérez-Silanes S, Fernández-Rubio C, Poveda A, Monzote L, González VM, Alonso-Collado P, Carrión J. Neglected Zoonotic Diseases: Advances in the Development of Cell-Penetrating and Antimicrobial Peptides against Leishmaniosis and Chagas Disease. Pathogens 2023; 12:939. [PMID: 37513786 PMCID: PMC10383258 DOI: 10.3390/pathogens12070939] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
In 2020, the WHO established the road map for neglected tropical diseases 2021-2030, which aims to control and eradicate 20 diseases, including leishmaniosis and Chagas disease. In addition, since 2015, the WHO has been developing a Global Action Plan on Antimicrobial Resistance. In this context, the achievement of innovative strategies as an alternative to replace conventional therapies is a first-order socio-sanitary priority, especially regarding endemic zoonoses in poor regions, such as those caused by Trypanosoma cruzi and Leishmania spp. infections. In this scenario, it is worth highlighting a group of natural peptide molecules (AMPs and CPPs) that are promising strategies for improving therapeutic efficacy against these neglected zoonoses, as they avoid the development of toxicity and resistance of conventional treatments. This review presents the novelties of these peptide molecules and their ability to cross a whole system of cell membranes as well as stimulate host immune defenses or even serve as vectors of molecules. The efforts of the biotechnological sector will make it possible to overcome the limitations of antimicrobial peptides through encapsulation and functionalization methods to obtain approval for these treatments to be used in clinical programs for the eradication of leishmaniosis and Chagas disease.
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Affiliation(s)
- Sara M Robledo
- Programa de Estudio y Control de Enfermedades Tropicales PECET, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia
| | - Silvia Pérez-Silanes
- Department of Pharmaceutical Technology and Chemistry, ISTUN Instituto de Salud Tropical, IdiSNA, Universidad de Navarra, 31008 Pamplona, Spain
| | - Celia Fernández-Rubio
- Department of Microbiology and Parasitology, ISTUN Instituto de Salud Tropical, IdiSNA, Universidad de Navarra, 31008 Pamplona, Spain
| | - Ana Poveda
- DNA Replication and Genome Instability Unit, Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Investigación en Zoonosis-CIZ, Facultad de Ciencias Químicas, Universidad Central del Ecuador, Quito 170521, Ecuador
| | - Lianet Monzote
- Department of Parasitology, Institute of Tropical Medicine "Pedro Kourí", Apartado Postal No. 601, Marianao 13, La Habana 10400, Cuba
| | - Víctor M González
- Grupo de Aptámeros, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Universitario Ramón y Cajal, Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - Paloma Alonso-Collado
- Department of Animal Health, Faculty of Veterinary Science, Complutense University of Madrid, 28040 Madrid, Spain
| | - Javier Carrión
- Department of Animal Health, Faculty of Veterinary Science, Complutense University of Madrid, 28040 Madrid, Spain
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wu C, Gan N, Ou C, Tang H, Zhou Y, Cao J. A homogenous “signal-on” aptasensor for antibiotics based on a single stranded DNA binding protein-quantum dot aptamer probe coupling exonuclease-assisted target recycling for signal amplification. RSC Adv 2017. [DOI: 10.1039/c6ra27337h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The method is based on replacement reaction, just by mixing the probes with targets for detection, which is simple and easy for manipulation.
