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Adegbenro A, Coleman S, Nesterova IV. Stoichiometric approach to quantitative analysis of biomolecules: the case of nucleic acids. Anal Bioanal Chem 2022; 414:1587-1594. [PMID: 34800148 PMCID: PMC8766926 DOI: 10.1007/s00216-021-03781-y] [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: 09/01/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023]
Abstract
Majority of protocols for quantitative analysis of biomarkers (including nucleic acids) require calibrations and target standards. In this work, we developed a principle for quantitative analysis that eliminates the need for a standard of a target molecule. The approach is based on stoichiometric reporting. While stoichiometry is a simple and robust analytical platform, its utility toward the analysis of biomolecules is very limited due to the lack of general methodologies for detecting the equivalence point. In this work, we engineer a new target/probe-binding model that enables detecting the equivalence point while maintaining an appropriate level of specificity. We establish the probe design principles through theoretical simulations and experimental confirmation. Further, we demonstrate the utility of the stoichiometric analysis via a proof-of-concept system based on oligonucleotide hybridization. Overall, the approach that requires neither standard nor calibration yields quantitative results with an adequate accuracy (> 90-110%) and a high specificity. The principles established in our work are very general and can extend beyond oligonucleotide targets toward quantitative analysis of many other biomolecules such as antibodies and proteins.
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Affiliation(s)
- Adeyinka Adegbenro
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Seth Coleman
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Irina V Nesterova
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, 60115, USA.
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Franco LS, Holechek SA, Caplan MR, Blattman JN. Sequence-specific detection of different strains of LCMV in a single sample using tentacle probes. Virol J 2017; 14:197. [PMID: 29029641 PMCID: PMC5640925 DOI: 10.1186/s12985-017-0863-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/05/2017] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Virus infections often result in quasispecies of viral strains that can have dramatic impacts on disease outcomes. However, sequencing of viruses to determine strain composition is time consuming and often cost-prohibitive. Rapid, cost-effective methods are needed for accurate measurement of virus diversity to understand virus evolution and can be useful for experimental systems. METHODS We have developed a novel molecular method for sequence-specific detection of RNA virus genetic variants called Tentacle Probes. The probes are modified molecular beacons that have dramatically improved false positive rates and specificity in routine qPCR. To validate this approach, we have designed Tentacle Probes for two different strains of Lymphocytic Choriomeningitis Virus (LCMV) that differ by only 3 nucleotide substitutions, the parental Armstrong and the more virulent Clone-13 strain. One of these mutations is a missense mutation in the receptor protein GP1 that leads to the Armstrong strain to cause an acute infection and Clone-13 to cause a chronic infection instead. The probes were designed using thermodynamic calculations for hybridization between target or non-target sequences and the probe. RESULTS Using this approach, we were able to distinguish these two strains of LCMV individually by a single nucleotide mutation. The assay showed high reproducibility among different concentrations of viral cDNA, as well as high specificity and sensitivity, especially for the Clone-13 Tentacle Probe. Furthermore, in virus mixing experiments we were able to detect less than 10% of Clone-13 cDNA diluted in Armstrong cDNA. CONCLUSIONS Thus, we have developed a fast, cost-effective approach for identifying Clone-13 strain in a mix of other LCMV strains.
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Affiliation(s)
- Lina S Franco
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Susan A Holechek
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Simon A. Levin Mathematical, Computational and Modeling Sciences Center, Arizona State University, Tempe, AZ, USA
| | - Michael R Caplan
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
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Qin Y, Zhang L, Li S, Zhao J, Huang Y, Zhao S, Liu YM. A microchip electrophoresis-based fluorescence signal amplification strategy for highly sensitive detection of biomolecules. Chem Commun (Camb) 2017; 53:455-458. [PMID: 27966686 DOI: 10.1039/c6cc08911a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We have developed a microchip electrophoresis (MCE)-based fluorescence signal amplification strategy as a universal MCE method for the detection of trace biomolecules. This strategy exhibits high sensitivity and specificity for target molecules, and has been applied for the detection of interferon-gamma (IFN-γ) in human plasma with satisfactory results.
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Affiliation(s)
- Yingfeng Qin
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China.
| | - Liangliang Zhang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China.
| | - Shuting Li
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China.
| | - Jingjin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China.
| | - Yong Huang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China.
