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Bian T, Pei Y, Gao S, Zhou S, Sun X, Dong M, Song J. Xeno Nucleic Acids as Functional Materials: From Biophysical Properties to Application. Adv Healthc Mater 2024:e2401207. [PMID: 39036821 DOI: 10.1002/adhm.202401207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/14/2024] [Indexed: 07/23/2024]
Abstract
Xeno nucleic acid (XNA) are artificial nucleic acids, in which the chemical composition of the sugar moiety is changed. These modifications impart distinct physical and chemical properties to XNAs, leading to changes in their biological, chemical, and physical stability. Additionally, these alterations influence the binding dynamics of XNAs to their target molecules. Consequently, XNAs find expanded applications as functional materials in diverse fields. This review provides a comprehensive summary of the distinctive biophysical properties exhibited by various modified XNAs and explores their applications as innovative functional materials in expanded fields.
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Affiliation(s)
- Tianyuan Bian
- Academy of Medical Engineering and Translational Medicine (AMT), Tianjin University, Tianjin, 300072, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Yufeng Pei
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Shitao Gao
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
- College of Materials Science and Engineering, Zhejiang University of Technology, ChaoWang Road 18, HangZhou, 310014, China
| | - Songtao Zhou
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xinyu Sun
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Aarhus, DK-8000, Denmark
| | - Jie Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
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Li P, Zhu C, Liu LS, Han CTJ, Chu HC, Li Z, Mao Z, Wang F, Lo PK. Ultra-stable threose nucleic acid-based biosensors for rapid and sensitive nucleic acid detection and in vivo imaging. Acta Biomater 2024; 177:472-485. [PMID: 38296012 DOI: 10.1016/j.actbio.2024.01.031] [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: 09/09/2023] [Revised: 01/04/2024] [Accepted: 01/22/2024] [Indexed: 02/13/2024]
Abstract
The human genome's nucleotide sequence variation, such as single nucleotide mutations, can cause numerous genetic diseases. However, detecting nucleic acids accurately and rapidly in complex biological samples remains a major challenge. While natural deoxyribonucleic acid (DNA) has been used as biorecognition probes, it has limitations like poor specificity, reproducibility, nuclease-induced enzymatic degradation, and reduced bioactivity on solid surfaces. To address these issues, we introduce a stable and reliable biosensor called graphene oxide (GO)- threose nucleic acid (TNA). It comprises chemically modified TNA capture probes on GO for detecting and imaging target nucleic acids in vitro and in vivo, distinguishing single nucleobase mismatches, and monitoring dynamic changes in target microRNA (miRNA). By loading TNA capture probes onto the GO substrate, the GO-TNA sensing platform for nucleic acid detection demonstrates a significant 88-fold improvement in the detection limit compared to TNA probes alone. This platform offers a straightforward preparation method without the need for costly and labor-intensive isolation procedures or complex chemical reactions, enabling real-time analysis. The stable TNA-based GO sensing nanoplatform holds promise for disease diagnosis, enabling rapid and accurate detection and imaging of various disease-related nucleic acid molecules at the in vivo level. STATEMENT OF SIGNIFICANCE: The study's significance lies in the development of the GO-TNA biosensor, which addresses limitations in nucleic acid detection. By utilizing chemically modified nucleic acid analogues, the biosensor offers improved reliability and specificity, distinguishing single nucleobase mismatches and avoiding false signals. Additionally, its ability to detect and image target nucleic acids in vivo facilitates studying disease mechanisms. The simplified preparation process enhances practicality and accessibility, enabling real-time analysis. The biosensor's potential applications extend beyond healthcare, contributing to environmental analysis and food safety. Overall, this study's findings have substantial implications for disease diagnosis, biomedical research, and diverse applications, advancing nucleic acid detection and its impact on various fields.
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Affiliation(s)
- Pan Li
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China
| | - Chiying Zhu
- Shenzhen Clinical Medical College, Guangzhou University of Chinese Medicine, 518116 Shenzhen, P. R. China
| | - Ling Sum Liu
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, London W12 0BZ, United Kingdom
| | - Chang Tristan Juin Han
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China
| | - Hoi Ching Chu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China
| | - Zhenhua Li
- The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), 523059 Dongguan, P. R. China
| | - Zhengwei Mao
- Department of Polymer Science and Engineering, Zhejiang University, 310027 Hangzhou, P. R. China.
| | - Fei Wang
- The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), 523059 Dongguan, P. R. China.
| | - Pik Kwan Lo
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China; Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, 518057 Shenzhen, P. R. China.
