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Narayan C, Veeramani S, Thiel WH. Optimization of RNA Aptamer SELEX Methods: Improved Aptamer Transcript 3'-End Homogeneity, PAGE Purification Yield, and Target-Bound Aptamer RNA Recovery. Nucleic Acid Ther 2022; 32:74-80. [PMID: 34757856 PMCID: PMC8817694 DOI: 10.1089/nat.2021.0060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Since its inception in the early 1990s, SELEX remains the gold standard for discovering RNA aptamers specific for proteins and small molecules. The SELEX process has undergone countless modifications and now encompasses a breadth of innovative selection schemes to pare an aptamer library toward target-specific aptamers. Common to all these RNA aptamer SELEX processes are the steps for the preparation of DNA template and in vitro transcription of aptamer RNA. These steps have remained mostly unchanged over the past three decades and would benefit from optimization. We focused on three key areas: improving the homogeneity of in vitro transcribed aptamer RNA, increasing the efficiency of in vitro transcribed aptamer RNA purification by PAGE, and improving the quality of target-bound aptamer RNA recovered during SELEX. Together, these optimizations contribute toward a more efficient SELEX process and are applicable to both protein-based and cell-based RNA aptamer selections.
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Affiliation(s)
- Chandan Narayan
- Department of Internal Medicine and University of Iowa, Iowa City, Iowa, USA
| | - Suresh Veeramani
- Department of Internal Medicine and University of Iowa, Iowa City, Iowa, USA.,Department of Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA.,Address correspondence to: Suresh Veeramani, DVM, PhD, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - William H. Thiel
- Department of Internal Medicine and University of Iowa, Iowa City, Iowa, USA.,Address correspondence to: William H. Thiel, PhD, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
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Narayan C, Kwon J, Kim C, Kim SJ, Jang SK. Virus-based SELEX (viro-SELEX) allows development of aptamers targeting knotty proteins. Analyst 2020; 145:1473-1482. [PMID: 31868873 DOI: 10.1039/c9an01943j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
It has been 100 years since the worst flu (Spanish flu) mankind has ever experienced. Rapid, accurate diagnosis and subtyping of flu are still an urgent unmet medical need. By using surrogate virus-based SELEX (viro-SELEX), we report here multiple advances incorporated into the field of flu diagnostics: (i) aptamers that can bind to the native virus well even though they cannot bind strongly to a recombinant protein (hemagglutinin); (ii) a couple of aptamers that can target a broad range of strains belonging to the H1N1 subtype and detect only the H1N1 subtype and nothing else; (iii) a highly sensitive lateral flow assay system (limit of detection is 0.08 HAU) using fluorescence-tagged aptamers. The viro-SELEX method of aptamer selection in conjunction with a fluorescent tag on aptamers is a very useful approach to develop highly sensitive, specific, portable, rapid, and quantitative point-of-care testing diagnostic tools for the future.
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Affiliation(s)
- Chandan Narayan
- Molecular virology Laboratory, Department of Life Sciences, Postech Biotech Center, Pohang University of Science and Technology, Cheongam-ro 77, Nam-gu, Pohang-si, Gyeongsangbuk-do 37673, Republic of Korea.
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Bergevin C, Narayan C, Williams J, Mhatre N, Steeves JK, Bernstein JG, Story B. Overtone focusing in biphonic tuvan throat singing. eLife 2020; 9:50476. [PMID: 32048990 PMCID: PMC7064340 DOI: 10.7554/elife.50476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 01/31/2020] [Indexed: 11/13/2022] Open
Abstract
Khoomei is a unique singing style originating from the republic of Tuva in central Asia. Singers produce two pitches simultaneously: a booming low-frequency rumble alongside a hovering high-pitched whistle-like tone. The biomechanics of this biphonation are not well-understood. Here, we use sound analysis, dynamic magnetic resonance imaging, and vocal tract modeling to demonstrate how biphonation is achieved by modulating vocal tract morphology. Tuvan singers show remarkable control in shaping their vocal tract to narrowly focus the harmonics (or overtones) emanating from their vocal cords. The biphonic sound is a combination of the fundamental pitch and a focused filter state, which is at the higher pitch (1-2 kHz) and formed by merging two formants, thereby greatly enhancing sound-production in a very narrow frequency range. Most importantly, we demonstrate that this biphonation is a phenomenon arising from linear filtering rather than from a nonlinear source.