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China.
| | - Yi-Ming Liu
- Department of Chemistry and Biochemistry, Jackson State University, 1400 Lynch St., Jackson, MS 39217, USA
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Kikuchi N, Kolpashchikov DM. Split Spinach Aptamer for Highly Selective Recognition of DNA and RNA at Ambient Temperatures. Chembiochem 2016; 17:1589-92. [PMID: 27305425 DOI: 10.1002/cbic.201600323] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Indexed: 12/25/2022]
Abstract
Split spinach aptamer (SSA) probes for fluorescent analysis of nucleic acids were designed and tested. In SSA design, two RNA or RNA/DNA strands hybridized to a specific nucleic acid analyte and formed a binding site for low-fluorescent 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) dye, which resulted in up to a 270-fold increase in fluorescence. The major advantage of the SSA over state-of-the art fluorescent probes is high selectivity: it produces only background fluorescence in the presence of a single-base-mismatched analyte, even at room temperature. SSA is therefore a promising tool for label-free analysis of nucleic acids at ambient temperatures.
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Affiliation(s)
- Nanami Kikuchi
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA.
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Gulur Srinivas AR, Barker D, Travas-Sejdic J. ‘Switch-on’ DNA sensor based on poly (p-phenylene vinylenes) bound tentacle probes. PURE APPL CHEM 2015. [DOI: 10.1515/pac-2014-1114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
AbstractThe development of highly sensitive and selective DNA sensors has fuelled applications in a wide range of fields including medical diagnostics, forensics, biodefense, food contamination and environment monitoring. We demonstrate a novel superquenching based DNA sensor with “switch-on” readout using poly(p-phenylenevinylene) (PPV) coated magnetic beads (PPV-MagSi) and quencher functionalized tentacle probes (TP). The sensor design utilizes signal amplification properties of PPV and cooperativity of TPs to monitor hybridization of target oligonucleotides (ONs). The switch-on sensor exhibits excellent sensitivity and selectively discriminates mismatches in the target DNA sequence. Two novel anionic PPVs – poly (6,6′-((2-methyl-5-((E)-4-((E)-prop-1-en-1-yl)styryl)-1,4-phenylene)-bis(oxy) dihexanoic acid) (PMDH) and poly (6,6′-((2-((E)-2,5-bis(2-methoxyethoxy)-4-((E)-prop-1-en-1-yl)styryl)-5-methyl-1,4-phenylene)-bis-(oxy)) di-hexanoic acid) (PDMonoG) were tested and compared against each other as part of the sensor design. The employed hairpin TPs possess further advantages of avoiding labelling of target ON, increased selectivity and sensitivity; faster assay time, and capability of magnetically controlled deployment and separation of PPV-MagSi beads.
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Affiliation(s)
- Anupama R. Gulur Srinivas
- 1Polymer Electronics Research Centre, School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - David Barker
- 1Polymer Electronics Research Centre, School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
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6
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Poritz MA, Ririe KM. Getting things backwards to prevent primer dimers. J Mol Diagn 2014; 16:159-62. [PMID: 24457120 DOI: 10.1016/j.jmoldx.2014.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 12/30/2013] [Accepted: 01/09/2014] [Indexed: 02/04/2023] Open
Abstract
This Commentary highlights the article by Satterfield that describes a new class of primer technology-cooperative primers, which prevent primer-dimer amplification.
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Satterfield BC. Cooperative primers: 2.5 million-fold improvement in the reduction of nonspecific amplification. J Mol Diagn 2013; 16:163-73. [PMID: 24370857 DOI: 10.1016/j.jmoldx.2013.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 10/26/2013] [Accepted: 10/30/2013] [Indexed: 10/25/2022] Open
Abstract
The increasing need to multiplex nucleic acid reactions presses test designers to the limits of amplification specificity in PCR. Although more than a dozen hot starts have been developed for PCR to reduce primer-dimer formation, none can stop the propagation of primer-dimers once formed. Even a small number of primer-dimers can result in false-negatives and/or false-positives. Herein, we demonstrate a new class of primer technology that greatly reduces primer-dimer propagation, showing successful amplification of 60 template copies with no signal dampening in a background of 150,000,000 primer-dimers. In contrast, normal primers, with or without a hot start, experienced signal dampening with as few as 60 primer-dimers and false-negatives with only 600 primer-dimers. This represents more than a 2.5 million-fold improvement in reduction of nonspecific amplification. We also show how a probe can be incorporated into the cooperative primer, with 2.5 times more signal than conventional fluorescent probes.
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Genetic encoding of fluorescent RNA ensures a bright future for visualizing nucleic acid dynamics. Trends Biotechnol 2012; 30:621-6. [PMID: 23127753 DOI: 10.1016/j.tibtech.2012.09.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 09/19/2012] [Indexed: 11/22/2022]
Abstract
Recently RNA localization has been appreciated as an essential post-transcriptional mechanism to program local proteome composition and function. Although RNA has been visualized using diverse techniques, the use of the bacteriophage MS2 method to encode genetically fluorescent RNA has revolutionized the study of RNA dynamics in living cells. Here, I highlight the strength of MS2 compared to other techniques, and how further evolution of this system will enable the visualization of RNA in the context of complex live-cell dynamics. Although the generation of MS2-fluorescence resonance energy transfer (FRET) and MS2-bifluorescence complementation (BiFC) will require further development, it has the potential to increase significantly the signal-to-noise ratio, which is the major obstacle to rapid live-cell imaging of RNA.