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Affiliation(s)
- Caiye wu
- Faculty of Marine
- Ningbo University
- Ningbo
- China
- Faculty of Material Science and Chemical Engineering
| | - Ning Gan
- Faculty of Material Science and Chemical Engineering
- Ningbo University
- Ningbo
- China
| | | | - Haiqing Tang
- School of Food Science and Technology
- Zhejiang Pharmaceutical College
- Ningbo
- China
| | - You Zhou
- Faculty of Material Science and Chemical Engineering
- Ningbo University
- Ningbo
- China
| | - Jinxuan Cao
- Faculty of Marine
- Ningbo University
- Ningbo
- China
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Primary and Secondary Sequence Structure Requirements for Recognition and Discrimination of Target RNAs by Pseudomonas aeruginosa RsmA and RsmF. J Bacteriol 2016; 198:2458-69. [PMID: 27381913 DOI: 10.1128/jb.00343-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/27/2016] [Indexed: 01/13/2023] Open
Abstract
UNLABELLED CsrA family RNA-binding proteins are widely distributed in bacteria and regulate gene expression at the posttranscriptional level. Pseudomonas aeruginosa has a canonical member of the CsrA family (RsmA) and a novel, structurally distinct variant (RsmF). To better understand RsmF binding properties, we performed parallel systematic evolution of ligands by exponential enrichment (SELEX) experiments for RsmA and RsmF. The initial target library consisted of 62-nucleotide (nt) RNA transcripts with central cores randomized at 15 sequential positions. Most targets selected by RsmA and RsmF were the expected size and shared a common consensus sequence (CANGGAYG) that was positioned in a hexaloop region of the stem-loop structure. RsmA and RsmF also selected for longer targets (≥96 nt) that were likely generated by rare PCR errors. Most of the long targets contained two consensus-binding sites. Representative short (single consensus site) and long (two consensus sites) targets were tested for RsmA and RsmF binding. Whereas RsmA bound the short targets with high affinity, RsmF was unable to bind the same targets. RsmA and RsmF both bound the long targets. Mutation of either consensus GGA site in the long targets reduced or eliminated RsmF binding, suggesting a requirement for two tandem binding sites. Conversely, RsmA bound long targets containing only a single GGA site with unaltered affinity. The RsmF requirement for two binding sites was confirmed with tssA1, an in vivo regulatory target of RsmA and RsmF. Our findings suggest that RsmF binding requires two GGA-containing sites, while RsmA binding requirements are less stringent. IMPORTANCE The CsrA family of RNA-binding proteins is widely conserved in bacteria and plays important roles in the posttranscriptional regulation of protein synthesis. P. aeruginosa has two CsrA proteins, RsmA and RsmF. Although RsmA and RsmF share a few RNA targets, RsmF is unable to bind to other targets recognized by RsmA. The goal of the present study was to better understand the basis for differential binding by RsmF. Our data indicate that RsmF binding requires target RNAs with two consensus-binding sites, while RsmA recognizes targets with just a single binding site. This information should prove useful to future efforts to define the RsmF regulon and its contribution to P. aeruginosa physiology and virulence.
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Prakash JS, Rajamanickam K. Aptamers and Their Significant Role in Cancer Therapy and Diagnosis. Biomedicines 2015; 3:248-269. [PMID: 28536411 PMCID: PMC5344239 DOI: 10.3390/biomedicines3030248] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/07/2015] [Indexed: 02/07/2023] Open
Abstract
Aptamers are nucleic acid/peptide molecules that can be generated by a sophisticated, well-established technique known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Aptamers can interact with their targets through structural recognition, as in antibodies, though with higher specificity. With this added advantage, they can be made useful for clinical applications such as targeted therapy and diagnosis. In this review, we have discussed the steps involved in SELEX process and modifications executed to attain high affinity nucleic acid aptamers. Moreover, our review also highlights the therapeutic applications of aptamer functionalized nanoparticles and nucleic acids as chemo-therapeutic agents. In addition, we have described the development of "aptasensor" in clinical diagnostic application for detecting cancer cells and the use of aptamers in different routine imaging techniques, such as Positron Emission Tomography/Computed Tomography, Ultrasound, and Magnetic Resonance Imaging.
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Affiliation(s)
- Joy Sebastian Prakash
- Faculty of Allied Health Sciences (FAHS), Chettinad Academy of Research and Education, Kelambakkam, Chennai 603103, Tamil Nadu, India.
| | - Karunanithi Rajamanickam
- Faculty of Allied Health Sciences (FAHS), Chettinad Academy of Research and Education, Kelambakkam, Chennai 603103, Tamil Nadu, India.
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Davydova A, Vorobjeva M, Pyshnyi D, Altman S, Vlassov V, Venyaminova A. Aptamers against pathogenic microorganisms. Crit Rev Microbiol 2015; 42:847-65. [PMID: 26258445 PMCID: PMC5022137 DOI: 10.3109/1040841x.2015.1070115] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An important current issue of modern molecular medicine and biotechnology is the search for new approaches to early diagnostic assays and adequate therapy of infectious diseases. One of the promising solutions to this problem might be a development of nucleic acid aptamers capable of interacting specifically with bacteria, protozoa, and viruses. Such aptamers can be used for the specific recognition of infectious agents as well as for blocking of their functions. The present review summarizes various modern SELEX techniques used in this field, and of several currently identified aptamers against viral particles and unicellular organisms, and their applications. The prospects of applying nucleic acid aptamers for the development of novel detection systems and antibacterial and antiviral drugs are discussed.