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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] [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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Mana T, Kundu J, Lahiri H, Bera S, Kolay J, Sinha S, Mukhopadhyay R. Molecularly resolved, label-free nucleic acid sensing at solid-liquid interface using non-ionic DNA analogues. RSC Adv 2022; 12:9263-9274. [PMID: 35424880 PMCID: PMC8985177 DOI: 10.1039/d2ra00386d] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/07/2022] [Indexed: 01/10/2023] Open
Abstract
Nucleic acid-based biosensors, where the capture probe is a nucleic acid, e.g., DNA or its synthetic analogue xeno nucleic acid (XNA), offer interesting ways of eliciting clinically relevant information from hybridization/dehybridization signals. In this respect, the application of XNA probes is attractive since the drawbacks of DNA probes might be overcome. Within the XNA probe repertoire, peptide nucleic acid (PNA) and morpholino (MO) are promising since their backbones are non-ionic. Therefore, in the absence of electrostatic charge repulsion between the capture probe and the target nucleic acid, a stable duplex can be formed. In addition, these are nuclease-resistant probes. Herein, we have tested the molecularly resolved nucleic acid sensing capacity of PNA and MO capture probes using a fluorescent label-free single molecule force spectroscopy approach. As far as single nucleobase mismatch discrimination is concerned, both PNA and MO performed better than DNA, while the performance of the MO probe was the best. We propose that the conformationally more rigid backbone of MO, compared to the conformationally flexible PNA, is an advantage for MO, since the probe orientation can be made more upright on the surface and therefore MO can be more effectively accessed by the target sequences. The performance of the XNA probes has been compared to that of the DNA probe, using fixed nucleobase sequences, so that the effect of backbone variation could be investigated. To our knowledge, this is the first report on molecularly resolved nucleic acid sensing by non-ionic capture probes, here, MO and PNA. Improved nucleic acid sensing in terms of single nucleobase mismatch discrimination, as achieved by the surface-confined non-ionic PNA and MO capture probes, is exemplified by single molecule force spectroscopy.![]()
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Affiliation(s)
- Tanushree Mana
- School of Biological Sciences, Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India +91 33 2473 2805 +91 33 2473 4971 extn 1506
| | - Jayanta Kundu
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India
| | - Hiya Lahiri
- School of Biological Sciences, Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India +91 33 2473 2805 +91 33 2473 4971 extn 1506
| | - Sudipta Bera
- School of Biological Sciences, Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India +91 33 2473 2805 +91 33 2473 4971 extn 1506
| | - Jayeeta Kolay
- School of Biological Sciences, Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India +91 33 2473 2805 +91 33 2473 4971 extn 1506
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India
| | - Rupa Mukhopadhyay
- School of Biological Sciences, Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India +91 33 2473 2805 +91 33 2473 4971 extn 1506
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Teixeira H, Sousa AL, Azevedo AS. Bioinformatic Tools and Guidelines for the Design of Fluorescence In Situ Hybridization Probes. Methods Mol Biol 2021; 2246:35-50. [PMID: 33576981 DOI: 10.1007/978-1-0716-1115-9_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Fluorescence in situ hybridization (FISH) is a well-established technique that allows the detection of microorganisms in diverse types of samples (e.g., clinical, food, environmental samples, and biofilm communities). The FISH probe design is an essential step in this technique. For this, two strategies can be used, the manual form based on multiple sequence alignment to identify conserved regions and programs/software specifically developed for the selection of the sequence of the probe. Additionally, databases/software for the theoretical evaluation of the probes in terms of specificity, sensitivity, and thermodynamic parameters (melting temperature and Gibbs free energy change) are used. The purpose of this chapter is to describe the essential steps and guidelines for the design of FISH probes (e.g., DNA and Nucleic Acid Mimic (NAM) probes), and its theoretical evaluation through the application of diverse bioinformatic tools.
