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Zoughi S, Faridbod F, Moradi S. Rapid enzyme-free detection of miRNA-21 in human ovarian cancerous cells using a fluorescent nanobiosensor designed based on hairpin DNA-templated silver nanoclusters. Anal Chim Acta 2024; 1320:342968. [PMID: 39142796 DOI: 10.1016/j.aca.2024.342968] [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: 05/17/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 08/16/2024]
Abstract
BACKGROUND Cancer is known as one of the main non-communicable diseases and the leading cause of death in the new era. Early diagnosis of cancer requires the identification of special biomarkers. Currently, microRNAs (miRNAs) have attracted the attention of researchers as useful biomarkers for cancer early detection. Hence, various methods have been recently developed for detecting and monitoring miRNAs. Among all miRNAs, detection of miRNA-21 (miR-21) is important because it is abnormally overexpressed in most cancers. Here, a new biosensor based on silver nanoclusters (AgNCs) is introduced for detecting miR-21. RESULTS As a fluorescent probe, a rationally designed hairpin sequence containing a poly-cytosine motif was used to facilitate the formation of AgNCs. A guanine-rich sequence was also employed to enhance the sensing signal. It was found that in the absence of miR-21, adding a guanine-rich sequence to the detecting probe caused only a slight change in the fluorescence emission intensity of AgNCs. While in the presence of miR-21, the emission signal enhanced. A direct correlation was observed between the increase in the fluorescence of AgNCs and the concentration of miR-21. The performance of the proposed biosensor was characterized thoroughly and confirmed. The biosensor detected miR-21 in an applicable linear range from 9 pM to 1.55 nM (LOD: 2 pM). SIGNIFICANCE The designed biosensor was successfully applied for detecting miR-21 in human plasma samples and also in human normal and lung and ovarian cancer cells. This biosensing strategy can be used as a model for detecting other miRNAs. The designed nanobiosensor can measure miR-21 without using any enzymes, with fewer experimental steps, and at a low cost compared to the reported biosensors in this field.
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Affiliation(s)
- Sheida Zoughi
- Analytical Chemistry Department, Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Farnoush Faridbod
- Analytical Chemistry Department, Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran.
| | - Sharif Moradi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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2
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Slott S, Krüger-Jensen CS, Ferreira da Silva I, Pedersen NB, Astakhova K. Mutations in microRNA-128-2-3p identified with amplification-free hybridization assay. PLoS One 2023; 18:e0289556. [PMID: 37607185 PMCID: PMC10443835 DOI: 10.1371/journal.pone.0289556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/20/2023] [Indexed: 08/24/2023] Open
Abstract
We describe a quantitative detection method for mutated microRNA in human plasma samples. Specific oligonucleotides designed from a Peyrard-Bishop model allowed accurate prediction of target:probe recognition affinity and specificity. Our amplification-free tandem bead-based hybridization assay had limit of detection of 2.2 pM. Thereby, the assay allowed identification of single-nucleotide polymorphism mismatch profiles in clinically relevant microRNA-128-2-3p, showing terminal mutations that correlate positively with inflammatory colitis and colorectal cancer.
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Affiliation(s)
- Sofie Slott
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Izabela Ferreira da Silva
- Programa Interunidades de Pós-Graduacão em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte-MG, Brazil
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte-MG, Brazil
- Bioinformatics Core, Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, House of Biomedicine II, Belvaux, Luxembourg
| | - Nadia Bom Pedersen
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
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3
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Martino S, Tammaro C, Misso G, Falco M, Scrima M, Bocchetti M, Rea I, De Stefano L, Caraglia M. microRNA Detection via Nanostructured Biochips for Early Cancer Diagnostics. Int J Mol Sci 2023; 24:7762. [PMID: 37175469 PMCID: PMC10178165 DOI: 10.3390/ijms24097762] [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: 03/21/2023] [Revised: 04/15/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
MicroRNA (miRNA) are constituted of approximately 22 nucleotides and play an important role in the regulation of many physiological functions and diseases. In the last 10 years, an increasing interest has been recorded in studying the expression profile of miRNAs in cancer. Real time-quantitative polymerase chain reaction (RT-qPCR), microarrays, and small RNA sequencing represent the gold standard techniques used in the last 30 years as detection methods. The advent of nanotechnology has allowed the fabrication of nanostructured biosensors which are widely exploited in the diagnostic field. Nanostructured biosensors offer many advantages: (i) their small size allows the construction of portable, wearable, and low-cost products; (ii) the large surface-volume ratio enables the loading of a great number of biorecognition elements (e.g., probes, receptors); and (iii) direct contact of the recognition element with the analyte increases the sensitivity and specificity inducing low limits of detection (LOD). In this review, the role of nanostructured biosensors in miRNA detection is explored, focusing on electrochemical and optical sensing. In particular, four types of nanomaterials (metallic nanoparticles, graphene oxide, quantum dots, and nanostructured polymers) are reported for both detection strategies with the aim to show their distinct properties and applications.