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Affiliation(s)
- Anna Davydova
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Maria Vorobjeva
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Dmitrii Pyshnyi
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Sidney Altman
- b Department of Molecular, Cellular and Developmental Biology , Yale University , New Haven , CT , USA
| | - Valentin Vlassov
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Alya Venyaminova
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
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Xi Z, Huang R, Li Z, He N, Wang T, Su E, Deng Y. Selection of HBsAg-Specific DNA Aptamers Based on Carboxylated Magnetic Nanoparticles and Their Application in the Rapid and Simple Detection of Hepatitis B Virus Infection. ACS APPLIED MATERIALS & INTERFACES 2015; 7:11215-23. [PMID: 25970703 DOI: 10.1021/acsami.5b01180] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Aptamers are short single-stranded DNA or RNA oligonucleotides and can be selected from synthetic combinatorial libraries in vitro. They have a high binding affinity and specificity for their targets. Agarose gels, nitrocellulose membranes, and adsorptive microplates are often used as carriers to immobilize targets in the SELEX (systematic evolution of ligands by exponential enrichment) process, but the subsequent separation step is tedious and time-consuming. Therefore, we used magnetic nanoparticles (MNPs) as carriers to immobilize the target, hepatitis B surface antigen (HBsAg), which is convenient for fast magnetic separation. In this study, we first selected DNA aptamers against HBsAg by immobilizing HBsAg on the surface of carboxylated MNPs. The ssDNA library of each selection round was prepared by asymmetric PCR amplification for the next selection round. To obtain aptamer sequences, the final selected products were purified by gel electrophoresis, then cloned, and sequenced. DNA aptamers that specifically bind to HBsAg were successfully obtained after 13 selection rounds. The selected aptamers were used to construct a chemiluminescence aptasensor based on magnetic separation and immunoassay to detect HBsAg from pure protein or actual serum samples. There was a linear relationship between HBsAg concentration and chemiluminescent intensity in the range of 1-200 ng/mL. The aptasensor worked well even in the presence of interfering substances and was highly specific in the detection of HBsAg in serum samples, with a detection limit 0.1 ng/mL lower than the 0.5 ng/mL limit of an ELISA in use at the hospital. This aptasensor can contribute to better detection of hepatitis B virus infection.
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Affiliation(s)
- Zhijiang Xi
- †State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
- ‡School of Life and Science, Yangtze University, Jingzhou 434025, P. R. China
| | - Rongrong Huang
- †State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
| | - Zhiyang Li
- †State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
| | - Nongyue He
- †State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
- §Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Packaging and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Ting Wang
- †State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
| | - Enben Su
- †State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
- ∥Getein Biotechnology Co., Ltd., Nanjing 210000, P. R. China
| | - Yan Deng
- †State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
- §Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Packaging and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou 412007, P. R. China
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7
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Weinert U, Vogel M, Reinemann C, Strehlitz B, Pollmann K, Raff J. S-layer proteins as an immobilization matrix for aptamers on different sensor surfaces. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400204] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Ulrike Weinert
- Helmholtz-Zentrum Dresden-Rossendorf; Helmholtz Institute Freiberg for Resource Technology; Dresden Germany
| | - Manja Vogel
- Helmholtz-Zentrum Dresden-Rossendorf; Helmholtz Institute Freiberg for Resource Technology; Dresden Germany
- Helmholtz-Zentrum Dresden-Rossendorf; Institute of Resource Ecology; Dresden Germany
| | - Christine Reinemann
- Department Environmental and Biotechnology Centre; Helmholtz Centre for Environmental Research (UFZ); Leipzig Germany
| | - Beate Strehlitz
- Department Environmental and Biotechnology Centre; Helmholtz Centre for Environmental Research (UFZ); Leipzig Germany
| | - Katrin Pollmann