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Affiliation(s)
- Christopher Bergevin
- Physics and Astronomy, York University, Toronto, Canada.,Centre for Vision Research, York University, Toronto, Canada.,Fields Institute for Research in Mathematical Sciences, Toronto, Canada.,Kavli Institute of Theoretical Physics, University of California, Santa Barbara, United States
| | - Chandan Narayan
- Languages, Literatures and Linguistics, York University, Toronto, Canada
| | - Joy Williams
- York MRI Facility, York University, Toronto, Canada
| | | | - Jennifer Ke Steeves
- Centre for Vision Research, York University, Toronto, Canada.,Psychology, York University, Toronto, Canada
| | - Joshua Gw Bernstein
- National Military Audiology & Speech Pathology Center, Walter Reed National Military Medical Center, Bethesda, United States
| | - Brad Story
- Speech, Language, and Hearing Sciences, University of Arizona, Tucson, United States
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Kwon J, Narayan C, Kim C, Han MJ, Kim M, Jang SK. Development of a Subtype-Specific Diagnostic System for Influenza Virus H3N2 Using a Novel Virus-Based Systematic Evolution of Ligands by Exponential Enrichment (Viro-SELEX). J Biomed Nanotechnol 2019; 15:1609-1621. [PMID: 31196363 DOI: 10.1166/jbn.2019.2789] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Aptamers are oligonucleotide molecules that bind to specific target molecules generated by systematic evolution of ligands by exponential enrichment (SELEX). Aptamers have high future potential for use in diagnostics and therapeutics as molecular probes that recognize target molecules. To develop aptamers against a target protein using a SELEX process, it is necessary to purify the target protein. Purifying a membrane protein, however, is usually a challenging task. Here, we report a novel approach to developing aptamers against membrane proteins. Surrogate viruses containing target proteins on the surface of an enveloped virus (e.g., baculovirus), instead of purified proteins, were used in a new SELEX process. We designated this new SELEX process as "surrogate virus-based SELEX (viro-SELEX)." Using viro-SELEX, we developed a pair of aptamers that specifically interact with the hemagglutinin protein of influenza subtype H3N2. Using the aptamer pair and a lateral flow assay system, we developed a very sensitive point-of-care diagnostic system for specifically detecting influenza virus subtype H3N2.
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Tantry SJ, Degiacomi G, Sharma S, Jena LK, Narayan A, Guptha S, Shanbhag G, Menasinakai S, Mallya M, Awasthy D, Balakrishnan G, Kaur P, Bhattacharjee D, Narayan C, Reddy J, Naveen Kumar C, Shandil R, Boldrin F, Ventura M, Manganelli R, Hartkoorn RC, Cole ST, Panda M, Markad SD, Ramachandran V, Ghorpade SR, Dinesh N. Whole cell screen based identification of spiropiperidines with potent antitubercular properties. Bioorg Med Chem Lett 2015; 25:3234-45. [DOI: 10.1016/j.bmcl.2015.05.087] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 05/23/2015] [Accepted: 05/26/2015] [Indexed: 11/24/2022]
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Raghavendra Achar VG, Barde SP, Mallya MV, Awasthy D, Narayan C. Optimization of Compound Plate Preparation to Address Precipitation Issue in Mammalian A549 Cytotoxicity Assay. ACTA ACUST UNITED AC 2015; 21:423-31. [PMID: 26185254 DOI: 10.1177/2211068215594768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Indexed: 11/16/2022]
Abstract
This study illustrates the optimization of low-volume dispensing on a liquid handling system (LHS) to overcome the precipitation of compounds in the mammalian cytotoxicity assay with low dimethyl sulfoxide (DMSO) tolerance. All compounds at AstraZeneca Bangalore are tested in the mammalian cytotoxicity assay. In order to maintain the DMSO levels, serially diluted plates were prepared in DMSO/water. It was observed that some of the compounds precipitated. The IC50 data for such compounds were therefore erratic. To circumvent the problem of compound precipitation, the LHS was optimized to dispense low volumes (<1 µL). The plates were serially diluted using neat DMSO. Since the dilution was done using neat DMSO, there were no issues with precipitation. The serially diluted sample (0.5 µL) from the plate was stamped onto the assay plate to give the desired DMSO concentration. No significant differences in IC50 data were observed for 1 µL dispenses made from DMSO/water and 0.5 µL dispenses from neat DMSO for the samples with no precipitation issues. These data therefore gave us the confidence to switch over to 0.5 µL dispenses for the cytotoxicity assay to address the precipitation issue. However, precipitation of samples in the assay buffer is beyond the scope of this discussion.