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Affiliation(s)
- Sara Martino
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (S.M.); (C.T.); (M.F.); (M.B.); (M.C.)
- Unit of Naples, National Research Council, Institute of Applied Sciences and Intelligent Systems, 80138 Naples, Italy;
| | - Chiara Tammaro
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (S.M.); (C.T.); (M.F.); (M.B.); (M.C.)
| | - Gabriella Misso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (S.M.); (C.T.); (M.F.); (M.B.); (M.C.)
| | - Michela Falco
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (S.M.); (C.T.); (M.F.); (M.B.); (M.C.)
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, 83031 Ariano Irpino, Italy;
| | - Marianna Scrima
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, 83031 Ariano Irpino, Italy;
| | - Marco Bocchetti
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (S.M.); (C.T.); (M.F.); (M.B.); (M.C.)
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, 83031 Ariano Irpino, Italy;
| | - Ilaria Rea
- Unit of Naples, National Research Council, Institute of Applied Sciences and Intelligent Systems, 80138 Naples, Italy;
| | - Luca De Stefano
- Unit of Naples, National Research Council, Institute of Applied Sciences and Intelligent Systems, 80138 Naples, Italy;
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (S.M.); (C.T.); (M.F.); (M.B.); (M.C.)
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, 83031 Ariano Irpino, Italy;
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4
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Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that regulate gene expression. They play an important role in many biological processes including human diseases. However, miRNAs are challenging to detect due to their short sequence length and low copy number. A number of conventional (e.g., Northern blot, microarray, and RT-qPCR) and emerging (e.g., nanostructured materials and electrochemical methods) techniques have been developed to detect miRNA, each with their own strengths and weaknesses. Some of these techniques have been combined to detect miRNAs as disease biomarkers in point-of-care (POC) settings. Nonetheless, there is still potential for further innovation to facilitate the detection of miRNAs.
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Affiliation(s)
- Afrah Bawazeer
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - David C Prince
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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5
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Petrou L, Latvanen E, Seichepine F, Kim SH, Bennett PR, Sykes L, MacIntyre DA, Terzidou V, Ladame S. Lateral Flow Test (LFT) Detects Cell‐Free MicroRNAs Predictive of Preterm Birth Directly from Human Plasma. ADVANCED NANOBIOMED RESEARCH 2022. [DOI: 10.1002/anbr.202200026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Loukia Petrou
- Department of Bioengineering Imperial College London W12 0BZ London UK
| | - Elmeri Latvanen
- Department of Bioengineering Imperial College London W12 0BZ London UK
| | | | - Sung Hye Kim
- March of Dimes European Preterm Birth Research Centre Imperial College London W12 0NN London UK
- Institute of Reproductive and Developmental Biology Imperial College London W12 0NN London UK
| | - Phillip R. Bennett
- March of Dimes European Preterm Birth Research Centre Imperial College London W12 0NN London UK
- Institute of Reproductive and Developmental Biology Imperial College London W12 0NN London UK
- Queen Charlotte's and Chelsea Hospital Imperial College NHS Trust W12 0HS London UK
- Department of Obstetrics & Gynaecology Chelsea and Westminster Hospital NHS Trust SW10 9NH London UK
| | - Lynne Sykes
- March of Dimes European Preterm Birth Research Centre Imperial College London W12 0NN London UK
- Institute of Reproductive and Developmental Biology Imperial College London W12 0NN London UK
- The Parasol Foundation Centre for Women's Health and Cancer Research St Mary's Hospital Imperial College NHS Trust W2 1NY London UK
| | - David A. MacIntyre
- March of Dimes European Preterm Birth Research Centre Imperial College London W12 0NN London UK
- Institute of Reproductive and Developmental Biology Imperial College London W12 0NN London UK
| | - Vasso Terzidou
- March of Dimes European Preterm Birth Research Centre Imperial College London W12 0NN London UK
- Institute of Reproductive and Developmental Biology Imperial College London W12 0NN London UK
- Department of Obstetrics & Gynaecology Chelsea and Westminster Hospital NHS Trust SW10 9NH London UK
| | - Sylvain Ladame
- Department of Bioengineering Imperial College London W12 0BZ London UK
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6
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Manicardi A, Cadoni E, Madder A. Hydrolysis of 5-methylfuran-2-yl to 2,5-dioxopentanyl allows for stable bio-orthogonal proximity-induced ligation. Commun Chem 2021; 4:146. [PMID: 36697666 PMCID: PMC9814669 DOI: 10.1038/s42004-021-00584-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/14/2021] [Indexed: 01/28/2023] Open
Abstract