- Helmholtz-Zentrum Dresden-Rossendorf; Helmholtz Institute Freiberg for Resource Technology; Dresden Germany
| | - Johannes Raff
- Helmholtz-Zentrum Dresden-Rossendorf; Helmholtz Institute Freiberg for Resource Technology; Dresden Germany
- Helmholtz-Zentrum Dresden-Rossendorf; Institute of Resource Ecology; Dresden Germany
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8
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Wu Y, Zhan S, Wang L, Zhou P. Selection of a DNA aptamer for cadmium detection based on cationic polymer mediated aggregation of gold nanoparticles. Analyst 2015; 139:1550-61. [PMID: 24496116 DOI: 10.1039/c3an02117c] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The demand for selection of aptamers against various small chemical molecules has substantially increased in recent years. To incubate and separate target-specific aptamers, the conventional SELEX procedures generally need to immobilize target molecules on a matrix, which may be impotent to screen aptamers toward small molecules without enough sites for immobilization. Herein we chose Cd(II) as a model of a small molecule with less sites, and proposed a novel SELEX strategy of immobilizing ssDNA libraries rather than target molecules on a matrix, for selection of aptamers with high affinity to Cd(II). After eleven rounds of positive and negative selection, twelve T and G-rich of nonrepeating ssDNA sequences were identified, of which the Cd-4 aptamer displayed the highest binding affinity to Cd(II). The secondary structures of these sequences revealed that a stem-loop structure folded by the domain of their 30-random sequence is critical for aptamers to bind targets. Then the interaction between the selected Cd-4 aptamer and Cd(II) was confirmed by CD analysis, and the binding specificity toward other competitive metal ions was also investigated. The dissociation constant (Kd) of Cd-4 aptamer was determined as 34.5 nM for Cd(II). Moreover, the Cd-4 aptamer was considered a recognition element for the colorimetric detection of Cd(II) based on the aggregation of AuNPs by cationic polymer. Through spectroscopic quantitative analysis, Cd(II) in aqueous solution can be detected as low as 4.6 nM. The selected Cd-4 aptamer will offer a new substitute for the detection of Cd(II) or other applications like recovery of cadmium from polluted samples.
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Affiliation(s)
- Yuangen Wu
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China.
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9
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Martin JA, Chávez JL, Chushak Y, Chapleau RR, Hagen J, Kelley-Loughnane N. Tunable stringency aptamer selection and gold nanoparticle assay for detection of cortisol. Anal Bioanal Chem 2014; 406:4637-47. [PMID: 24880870 DOI: 10.1007/s00216-014-7883-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/25/2014] [Accepted: 05/07/2014] [Indexed: 01/17/2023]
Abstract
The first-known aptamer for the stress biomarker cortisol was selected using a tunable stringency magnetic bead selection strategy. The capture DNA probe immobilized on the beads was systematically lengthened to increase the number of bases bound to the complementary pool primer regions following selection enrichment. This resulted in a single sequence (15-1) dominating the final round 15 pool, where the same sequence was the second-highest copy number candidate in the enriched pool with the shorter capture DNA probe (round 13). A thorough analysis of the next-generation sequencing results showed that a high copy number may only correlate with enhanced affinity under certain stringency and enrichment conditions, in contrast with prior published reports. Aptamer 15-1 demonstrated enhanced binding to cortisol (K(d) = 6.9 ± 2.8 μM by equilibrium dialysis; 16.1 ± 0.6 μM by microscale thermophoresis) when compared with the top sequence from round 13 and the negative control progesterone. Whereas most aptamer selections terminate at the selection round demonstrating the highest enrichment, this work shows that extending the selection with higher stringency conditions leads to lower amounts eluted by the target but higher copy numbers of a sequence with enhanced binding. The structure-switching aptamer was applied to a gold nanoparticle assay in buffer and was shown to discriminate between cortisol and two other stress biomarkers, norepinephrine and epinephrine, and a structurally analogous biomarker of liver dysfunction, cholic acid. We believe this approach enhances aptamer selection and serves as proof-of-principle work toward development of point-of-care diagnostics for medical, combat, or bioterrorism targets.
