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Mana T, Bhattacharya B, Lahiri H, Mukhopadhyay R. XNAs: A Troubleshooter for Nucleic Acid Sensing. ACS Omega 2022; 7:15296-15307. [PMID: 35571783 PMCID: PMC9096816 DOI: 10.1021/acsomega.2c00581] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
The strategies for nucleic acid sensing based on nucleic acid hybridization between the target sequence and the capture probe sequence are considered to be largely successful as far as detection of a specific target of known sequence is concerned. However, when compared with other complementary methods, like direct sequencing, a number of results are still found to be either "false positives" or "false negatives". This suggests that modifications in these strategies are necessary to make them more accurate. In this minireview, we propose that one way toward improvement could be replacement of the DNA capture probes with the xeno nucleic acid or XNA capture probes. This is because the XNAs, especially the locked nucleic acid, the peptide nucleic acid, and the morpholino, have shown better single nucleobase mismatch discrimination capacity than the DNA capture probes, indicating their capacity for more precise detection of nucleic acid sequences, which is beneficial for detection of gene stretches having point mutations. Keeping the current trend in mind, this minireview will include the recent developments in nanoscale, fluorescent label-free applications, and present the cases where the XNA probes show clear advantages over the DNA probes.
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Affiliation(s)
- Tanushree Mana
- School
of Biological Sciences, Indian Association
for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Budhaditya Bhattacharya
- School
of Biological Sciences, Indian Association
for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Hiya Lahiri
- School
of Biological Sciences, Indian Association
for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Rupa Mukhopadhyay
- School
of Biological Sciences, Indian Association
for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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Levicky R, Koniges U, Tercero N. Diagnostic Applications of Morpholinos and Label-Free Electrochemical Detection of Nucleic Acids. Methods Mol Biol 2017; 1565:181-90. [PMID: 28364243 DOI: 10.1007/978-1-4939-6817-6_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Diagnostic applications of morpholinos take advantage of their unique properties including backbone charge neutrality, a weak impact of ionic strength on their hybridization behavior, and their resistance to enzymatic degradation. This chapter overviews how these properties have advanced transduction and other capabilities useful for the analysis of nucleic acids. In many cases, the benefits stem from electrostatic mechanisms; for example, use of low ionic strengths improves sensitivity of detection while decreasing background signals because only the nucleic acid analyte is charged. While most literature reports focus on in vitro assays in buffer, morpholinos have been also used for biodistribution measurements of species such as fungal rRNA and miRNA. After reviewing the diagnostic applications of morpholinos, the chapter describes preparation of morpholino monolayers on metal supports for electrochemical diagnostics and the procedure for performing label-free detection of DNA from changes in surface capacitance.
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Bizid S, Blili S, Mlika R, Haj Said A, Korri-youssoufi H. Direct Electrochemical DNA Sensor based on a new redox oligomer modified with ferrocene and carboxylic acid: Application to the detection of Mycobacterium tuberculosis mutant strain. Anal Chim Acta 2017; 994:10-8. [DOI: 10.1016/j.aca.2017.09.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/23/2017] [Accepted: 09/14/2017] [Indexed: 11/22/2022]
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Ho TH, Guillon F, Bigey P, Bedioui F, Lazerges M. Analysis of the evolution of the detection limits of electrochemical nucleic acid biosensors II. Anal Bioanal Chem 2017; 409:4335-52. [DOI: 10.1007/s00216-017-0377-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/11/2017] [Accepted: 04/21/2017] [Indexed: 01/07/2023]
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He Y, Zhang J, Ruffin S, Ji L, Wang K, Levicky R, Xia X. An Electrochemical Study of the Surface Hybridization Process of Morpholino-DNA: Thermodynamics and Kinetics. ELECTROANAL 2016. [DOI: 10.1002/elan.201501109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yakai He
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing, Jiangsu 163 Xianlin Avenue 210023 P. R. China
| | - Jing Zhang
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing, Jiangsu 163 Xianlin Avenue 210023 P. R. China
| | - Sade Ruffin
- Department of Chemical and Biomolecular Engineering; New York University Polytechnic School of Engineering; 6 MetroTech Center Brooklyn, New York 11201
| | - Lina Ji
- State Key Laboratory of Pharmaceutical Biotechnology; School of Life Sciences; Nanjing University; Nanjing, Jiangsu 163 Xianlin Avenue 210023 P. R. China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing, Jiangsu 163 Xianlin Avenue 210023 P. R. China
| | - Rastislav Levicky
- Department of Chemical and Biomolecular Engineering; New York University Polytechnic School of Engineering; 6 MetroTech Center Brooklyn, New York 11201
| | - Xinghua Xia
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing, Jiangsu 163 Xianlin Avenue 210023 P. R. China
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Abstract
Advances and applications of synthetic genetic polymers (xeno-nucleic acids) are reviewed in this article. The types of synthetic genetic polymers are summarized. The basic properties of them are elaborated and their technical applications are presented. Challenges and prospects of synthetic genetic polymers are discussed.