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Satterfield BC, Bartosiewicz M, West JAA, Caplan MR. Surpassing specificity limits of nucleic acid probes via cooperativity. J Mol Diagn 2010; 12:359-67. [PMID: 20304941 DOI: 10.2353/jmoldx.2010.090056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The failure to correctly identify single nucleotide polymorphisms (SNPs) significantly contributes to the misdiagnosis of infectious disease. Contrary to the strategy of creating shorter probes to improve SNP differentiation, we created larger probes that appeared to increase selectivity. Specifically, probes with enhanced melting temperature differentials (>13x improvement) to SNPs were generated by linking two probes that consist of both a capture sequence and a detection sequence; these probes act cooperatively to improve selectivity over a wider range of reaction conditions. These cooperative probe constructs (Tentacle probes) were then compared by modeling thermodynamic and hybridization characteristics to both Molecular Beacons (stem loop DNA probes) and Taqman probes (a linear oligonucleotide). The biophysical models reveal that cooperative probes compared with either Molecular beacons or Taqman probes have enhanced specificity. This was a result of increased melting temperature differentials and the concentration-independent hybridization revealed between wild-type and variant sequences. We believe these findings of order of magnitude enhanced melting temperature differentials with probes possessing concentration independence and more favorable binding kinetics have the potential to significantly improve molecular diagnostic assay functionality.
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Affiliation(s)
- Brent C Satterfield
- Arcxis Biotechnologies, 6920 Koll Center Pkwy, Suite 215, Pleasanton, CA 94566, USA
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Tosar JP, Keel K, Laíz J. Two independent label-free detection methods in one electrochemical DNA sensor. Biosens Bioelectron 2009; 24:3036-42. [PMID: 19359160 DOI: 10.1016/j.bios.2009.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 03/05/2009] [Accepted: 03/11/2009] [Indexed: 11/27/2022]
Abstract
Two direct reagent-free detection methods were tested with Au/polypyrrole/oligonucleotide modified electrodes. Detection by monitoring guanine oxidation was realized amperometrically using an experimental setup which does not require any expensive electrochemical equipment and is therefore suitable for in situ detection. Target detection was also realized by monitoring the decrease in the amplitude of polypyrrole oxidation and reduction peaks in cyclic voltammetry experiments after incubation or injection of target into the electrochemical cell. Detection of 53 pM target within a 2000x excess of non-complementary sequences was possible. The possibility of a dual detection scheme in the same biosensor, with both detection schemes being totally independent from one another is very promising for genosensor design since it would result in a significant decrease in the number of false positive and false negative samples.
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Affiliation(s)
- Juan Pablo Tosar
- Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo, Uruguay
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Abstract
Commonly used techniques for analyzing gene expression, such as polymerase chain reaction (PCR), microarrays, and in situ hybridization, have proven invaluable in understanding RNA processing and regulation. However, these techniques rely on the use of lysed and/or fixed cells and are therefore limited in their ability to provide important spatial-temporal information. This has led to the development of numerous techniques for imaging RNA in living cells, some of which have already provided important insight into the dynamic role RNA plays in dictating cell behavior. Here we review the fluorescent probes that have allowed for RNA imaging in living cells and discuss their utility and limitations. Common challenges faced by fluorescent probes, such as probe design, delivery, and target accessibility, are also discussed. It is expected that continued advancements in live cell imaging of RNA will open new and exciting opportunities in a wide range of biological and medical applications.
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Affiliation(s)
- Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332;
| | - Won Jong Rhee
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332;
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Satterfield BC, Caplan MR, West JAA. Tentacle probe sandwich assay in porous polymer monolith improves specificity, sensitivity and kinetics. Nucleic Acids Res 2008; 36:e129. [PMID: 18790801 PMCID: PMC2577359 DOI: 10.1093/nar/gkn564] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Revised: 08/18/2008] [Accepted: 08/19/2008] [Indexed: 12/02/2022] Open
Abstract
Nucleic acid sandwich assays improve low-density array analysis through the addition of a capture probe and a specific label, increasing specificity and sensitivity. Here, we employ photo-initiated porous polymer monolith (PPM) as a high-surface area substrate for sandwich assay analysis. PPMs are shown to enhance extraction efficiency by 20-fold from 2 microl of sample. We further compare the performance of labeled linear probes, quantum dot labeled probes, molecular beacons (MBs) and tentacle probes (TPs). Each probe technology was compared and contrasted with traditional hybridization methods using labeled sample. All probes demonstrated similar sensitivity and greater specificity than traditional hybridization techniques. MBs and TPs were able to bypass a wash step due to their 'on-off' signaling mechanism. TPs demonstrated reaction kinetics 37.6 times faster than MBs, resulting in the fastest assay time of 5 min. Our data further indicate TPs had the most sensitive detection limit (<1 nM) as well as the highest specificity (>1 x 10(4) improvement) among all tested probes in these experiments. By matching the enhanced extraction efficiencies of PPM with the selectivity of TPs, we have created a format for improved sandwich assays.