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Affiliation(s)
- Helena Teixeira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Ana L Sousa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.,INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Andreia S Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal. .,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal. .,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal. .,CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
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Lahiri H, Mishra S, Mukhopadhyay R. Nanoscale Nucleic Acid Recognition at the Solid-Liquid Interface Using Xeno Nucleic Acid Probes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8875-8888. [PMID: 30398876 DOI: 10.1021/acs.langmuir.8b02770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Challenges in reliable nucleic acid detection are manifold. The major ones are related to false positive or negative signals due to a lack of target specificity in detection and to low sensitivity, especially when a plethora of background sequences are present that can mask the specific recognition signal. Utilizing designed synthetic nucleic acids that are commonly called xeno nucleic acids could offer potential routes to meeting such challenges. In this article, we present the general framework of nucleic acid detection, especially for nanoscale applications, and discuss how and why the xeno nucleic acids could be truly an alternative to the DNA probes. Two specific cases, locked nucleic acid (LNA) and peptide nucleic acid (PNA), which are nuclease-resistant and can form thermally stable duplexes with DNA, are addressed. It is shown that the relative ease of the conformationally rigid LNA probe to be oriented upright on the substrate surface and of the nonionic PNA probe to result into high probe density assists in their use in nanoscale nucleic acid recognition. It is anticipated that success with these probes may lead to important developments such as PCR-independent approaches where the major aim is to detect a small number of target sequences present in the analyte medium.
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Affiliation(s)
- Hiya Lahiri
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
| | - Sourav Mishra
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
| | - Rupa Mukhopadhyay
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
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7
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Qiao W, Chiang HC, Xie H, Levicky R. Surface vs. solution hybridization: effects of salt, temperature, and probe type. Chem Commun (Camb) 2016; 51:17245-8. [PMID: 26459915 DOI: 10.1039/c5cc06674c] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hybridization thermodynamics on solid supports are compared with those in solution for two types of hybridization probe, DNA and uncharged morpholino oligonucleotides of identical sequences. Trends in hybridization affinity are discussed with respect to ionic strength, temperature, and surface behavior.
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Affiliation(s)
- Wanqiong Qiao
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Hao-Chun Chiang
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Hui Xie
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Rastislav Levicky
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
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8
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De Costa NTS, Heemstra JM. Differential DNA and RNA sequence discrimination by PNA having charged side chains. Bioorg Med Chem Lett 2014; 24:2360-3. [PMID: 24731279 DOI: 10.1016/j.bmcl.2014.03.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 12/14/2022]
Abstract
PNA sequences modified with charged side chains were evaluated for base-pairing sequence selectivity under physiological conditions. PNA having negatively charged aspartic acid side chains shows higher selectivity with RNA, while PNA having positively charged lysine side chains shows higher selectivity with DNA. These observations provide insight into the binding selectivity of modified PNA in antisense and antigene applications.
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Affiliation(s)
- N Tilani S De Costa
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112, USA; Center for Cell and Genome Science, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Jennifer M Heemstra
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112, USA; Center for Cell and Genome Science, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA.
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Ghosh S, Mishra S, Mukhopadhyay R. Enhancing sensitivity in a piezoresistive cantilever-based label-free DNA detection assay using ssPNA sensor probes. J Mater Chem B 2014; 2:960-970. [DOI: 10.1039/c3tb21392g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ghosh S, Mishra S, Mukhopadhyay R. Enhancing on-surface mismatch discrimination capability of PNA probes by AuNP modification of gold(111) surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:11982-90. [PMID: 23978256 DOI: 10.1021/la4019579] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Unambiguous identification of single base mismatches in nucleic acid sequences is of great importance in nucleic acid detection assays. However, ambiguities are often encountered with, and therefore, a strategy for attaining substantially large enhancement of mismatch discrimination has been worked upon in this study. Short single-stranded peptide nucleic acid (PNA) and deoxyribonucleic acid (DNA) sensor probes that are immobilized onto gold nanoparticle (AuNP) modified Au(111) surface have been applied for target DNA detection. It will be shown that while both PNA and the analogous DNA probes exhibit generally better target detection abilities on the AuNP-modified Au(111) surface (elicited from fluorescence-based measurement of on-surface Tm values), compared to the bare Au(111) surface, PNA supersedes DNA, for all sizes of AuNPs (10, 50, and 90 nm) applied, with the difference being quite drastic in the case of the smallest 10 nm AuNP. It is found that while the AuNP curvature plays a pivotal role in target detection abilities of the PNA probes, the changes in the surface roughness caused by AuNP treatment do not exert any significant influence. This study also presents a means for preparing PNA-AuNP hybrids without altering PNA functionality and without AuNP aggregation by working with the surface-affixed AuNPs.
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Affiliation(s)
- Srabani Ghosh
- Department of Biological Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata-700 032, India
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