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Affiliation(s)
- Qian Ma
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Danence Lee
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Yong Quan Tan
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Garrett Wong
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Zhiqiang Gao
- Department of Chemistry
- National University of Singapore
- Singapore 117543
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7
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Cao L, Zhao Y, Ji LN, Zhang J, Wang K, Xia XH. The Enhanced Enzymolysis Resistance of Surface-Immobilized DNA Caused by Hybridizing with Morpholino. ELECTROANAL 2013. [DOI: 10.1002/elan.201200612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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Lazerges M, Bedioui F. Analysis of the evolution of the detection limits of electrochemical DNA biosensors. Anal Bioanal Chem 2013; 405:3705-14. [DOI: 10.1007/s00216-012-6672-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 12/04/2012] [Accepted: 12/18/2012] [Indexed: 11/26/2022]
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Qiao W, Kalachikov S, Liu Y, Levicky R. Charge-neutral morpholino microarrays for nucleic acid analysis. Anal Biochem 2012; 434:207-14. [PMID: 23246344 DOI: 10.1016/j.ab.2012.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 11/21/2012] [Accepted: 12/03/2012] [Indexed: 12/14/2022]
Abstract
A principal challenge in microarray experiments is to facilitate hybridization between probe strands on the array with complementary target strands from solution while suppressing any competing interactions that the probes and targets may experience. Synthetic DNA analogs, whose hybridization to targets can exhibit qualitatively different dependence on experimental conditions than for nucleic acid probes, open up an attractive alternative for improving selectivity of array hybridization. Morpholinos (MOs), a class of uncharged DNA analogs, are investigated as microarray probes instead of DNA. MO microarrays were fabricated by contact printing of amino-modified probes onto aldehyde slides. In addition to covalent immobilization, MOs were found to efficiently immobilize through physical adsorption; such physically adsorbed probes could be removed by post-printing washes with surfactant solutions. Hybridization of double-stranded DNA targets to MO microarrays revealed a hybridization maximum at intermediate ionic strengths. The decline in hybridization at lower ionic strengths was attributed to an electrostatic barrier accumulated from hybridized DNA targets, whereas at higher ionic strengths it was attributed to stabilization of target secondary structure in solution. These trends, which illustrate ionic strength tuning of forming on-array relative to solution secondary structure, were supported by a stability analysis of MO/DNA and DNA/DNA duplexes in solution.
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Affiliation(s)
- Wanqiong Qiao
- Department of Chemical and Biomolecular Engineering, Polytechnic Institute of New York University, Brooklyn, NY 11201, USA
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Abstract
Morpholinos (MOs) are DNA analogues whose uncharged nature can bring fundamental advantages to surface hybridization technologies such as DNA microarrays, by using MOs as the immobilized, or "probe", species. Advancement of MO-based diagnostics, however, is challenged by limited understanding of the surface organization of MO molecules and of how this organization impacts hybridization kinetics and thermodynamics. The present study focuses on hybridization kinetics between monolayers of MO probes and DNA targets as a function of the instantaneous extent of hybridization (i.e., duplex coverage), total probe coverage, and ionic strength. Intriguingly, these experiments reveal distinct kinetic stages, none of which are consistent with Langmuir kinetics. The initial stage, in which duplex coverage remains relatively sparse, indicates confluence of two effects: blockage of target access to unhybridized probes by previously formed duplexes and deactivation of the solid support due to consumption of probe molecules. This interpretation is consistent with a surface organization in which unhybridized MO probes localize near the solid support, underneath a layer of MO-DNA duplexes. As duplex coverage builds, provided saturation is not reached first, the initial stage can transition to an unusual regime characterized by near independence of hybridization rate on duplex coverage, followed by a prolonged approach to equilibrium. The possible origins of these more complex latter behaviors are discussed. Comparison with published data for DNA and peptide nucleic acid (PNA) probes is carried out to look for universal trends in kinetics. This comparison reveals qualitative similarities when comparable surface organization of probes is expected. In addition, MO monolayers are found capable of a broad range of reactivities that span reported values for PNA and DNA probes.