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Affiliation(s)
- Jennifer A Martin
- Air Force Research Laboratory, Human Effectiveness Directorate, 711th Human Performance Wing, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
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10
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Ahn JY, Jo M, Dua P, Lee DK, Kim S. A sol-gel-based microfluidics system enhances the efficiency of RNA aptamer selection. Oligonucleotides 2011; 21:93-100. [PMID: 21413890 DOI: 10.1089/oli.2010.0263] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
RNA and DNA aptamers that bind to target molecules with high specificity and affinity have been a focus of diagnostics and therapeutic research. These aptamers are obtained by SELEX often requiring many rounds of selection and amplification. Recently, we have shown the efficient binding and elution of RNA aptamers against target proteins using a microfluidic chip that incorporates 5 sol-gel binding droplets within which specific target proteins are imbedded. Here, we demonstrate that our microfluidic chip in a SELEX experiment greatly improved selection efficiency of RNA aptamers to TATA-binding protein, reducing the number of selection cycles needed to produce high affinity aptamers by about 80%. Many aptamers were identical or homologous to those isolated previously by conventional filter-binding SELEX. The microfluidic chip SELEX is readily scalable using a sol-gel microarray-based target multiplexing. Additionally, we show that sol-gel embedded protein arrays can be used as a high-throughput assay for quantifying binding affinities of aptamers.
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Affiliation(s)
- Ji-Young Ahn
- Department of Molecular Biology and Genetics, Cornell University , Ithaca, New York
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12
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Abstract
SUMMARYHuman African trypanosomiasis (HAT) or sleeping sickness is caused by protozoan parasitesTrypanosoma brucei gambienseandT. b. rhodesiense. Despite the enormous technological progress in molecular parasitology in recent years, the diagnosis of HAT is still problematic due to the lack of specific tools. To date, there are two realities when it comes to HAT; the first one being the world of modern experimental laboratories, equipped with the latest state-of-the-art technology, and the second being the world of HAT diagnosis, where the latest semi-commercial test was introduced 30 years ago (Magnuset al.1978). Hence, it appears that the lack of progress in HAT diagnosis is not primarily due to a lack of scientific interest or a lack of research funds, but mainly results from the many obstacles encountered in the translation of basic research into field-applicable diagnostics. This review will provide an overview of current diagnostic methods and highlight specific difficulties in solving the shortcomings of these methods. Future perspectives for accurate, robust, affordable diagnostics will be discussed as well.
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Wang J, Munir A, Li Z, Zhou HS. Aptamer–Au NPs conjugates-enhanced SPR sensing for the ultrasensitive sandwich immunoassay. Biosens Bioelectron 2009; 25:124-9. [DOI: 10.1016/j.bios.2009.06.016] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 06/04/2009] [Accepted: 06/08/2009] [Indexed: 02/07/2023]
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Raddatz MSL, Dolf A, Endl E, Knolle P, Famulok M, Mayer G. Enrichment of cell-targeting and population-specific aptamers by fluorescence-activated cell sorting. Angew Chem Int Ed Engl 2008; 47:5190-3. [PMID: 18512861 DOI: 10.1002/anie.200800216] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Marie-Sophie L Raddatz
- Life and Medical Science, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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Raddatz M, Dolf A, Endl E, Knolle P, Famulok M, Mayer G. Enrichment of Cell‐Targeting and Population‐Specific Aptamers by Fluorescence‐Activated Cell Sorting. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800216] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Schultz C. Molecular tools for cell and systems biology. HFSP JOURNAL 2007; 1:230-48. [PMID: 19404424 DOI: 10.2976/1.2812442] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 10/24/2007] [Indexed: 01/25/2023]
Abstract
The sequencing of the genomes of key organisms and the subsequent identification of genes merely leads us to the next real challenge in modern biology-revealing the precise functions of these genes. Further, detailed knowledge of how the products of these genes behave in space and time is required, including their interactions with other molecules. In order to tackle these considerable tasks, a large and continuously expanding toolbox is required to probe the functions of proteins on a cellular level. Here, the currently available tools are described and future developments are projected. There is no doubt that only the close interplay between the life science disciplines in addition to advances in engineering will be able to meet the challenge.
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Affiliation(s)
- Carsten Schultz
- Gene Expression Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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17
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Famulok M, Hartig JS, Mayer G. Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem Rev 2007; 107:3715-43. [PMID: 17715981 DOI: 10.1021/cr0306743] [Citation(s) in RCA: 666] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael Famulok
- LIMES Institute, Program Unit Chemical Biology and Medicinal Chemistry, c/o Kekulé-Institut für Organische Chemie und Biochemie, Gerhard Domagk-Strasse 1, 53121 Bonn, Germany.
