1
|
Ban E, Kim A. PicoGreen assay for nucleic acid quantification - Applications, challenges, and solutions. Anal Biochem 2024; 692:115577. [PMID: 38789006 DOI: 10.1016/j.ab.2024.115577] [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: 01/18/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Various analytical methods and reagents have been employed for nucleic acid analysis in cells, biological fluids, and formulations. Standard techniques like gel electrophoresis and qRT-PCR are widely used for qualitative and quantitative nucleic acid analysis. However, these methods can be time-consuming and labor-intensive, with limitations such as inapplicability to small RNA at low concentrations and high costs associated with qRT-PCR reagents and instruments. As an alternative, PicoGreen (PG) has emerged as a valuable method for the quantitative analysis of nucleic acids. PG, a fluorescent dye, enables the quantitation of double-stranded DNA (dsDNA) or double-stranded RNA, including miRNA mimic and siRNA, in solution. It is also applicable to DNA and RNA analysis within cells using techniques like FACS and fluorescence microscopy. Despite its advantages, PG's fluorescence intensity is affected by various experimental conditions, such as pH, salts, and chemical reagents. This review explores the recent applications of PG as a rapid, cost-effective, robust, and accurate assay tool for nucleic acid quantification. We also address the limitations of PG and discuss approaches to overcome these challenges, recognizing the expanding range of its applications.
Collapse
Affiliation(s)
- Eunmi Ban
- College of Pharmacy, CHA University, Seongnam, 13488, South Korea
| | - Aeri Kim
- College of Pharmacy, CHA University, Seongnam, 13488, South Korea.
| |
Collapse
|
2
|
Hu Y, Li C, Hu M, Zhang Z, Fu R, Tang X, Wu T. Allosteric Nucleic Acid Enzyme: A Versatile Stimuli-Responsive Tool for Molecular Computing and Biosensing Nanodevices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2300207. [PMID: 36978231 DOI: 10.1002/smll.202300207] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Allostery is a naturally occurring mechanism in which effector binding induces the modulation and fine control of a related biomolecule function. Deoxyribozyme (DNAzyme) with catalytic activity and substrate recognition ability is ideal to be regulated by allosteric strategies. However, the current regulations frequently confront various obstacles, such as severe activity decay, signal leakage, and limited effectors. In this work, a rational regulation strategy for developing versatile effectors-responsive allosteric nucleic acid enzyme (ANAzyme) by introducing an allosteric domain in response to diverse effectors is established. The enzyme-like activity of this re-engineered ANAzyme can be modulated in a more predictable and fine way compared with the previous DNAzyme regulation strategies. Based on the allosteric strategy, the construction of allosterically coregulatory nanodevices and a series of basic logic gates and logic circuits are achieved, demonstrating that the proposed ANAzyme-regulated strategy showed great potential in molecular computing. Given these facts, the rational design of ANAzyme with the allosteric domain presented here can expand the available toolbox to develop a variety of stimuli-responsive allosteric DNA materials, including molecular machines, computing systems, biosensing platforms, and gene-silencing tools.
Collapse
Affiliation(s)
- Yuqiang Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Changjiang Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Minghao Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Zhen Zhang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Ruolan Fu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| |
Collapse
|
3
|
Guillen D, Schievelbein M, Patel K, Jose D, Ouellet J. A simple and affordable kinetic assay of nucleic acids with SYBR Gold gel staining. PLoS One 2020; 15:e0229527. [PMID: 32126098 PMCID: PMC7053750 DOI: 10.1371/journal.pone.0229527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/07/2020] [Indexed: 11/18/2022] Open
Abstract
Labeling substrates or products are paramount in determining enzymatic kinetic parameters. Several options are available; many laboratories use either radioactive or fluorescent labeling because of their high sensitivity. However, those methods have their own drawbacks such as half-life decay, expensive and hazardous. Here, we propose a novel, simple, economical and fast alternative to substrate labeling for studying the kinetics of nucleic acids: post-migration gel staining with SYBR Gold. Cleavage rates similar to the ones reported in the literature for the I-R3 DNA-cleaving DNA enzyme in the presence of zinc chloride are an indication of the quality of the new method. Moreover, the activity of the hammerhead ribozyme was also monitored by our method to illustrate its versatility. This labeling-free method has several advantages such as its ease of use as well as cost effective and versatility with both non-structured and structured RNAs or DNAs.
Collapse
Affiliation(s)
- Danielle Guillen
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey, United States of America
| | - Mika Schievelbein
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey, United States of America
| | - Kushkumar Patel
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey, United States of America
| | - Davis Jose
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey, United States of America
| | - Jonathan Ouellet
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey, United States of America
- * E-mail:
| |
Collapse
|
4
|
Khachigian LM. Deoxyribozymes as Catalytic Nanotherapeutic Agents. Cancer Res 2019; 79:879-888. [DOI: 10.1158/0008-5472.can-18-2474] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/24/2018] [Accepted: 12/14/2018] [Indexed: 11/16/2022]
|
5
|
Discovering a new catabolic pathway of D-ribonate in Mycobacterium smegmatis. Biochem Biophys Res Commun 2018; 505:1107-1111. [DOI: 10.1016/j.bbrc.2018.10.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 10/05/2018] [Indexed: 11/19/2022]
|
6
|
Eriksson J, Langel Ü. Quantitative Microplate Assay for Real-Time Nuclease Kinetics. PLoS One 2016; 11:e0154099. [PMID: 27101307 PMCID: PMC4839650 DOI: 10.1371/journal.pone.0154099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/08/2016] [Indexed: 01/08/2023] Open
Abstract
Utilizing the phenomenon of nucleases exposing oligonucleotide phosphate backbones to phosphatases we present a novel quantitative method for kinetics of nuclease catalysis. Inorganic phosphate released from nuclease products by phosphatases could be quantified in real-time by a fluorescent sensor of inorganic phosphate. Two different nucleases were employed, showing the versatility of this assay for multiple turnover label-free nuclease studies.
Collapse
Affiliation(s)
- Jonas Eriksson
- Department of Neurochemistry, Stockholm University, Stockholm, Sweden
- * E-mail:
| | - Ülo Langel
- Department of Neurochemistry, Stockholm University, Stockholm, Sweden
| |
Collapse
|