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Affiliation(s)
- Yatao Liu
- Department of Chemical and Biological Engineering, Polytechnic Institute of New York University, 6 MetroTech Center, Brooklyn, New York 11201, USA
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11
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Abstract
Surface hybridization, in which nucleic acids from solution bind to complementary "probe" strands immobilized on a solid support, is widely used to analyze composition of nucleic acid mixtures. Most often, detection is accomplished with fluorescent techniques whose sensitivity can be extended down to individual molecules. Applications, however, benefit as much if not more from convenience, accuracy, and affordability of the diagnostic test. By eliminating the need for fluorescent labeling and more complex sample workup, label-free electrochemical assays have significant advantages provided transduction remains sufficiently sensitive for applications. To this end, we have been exploring morpholinos, which are uncharged DNA analogues, as the immobilized probe species in surface hybridization assays based on measurement of interfacial capacitance. Through comparison of experimental trends with those predicted from basic physical models, the origins of diagnostic contrast in capacitive sensing are reviewed for assays based on morpholino as well as on DNA probes.
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Affiliation(s)
- R O'Connor
- Department of Chemical and Biological Engineering, Polytechnic Institute of New York University, Brooklyn, New York 11201, USA
| | - N Tercero
- Department of Chemical and Biological Engineering, Polytechnic Institute of New York University, Brooklyn, New York 11201, USA
| | - W Qiao
- Department of Chemical and Biological Engineering, Polytechnic Institute of New York University, Brooklyn, New York 11201, USA
| | - R Levicky
- Department of Chemical and Biological Engineering, Polytechnic Institute of New York University, Brooklyn, New York 11201, USA
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12
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Abstract
Impedance and cyclic voltammetry methods, complemented by Poisson-Boltzmann (PB) modeling, are used to study hybridization of DNA analyte strands to monolayers of morpholino oligomers (MOs) immobilized by one end to mercaptopropanol-passivated gold electrodes. MOs, like peptide nucleic acids (PNAs), are uncharged molecules that recognize nucleic acids following conventional base-pairing rules. The capacitive response to hybridization, determined from real-time impedance measurements, is analyzed with emphasis on understanding the underlying structural changes and on providing a foundation for label-free diagnostics. The capacitive response is correlated with the instantaneous surface molecular populations by labeling DNA and MO strands with ferrocene tags and using cyclic voltammetry to monitor their respective coverages in real-time. This approach allows analysis of hybridization-induced changes in interfacial capacitance as a function of duplex coverage, the DC bias used for readout, buffer molarity, and probe coverage. The results indicate that unhybridized MO layers exist in a compact state on the solid support. For hybridized layers, the intrinsic signal per hybridization event is strongly enhanced at low ionic strengths but, interestingly, does not depend on the readout bias in the sampled range negative of the capacitive minimum. A PB model incorporating an effective medium description of the hybridizing films is used to establish how hybridization-derived changes in dielectric composition and charge distribution at the surface translate into experimentally observed variations in interfacial capacitance.
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Affiliation(s)
- Napoleon Tercero
- Department of Chemical & Biological Engineering, Polytechnic Institute of NYU, 6 MetroTech Center, Brooklyn, NY 11201
| | | | - Rastislav Levicky
- Department of Chemical & Biological Engineering, Polytechnic Institute of NYU, 6 MetroTech Center, Brooklyn, NY 11201
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13
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Abstract
Synthetic nucleic acid mimics provide opportunity for redesigning the specificity and affinity of hybridization with natural DNA or RNA. Such redesign is of great interest for diagnostic applications where it can enhance the desired signal against a background of competing interactions. This report compares hybridization of DNA analyte strands with morpholinos (MOs), which are uncharged nucleic acid mimics, to the corresponding DNA-DNA case in solution and on surfaces. In solution, MO-DNA hybridization is found to be independent of counterion concentration, in contrast to DNA-DNA hybridization. On surfaces, when immobilized MO or DNA "probe" strands hybridize with complementary DNA "targets" from solution, both the MO-DNA and DNA-DNA processes depend on ionic strength but exhibit qualitatively different behaviors. At lower ionic strengths, MO-DNA surface hybridization exhibits hallmarks of kinetic limitations when separation between hybridized probe sites becomes comparable to target dimensions, whereas extents of DNA-DNA surface hybridization are instead consistent with limits imposed by buildup of surface (Donnan) potential. The two processes also fundamentally differ at high ionic strength, under conditions when electrostatic effects are weak. Here, variations in probe coverage have a much diminished impact on MO-DNA than on DNA-DNA hybridization for similarly crowded surface conditions. These various observations agree with a structural model of MO monolayers in which MO-DNA duplexes segregate to the buffer interface while unhybridized probes localize near the solid support. A general perspective is presented on using uncharged DNA analogues, which also include compounds such as peptide nucleic acids (PNA), in surface hybridization applications.
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Affiliation(s)
- Ping Gong
- Seventh Sense Biosystems Inc., 101 Binney Street, Cambridge, Massachusetts 02142, USA
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