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Affiliation(s)
- Brent C. Satterfield
- Harrington Department of Bioengineering, Arizona State
University Tempe, AZ, Cooperative Diagnostics, Greenwood, SC and
Arcxis Biotechnologies, Pleasanton, CA, USA
| | - Michael R. Caplan
- Harrington Department of Bioengineering, Arizona State
University Tempe, AZ, Cooperative Diagnostics, Greenwood, SC and
Arcxis Biotechnologies, Pleasanton, CA, USA
| | - Jay A. A. West
- Harrington Department of Bioengineering, Arizona State
University Tempe, AZ, Cooperative Diagnostics, Greenwood, SC and
Arcxis Biotechnologies, Pleasanton, CA, USA
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Marras SAE. Interactive fluorophore and quencher pairs for labeling fluorescent nucleic acid hybridization probes. Mol Biotechnol 2007; 38:247-55. [PMID: 17985254 DOI: 10.1007/s12033-007-9012-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 10/15/2007] [Indexed: 01/08/2023]
Abstract
The use of fluorescent nucleic acid hybridization probes that generate a fluorescence signal only when they bind to their target enables real-time monitoring of nucleic acid amplification assays. Real-time nucleic acid amplification assays markedly improves the ability to obtain qualitative and quantitative results. Furthermore, these assays can be carried out in sealed tubes, eliminating carryover contamination. Fluorescent nucleic acid hybridization probes are available in a wide range of different fluorophore and quencher pairs. Multiple hybridization probes, each designed for the detection of a different nucleic acid sequence and each labeled with a differently colored fluorophore, can be added to the same nucleic acid amplification reaction, enabling the development of high-throughput multiplex assays. In order to develop robust, highly sensitive and specific real-time nucleic acid amplification assays it is important to carefully select the fluorophore and quencher labels of hybridization probes. Selection criteria are based on the type of hybridization probe used in the assay, the number of targets to be detected, and the type of apparatus available to perform the assay. This article provides an overview of different aspects of choosing appropriate labels for the different types of fluorescent hybridization probes used with different types of spectrofluorometric thermal cyclers currently available.
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Affiliation(s)
- Salvatore A E Marras
- Public Health Research Institute and the Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, 225 Warren Street, Newark, NJ, 07103, USA.
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Satterfield BC, Kulesh DA, Norwood DA, Wasieloski LP, Caplan MR, West JAA. Tentacle Probes: differentiation of difficult single-nucleotide polymorphisms and deletions by presence or absence of a signal in real-time PCR. Clin Chem 2007; 53:2042-50. [PMID: 17932130 DOI: 10.1373/clinchem.2007.091488] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND False-positive results are a common problem in real-time PCR identification of DNA sequences that differ from near neighbors by a single-nucleotide polymorphism (SNP) or deletion. Because of a lack of sufficient probe specificity, post-PCR analysis, such as a melting curve, is often required for mutation differentiation. METHODS Tentacle Probes, cooperative reagents with both a capture and a detection probe based on specific cell-targeting principles, were developed as a replacement for 2 chromosomal TaqMan-minor groove binder (MGB) assays previously developed for Yersinia pestis and Bacillus anthracis detection. We compared TaqMan-MGB probes to Tentacle Probes for SNP and deletion detection based on the presence or absence of a growth curve. RESULTS With the TaqMan-MGB Y. pestis yp48 assays, false-positive results for Yersinia pseudotuberculosis occurred at every concentration tested, and with the TaqMan-MGB B. anthracis gyrA assays, false-positive results occurred in 21 of 29 boil preps of environmental samples of near neighbors. With Tentacle Probes no false-positive results occurred. CONCLUSIONS The high specificity exhibited by Tentacle Probes may eliminate melting curve analysis for SNP and deletion mutation detection, allowing the diagnostic use of previously difficult targets.
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Affiliation(s)
- Brent C Satterfield
- Harrington Department of Bioengineering, Arizona State University, Tempe, AZ 85287-9709, USA
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