Ligation methodologies featuring bio-orthogonal units and leading to the formation of a stable adduct are the ideal candidates for being applied in a biological context. However, most of the available strategies rely on highly reactive species that require careful handling, or on the activation of pro-reactive functional groups. We here report on a proximity-induced ligation reaction that relies on a stable 2,5-dione, that can be conveniently generated under acidic conditions from a 2,5-dialkylfuran building block, and hydrazine nucleophiles. This bio-orthogonal ligation, which proceeds under physiological conditions, does not require any stimulus or trigger and leads to the formation of a pyridazinium adduct that demonstrates excellent stability under harsh conditions (24 h at 90 °C). The reaction was applied to the formation of PNA-PNA adducts, DNA- and RNA-templated ligations, and for the formation of peptide-peptide adducts in solution. This convenient methodology was further implemented on plastic and glass surfaces to realize self-addressable covalent constructs.
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Affiliation(s)
- Alex Manicardi
- grid.5342.00000 0001 2069 7798Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Ghent, Belgium
| | - Enrico Cadoni
- grid.5342.00000 0001 2069 7798Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Ghent, Belgium
| | - Annemieke Madder
- grid.5342.00000 0001 2069 7798Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Ghent, Belgium
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7
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Ren R, Sun M, Goel P, Cai S, Kotov NA, Kuang H, Xu C, Ivanov AP, Edel JB. Single-Molecule Binding Assay Using Nanopores and Dimeric NP Conjugates. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2103067. [PMID: 34323323 DOI: 10.1002/adma.202103067] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/25/2021] [Indexed: 06/13/2023]
Abstract
The ability to measure biomarkers, both specifically and selectively at the single-molecule level in biological fluids, has the potential to transform the diagnosis, monitoring, and therapeutic intervention of diseases. The use of nanopores has been gaining prominence in this area, not only for sequencing but more recently in screening applications. The selectivity of nanopore sensing can be substantially improved with the use of labels, but substantial challenges remain, especially when trying to differentiate between bound from unbound targets. Here highly sensitive and selective molecular probes made from nanoparticles (NPs) that self-assemble and dimerize upon binding to a biological target are designed. It is shown that both single and paired NPs can be successfully resolved and detected at the single-molecule nanopore sensing and can be used for applications such as antigen/antibody detection and microRNA (miRNA) sequence analysis. It is expected that such technology will contribute significantly to developing highly sensitive and selective strategies for the diagnosis and screening of diseases without the need for sample processing or amplification while requiring minimal sample volume.
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Affiliation(s)
- Ren Ren
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Maozhong Sun
- Key Lab of Synthetic and Biological Colloids, Ministry of Education, State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Pratibha Goel
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Shenglin Cai
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Nicholas A Kotov
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hua Kuang
- Key Lab of Synthetic and Biological Colloids, Ministry of Education, State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Chuanlai Xu
- Key Lab of Synthetic and Biological Colloids, Ministry of Education, State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Aleksandar P Ivanov
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Joshua B Edel
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
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8
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Brodyagin N, Katkevics M, Kotikam V, Ryan CA, Rozners E. Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications. Beilstein J Org Chem 2021; 17:1641-1688. [PMID: 34367346 PMCID: PMC8313981 DOI: 10.3762/bjoc.17.116] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/28/2021] [Indexed: 12/23/2022] Open
Abstract
Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA's chemistry, optimization of structure and function, applications as probes and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA's binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA therapeutics. While many modifications have improved on PNA's binding affinity and specificity, solubility and other biophysical properties, the original PNA is still most frequently used in diagnostic and other in vitro applications. Development of therapeutics and other in vivo applications of PNA has notably lagged behind and is still limited by insufficient bioavailability and difficulties with tissue specific delivery. Relatively high doses are required to overcome poor cellular uptake and endosomal entrapment, which increases the risk of toxicity. These limitations remain unsolved problems waiting for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Venubabu Kotikam