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Stoltenburg R, Reinemann C, Strehlitz B. SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands. ACTA ACUST UNITED AC 2007; 24:381-403. [PMID: 17627883 DOI: 10.1016/j.bioeng.2007.06.001] [Citation(s) in RCA: 934] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 05/31/2007] [Accepted: 06/01/2007] [Indexed: 02/07/2023]
Abstract
SELEX stands for systematic evolution of ligands by exponential enrichment. This method, described primarily in 1990 [Ellington, A.D., Szostak, J.W., 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822; Tuerk, C., Gold, L., 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510] aims at the development of aptamers, which are oligonucleotides (RNA or ssDNA) binding to their target with high selectivity and sensitivity because of their three-dimensional shape. Aptamers are all new ligands with a high affinity for considerably differing molecules ranging from large targets as proteins over peptides, complex molecules to drugs and organic small molecules or even metal ions. Aptamers are widely used, including medical and pharmaceutical basic research, drug development, diagnosis, and therapy. Analytical and separation tools bearing aptamers as molecular recognition and binding elements are another big field of application. Moreover, aptamers are used for the investigation of binding phenomena in proteomics. The SELEX method was modified over the years in different ways to become more efficient and less time consuming, to reach higher affinities of the aptamers selected and for automation of the process. This review is focused on the development of aptamers by use of SELEX and gives an overview about technologies, advantages, limitations, and applications of aptamers.
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Affiliation(s)
- Regina Stoltenburg
- UFZ, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
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Fischer NO, Tarasow TM, Tok JBH. Aptasensors for biosecurity applications. Curr Opin Chem Biol 2007; 11:316-28. [PMID: 17548236 DOI: 10.1016/j.cbpa.2007.05.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 05/18/2007] [Indexed: 10/23/2022]
Abstract
Nucleic acid (aptasensors) have found steadily increased utility and application over the past decade. In particular, aptamers have been touted as a valuable complement to and, in some cases, replacement for antibodies owing to their structural and functional robustness as well as their ease in generation and synthesis. They are thus attractive for biosecurity applications (e.g. pathogen detection) and are especially well suited because their in vitro generation process does not require infection of any host systems. Herein we provide a brief overview of the aptamers generated against pathogens and toxins over the past few years. In addition, a few recently described detection platforms using aptamers and potentially suitable applications for biosecurity will be discussed.
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Affiliation(s)
- Nicholas O Fischer
- BioSecurity and NanoSciences Laboratory, Chemistry, Materials & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
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König J, Julius C, Baumann S, Homann M, Göringer HU, Feldbrügge M. Combining SELEX and the yeast three-hybrid system for in vivo selection and classification of RNA aptamers. RNA (NEW YORK, N.Y.) 2007; 13:614-22. [PMID: 17283213 PMCID: PMC1831868 DOI: 10.1261/rna.334307] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aptamers are small nucleic acid ligands that bind to their targets with specificity and high affinity. They are generated by a combinatorial technology, known as SELEX. This in vitro approach uses iterative cycles of enrichment and amplification to select binders from nucleic acid libraries of high complexity. Here we combine SELEX with the yeast three-hybrid system in order to select for RNA aptamers with in vivo binding activity. As a target molecule, we chose the RNA recognition motif-containing RNA-binding protein Rrm4 from the corn pathogen Ustilago maydis. Rrm4 is an ELAV-like protein containing three N-terminal RNA recognition motifs (RRMs). It has been implicated in microtubule-dependent RNA transport during pathogenic development. After 11 SELEX cycles, four aptamer classes were identified. These sequences were further screened for their in vivo binding activity applying the yeast three-hybrid system. Of the initial aptamer classes only members of two classes were capable of binding in vivo. Testing representatives of both classes against Rrm4 variants mutated in one of the three RRM domains revealed that these aptamers interacted with the third RRM. Thus, the yeast three-hybrid system is a useful extension to the SELEX protocol for the identification and characterization of aptamers with in vivo binding activity.