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Affiliation(s)
| | - Shubhada Pramod Barde
- Compound Management, Department of Biosciences (Microbiology), AstraZeneca India Pvt. Ltd., Hebbal, Bangalore, India
| | - Meenakshy Venkatesh Mallya
- Compound Management, Department of Biosciences (Microbiology), AstraZeneca India Pvt. Ltd., Hebbal, Bangalore, India
| | - Disha Awasthy
- Compound Management, Department of Biosciences (Microbiology), AstraZeneca India Pvt. Ltd., Hebbal, Bangalore, India
| | - Chandan Narayan
- Compound Management, Department of Biosciences (Microbiology), AstraZeneca India Pvt. Ltd., Hebbal, Bangalore, India
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Hameed P S, Chinnapattu M, Shanbag G, Manjrekar P, Koushik K, Raichurkar A, Patil V, Jatheendranath S, Rudrapatna SS, Barde SP, Rautela N, Awasthy D, Morayya S, Narayan C, Kavanagh S, Saralaya R, Bharath S, Viswanath P, Mukherjee K, Bandodkar B, Srivastava A, Panduga V, Reddy J, Prabhakar KR, Sinha A, Jiménez-Díaz MB, Martínez MS, Angulo-Barturen I, Ferrer S, Sanz LM, Gamo FJ, Duffy S, Avery VM, Magistrado PA, Lukens AK, Wirth DF, Waterson D, Balasubramanian V, Iyer PS, Narayanan S, Hosagrahara V, Sambandamurthy VK, Ramachandran S. Aminoazabenzimidazoles, a Novel Class of Orally Active Antimalarial Agents. J Med Chem 2014; 57:5702-13. [DOI: 10.1021/jm500535j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Stefan Kavanagh
- Safety
Assessment, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | - María Belén Jiménez-Díaz
- Tres
Cantos Medicines Development Campus, Diseases of Developing World
(DDW), GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - María Santos Martínez
- Tres
Cantos Medicines Development Campus, Diseases of Developing World
(DDW), GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Iñigo Angulo-Barturen
- Tres
Cantos Medicines Development Campus, Diseases of Developing World
(DDW), GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Santiago Ferrer
- Tres
Cantos Medicines Development Campus, Diseases of Developing World
(DDW), GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Laura María Sanz
- Tres
Cantos Medicines Development Campus, Diseases of Developing World
(DDW), GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Francisco Javier Gamo
- Tres
Cantos Medicines Development Campus, Diseases of Developing World
(DDW), GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Sandra Duffy
- Discovery
Biology, Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Vicky M. Avery
- Discovery
Biology, Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | | | - Amanda K. Lukens
- Harvard School of Public Health, Boston, Massachusetts 02115, United States
| | - Dyann F. Wirth
- Harvard School of Public Health, Boston, Massachusetts 02115, United States
| | - David Waterson
- Medicines for Malaria Venture, International Center
Cointrin, Route de Pré-Bois 20, Post Office Box 1826, 1215 Geneva, Switzerland
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Naik M, Humnabadkar V, Tantry SJ, Panda M, Narayan A, Guptha S, Panduga V, Manjrekar P, Jena LK, Koushik K, Shanbhag G, Jatheendranath S, Manjunatha MR, Gorai G, Bathula C, Rudrapatna S, Achar V, Sharma S, Ambady A, Hegde N, Mahadevaswamy J, Kaur P, Sambandamurthy VK, Awasthy D, Narayan C, Ravishankar S, Madhavapeddi P, Reddy J, Prabhakar KR, Saralaya R, Chatterji M, Whiteaker J, McLaughlin B, Chiarelli LR, Riccardi G, Pasca MR, Binda C, Neres J, Dhar N, Signorino-Gelo F, McKinney JD, Ramachandran V, Shandil R, Tommasi R, Iyer PS, Narayanan S, Hosagrahara V, Kavanagh S, Dinesh N, Ghorpade SR. 4-Aminoquinolone Piperidine Amides: Noncovalent Inhibitors of DprE1 with Long Residence Time and Potent Antimycobacterial Activity. J Med Chem 2014; 57:5419-34. [DOI: 10.1021/jm5005978] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Laurent R. Chiarelli