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Christopher A Ryan
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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9
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Zhang W, Han Z, Liang Y, Zhang Q, Dou X, Guo G, Wang X. A pico-HPLC-LIF system for the amplification-free determination of multiple miRNAs in cells. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Huang G, Su C, Wang L, Fei Y, Yang J. The Application of Nucleic Acid Probe-Based Fluorescent Sensing and Imaging in Cancer Diagnosis and Therapy. Front Chem 2021; 9:705458. [PMID: 34141699 PMCID: PMC8204288 DOI: 10.3389/fchem.2021.705458] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/17/2021] [Indexed: 01/27/2023] Open
Abstract
It is well known that cancer incidence and death rates have been growing, but the development of cancer theranostics and therapeutics has been a challenging work. Recently, nucleic acid probe-based fluorescent sensing and imaging have achieved remarkable improvements in a variety of cancer management techniques, credited to their high sensitivity, good tolerance to interference, fast detection, and high versatility. Herein, nucleic acid probe-based fluorescent sensing and imaging are labeled with advanced fluorophores, which are essential for fast and sensitive detection of aberrant nucleic acids and other cancer-relevant molecules, consequently performing cancer early diagnosis and targeted treatment. In this review, we introduce the characteristics of nucleic acid probes, summarize the development of nucleic acid probe-based fluorescent sensing and imaging, and prominently elaborate their applications in cancer diagnosis and treatment. In discussion, some challenges and perspectives are elaborated in the field of nucleic acid probe-based fluorescent sensing and imaging.
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Affiliation(s)
- Ge Huang
- Department of Medicine, University of South China, Hengyang, China.,Department of Anesthesiology and Pain Medicine, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, China
| | - Chen Su
- Department of Anesthesiology and Pain Medicine, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, China
| | - Lijuan Wang
- Department of Medicine, University of South China, Hengyang, China.,Department of Anesthesiology and Pain Medicine, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, China
| | - Yanxia Fei
- Department of Anesthesiology and Pain Medicine, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, China
| | - Jinfeng Yang
- Department of Anesthesiology and Pain Medicine, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, China
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11
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Palanca-Ballester C, Rodriguez-Casanova A, Torres S, Calabuig-Fariñas S, Exposito F, Serrano D, Redin E, Valencia K, Jantus-Lewintre E, Diaz-Lagares A, Montuenga L, Sandoval J, Calvo A. Cancer Epigenetic Biomarkers in Liquid Biopsy for High Incidence Malignancies. Cancers (Basel) 2021; 13:cancers13123016. [PMID: 34208598 PMCID: PMC8233712 DOI: 10.3390/cancers13123016] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Early alterations in cancer include the deregulation of epigenetic events such as changes in DNA methylation and abnormal levels of non-coding (nc)RNAs. Although these changes can be identified in tumors, alternative sources of samples may offer advantages over tissue biopsies. Because tumors shed DNA, RNA, and proteins, biological fluids containing these molecules can accurately reflect alterations found in cancer cells, not only coming from the primary tumor, but also from metastasis and from the tumor microenvironment (TME). Depending on the type of cancer, biological fluids encompass blood, urine, cerebrospinal fluid, and saliva, among others. Such samples are named with the general term "liquid biopsy" (LB). With the advent of ultrasensitive technologies during the last decade, the identification of actionable genetic alterations (i.e., mutations) in LB is a common practice to decide whether or not targeted therapy should be applied. Likewise, the analysis of global or specific epigenetic alterations may also be important as biomarkers for diagnosis, prognosis, and even for cancer drug response. Several commercial kits that assess the DNA promoter methylation of single genes or gene sets are available, with some of them being tested as biomarkers for diagnosis in clinical trials. From the tumors with highest incidence, we can stress the relevance of DNA methylation changes in the following genes found in LB: SHOX2 (for lung cancer); RASSF1A, RARB2, and GSTP1 (for lung, breast, genitourinary and colon cancers); and SEPT9 (for colon cancer). Moreover, multi-cancer high-throughput methylation-based tests are now commercially available. Increased levels of the microRNA miR21 and several miRNA- and long ncRNA-signatures can also be indicative biomarkers in LB. Therefore, epigenetic biomarkers are attractive and may have a clinical value in cancer. Nonetheless, validation, standardization, and demonstration of an added value over the common clinical practice are issues needed to be addressed in the transfer of this knowledge from "bench to bedside".