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Affiliation(s)
- Julian König
- Department of Organismic Interactions, Max-Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, Marburg, Germany
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Mascini M, Papamichael K, Mevola I, Pravda M, Guilbault GG. Ghrelin Detection Using Spiegelmer‐Capture Molecules. ANAL LETT 2007. [DOI: 10.1080/00032710601102391] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Gopinath SCB, Misono TS, Kawasaki K, Mizuno T, Imai M, Odagiri T, Kumar PKR. An RNA aptamer that distinguishes between closely related human influenza viruses and inhibits haemagglutinin-mediated membrane fusion. J Gen Virol 2006; 87:479-487. [PMID: 16476969 DOI: 10.1099/vir.0.81508-0] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aptamers selected against various kinds of targets have shown remarkable specificity and affinity, similar to those displayed by antibodies to their antigens. To employ aptamers as genotyping reagents for the identification of pathogens and their strains, in vitro selections were carried out to find aptamers that specifically bind and distinguish the closely related human influenza A virus subtype H3N2. The selected aptamer, P30-10-16, binds specifically to the haemagglutinin (HA) region of the target strain A/Panama/2007/1999(H3N2) and failed to recognize other human influenza viruses, including another strain with the same subtype, H3N2. The aptamer displayed over 15-fold-higher affinity to the HA compared with the monoclonal antibody, and efficiently inhibited HA-mediated membrane fusion. These studies delineate the application of aptamers in the genotyping of viruses.
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Affiliation(s)
- Subash C B Gopinath
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1 Higashi, Tsukuba City, Ibaraki 305-8566, Japan
| | - Tomoko S Misono
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1 Higashi, Tsukuba City, Ibaraki 305-8566, Japan
| | - Kazunori Kawasaki
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1 Higashi, Tsukuba City, Ibaraki 305-8566, Japan
| | - Takafumi Mizuno
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1 Higashi, Tsukuba City, Ibaraki 305-8566, Japan
| | - Masaki Imai
- Department of Virology III, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Takato Odagiri
- Department of Virology III, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Penmetcha K R Kumar
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1 Higashi, Tsukuba City, Ibaraki 305-8566, Japan
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Famulok M, Mayer G. Intramers and aptamers: applications in protein-function analyses and potential for drug screening. Chembiochem 2005; 6:19-26. [PMID: 15637667 DOI: 10.1002/cbic.200400299] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Michael Famulok
- Rheinische Friedrich-Wilhelms Universität Bonn, Kekulé-Institut für Organische Chemie und Biochemie, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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Abstract
In the year 2003 there was a 17% increase in the number of publications citing work performed using optical biosensor technology compared with the previous year. We collated the 962 total papers for 2003, identified the geographical regions where the work was performed, highlighted the instrument types on which it was carried out, and segregated the papers by biological system. In this overview, we spotlight 13 papers that should be on everyone's 'must read' list for 2003 and provide examples of how to identify and interpret high-quality biosensor data. Although we still find that the literature is replete with poorly performed experiments, over-interpreted results and a general lack of understanding of data analysis, we are optimistic that these shortcomings will be addressed as biosensor technology continues to mature.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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Freede P, Brantl S. Transcriptional Repressor CopR: use of SELEX to study the copR operator indicates that evolution was directed at maximal binding affinity. J Bacteriol 2004; 186:6254-64. [PMID: 15342596 PMCID: PMC515161 DOI: 10.1128/jb.186.18.6254-6264.2004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CopR is one of the two copy number control elements of the streptococcal plasmid pIP501. It represses transcription of the repR mRNA encoding the essential replication initiator protein about 10- to 20-fold by binding to its operator region upstream of the repR promoter pII. CopR binds at two consecutive sites in the major groove of the DNA that share the consensus motif 5'-CGTG. Previously, the minimal operator was narrowed down to 17 bp, and equilibrium dissociation constants for DNA binding and dimerization were determined to be 0.4 nM and 1.4 microM, respectively. In this work, we used a SELEX procedure to study copR operator sequences of different lengths in combination with electrophoretic mobility shift assays of mutated copR operators as well as copy number determinations to assess the sequence requirements for CopR binding. The results suggest that in vivo evolution was directed at maximal binding affinity. Three simultaneous nucleotide exchanges outside the bases directly contacted by CopR only slightly affected CopR binding in vitro or copy numbers in vivo. Furthermore, the optimal spacer sequence was found to comprise 7 bp, to be AT rich, and to need an A/T and a T at the 3' positions, whereas broad variations in the sequences flanking the minimal 17-bp operator were well tolerated.
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Affiliation(s)
- Peggy Freede
- Friedrich-Schiller-Universität Jena, Biologisch-Pharmazeutische Fakultät, AG Bakteriengenetik, Hans-Knoll-Str. 2, Jena D-07745, Germany
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