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Giovanna Riccardi
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Maria Rosalia Pasca
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Claudia Binda
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - João Neres
- École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Neeraj Dhar
- École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | - John D. McKinney
- École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | | | | | | | | | | | - Stefan Kavanagh
- Safety Assessment, AstraZeneca, Alderley
Park, Macclesfield, Cheshire SK10 2NA, United Kingdom
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Hameed P S, Patil V, Solapure S, Sharma U, Madhavapeddi P, Raichurkar A, Chinnapattu M, Manjrekar P, Shanbhag G, Puttur J, Shinde V, Menasinakai S, Rudrapatana S, Achar V, Awasthy D, Nandishaiah R, Humnabadkar V, Ghosh A, Narayan C, Ramya VK, Kaur P, Sharma S, Werngren J, Hoffner S, Panduga V, Kumar CNN, Reddy J, Kumar KN M, Ganguly S, Bharath S, Bheemarao U, Mukherjee K, Arora U, Gaonkar S, Coulson M, Waterson D, Sambandamurthy VK, de Sousa SM. Novel N-Linked Aminopiperidine-Based Gyrase Inhibitors with Improved hERG and in Vivo Efficacy against Mycobacterium tuberculosis. J Med Chem 2014; 57:4889-905. [DOI: 10.1021/jm500432n] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Michelle Coulson
- Safety
Assessment, AstraZeneca, Alderley Park, Macclesfield, U.K
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Shirude PS, Shandil R, Sadler C, Naik M, Hosagrahara V, Hameed S, Shinde V, Bathula C, Humnabadkar V, Kumar N, Reddy J, Panduga V, Sharma S, Ambady A, Hegde N, Whiteaker J, McLaughlin RE, Gardner H, Madhavapeddi P, Ramachandran V, Kaur P, Narayan A, Guptha S, Awasthy D, Narayan C, Mahadevaswamy J, Vishwas KG, Ahuja V, Srivastava A, Prabhakar KR, Bharath S, Kale R, Ramaiah M, Choudhury NR, Sambandamurthy VK, Solapure S, Iyer PS, Narayanan S, Chatterji M. Azaindoles: noncovalent DprE1 inhibitors from scaffold morphing efforts, kill Mycobacterium tuberculosis and are efficacious in vivo. J Med Chem 2013; 56:9701-8. [PMID: 24215368 DOI: 10.1021/jm401382v] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report 1,4-azaindoles as a new inhibitor class that kills Mycobacterium tuberculosis in vitro and demonstrates efficacy in mouse tuberculosis models. The series emerged from scaffold morphing efforts and was demonstrated to noncovalently inhibit decaprenylphosphoryl-β-D-ribose2'-epimerase (DprE1). With "drug-like" properties and no expectation of pre-existing resistance in the clinic, this chemical class has the potential to be developed as a therapy for drug-sensitive and drug-resistant tuberculosis.
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Affiliation(s)
- Pravin S Shirude
- Department of Medicinal Chemistry, IMED Infection, AstraZeneca India , Bellary Road, Hebbal, Bangalore 560024, India
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