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Affiliation(s)
- Cora Palanca-Ballester
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- Roche-CHUS Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Susana Torres
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
| | - Silvia Calabuig-Fariñas
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Pathology, Universitat de València, 46010 Valencia, Spain
| | - Francisco Exposito
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Diego Serrano
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Esther Redin
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Karmele Valencia
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, 31008 Pamplona, Spain
| | - Eloisa Jantus-Lewintre
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
| | - Luis Montuenga
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
- Correspondence: (J.S.); (A.C.)
| | - Alfonso Calvo
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
- Correspondence: (J.S.); (A.C.)
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12
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Cai S, Pataillot-Meakin T, Shibakawa A, Ren R, Bevan CL, Ladame S, Ivanov AP, Edel JB. Single-molecule amplification-free multiplexed detection of circulating microRNA cancer biomarkers from serum. Nat Commun 2021; 12:3515. [PMID: 34112774 PMCID: PMC8192752 DOI: 10.1038/s41467-021-23497-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) play essential roles in post-transcriptional gene expression and are also found freely circulating in bodily fluids such as blood. Dysregulated miRNA signatures have been associated with many diseases including cancer, and miRNA profiling from liquid biopsies offers a promising strategy for cancer diagnosis, prognosis and monitoring. Here, we develop size-encoded molecular probes that can be used for simultaneous electro-optical nanopore sensing of miRNAs, allowing for ultrasensitive, sequence-specific and multiplexed detection directly in unprocessed human serum, in sample volumes as small as 0.1 μl. We show that this approach allows for femtomolar sensitivity and single-base mismatch selectivity. We demonstrate the ability to simultaneously monitor miRNAs (miR-141-3p and miR-375-3p) from prostate cancer patients with active disease and in remission. This technology can pave the way for next generation of minimally invasive diagnostic and companion diagnostic tests for cancer.
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Affiliation(s)
- Shenglin Cai
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK
| | - Thomas Pataillot-Meakin
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, London, W12 0BZ, UK
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Akifumi Shibakawa
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Ren Ren
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK
| | - Charlotte L Bevan
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK.
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, London, W12 0BZ, UK.
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK.
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK.
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13
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Gillespie P, Channon RB, Meng X, Islam MN, Ladame S, O'Hare D. Nucleic acid sensing via electrochemical oligonucleotide-templated reactions. Biosens Bioelectron 2021; 176:112891. [PMID: 33397596 DOI: 10.1016/j.bios.2020.112891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/29/2020] [Accepted: 12/09/2020] [Indexed: 12/20/2022]
Abstract
Short single-stranded nucleic acids as found in a variety of bodily fluids have recently emerged as minimally invasive biomarkers for a broad range of pathologies, most notably cancer. Because of their small size, low natural abundance and high sequence homology between family members they are challenging to detect using standard technologies suitable for use at the point-of-care. Herein we report the design, engineering and testing of a novel sensing strategy: electrochemically active molecular probes based on peptide nucleic acid (PNA) scaffolds for the detection of single-stranded oligonucleotides, in particular microRNAs (or miRs). As a proof-of-principle, a wide range of probes were designed and tested to detect miR-141, a known diagnostic biomarker for prostate cancer. Optimal quantitative sensing of miR-141 was achieved via the first example of an electrochemical oligonucleotide-templated reaction (EOTR), whereby two PNA probes - functionalized with an aniline and a 1,4-catechol respectively - preferentially react with each other upon simultaneous hybridization to the same RNA target strand, serving here as a template. Quantitative, electrochemical detection of the product of this bio-orthogonal reaction showed direct correlation between adduct formation and miR-141 concentration. Coupling the specificity of OTR with the speed and sensitivity of electrochemical sensing delivers EOTRs as a promising new technique for fast, low-cost, quantitative and sequence-specific detection of short nucleic acids from liquid biopsies.
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Affiliation(s)
- Philip Gillespie
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Robert B Channon
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Xiaotong Meng
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Md Nazmul Islam
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK; School of Health and Life Sciences, Teesside University, Middlesbrough, Tees Valley, TS1 3BA, UK
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
| | - Danny O'Hare
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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14
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Rodriguez-Casanova A, Costa-Fraga N, Bao-Caamano A, López-López R, Muinelo-Romay L, Diaz-Lagares A. Epigenetic Landscape of Liquid Biopsy in Colorectal Cancer. Front Cell Dev Biol 2021; 9:622459. [PMID: 33614651 PMCID: PMC7892964 DOI: 10.3389/fcell.2021.622459] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies and is a major cause of cancer-related deaths worldwide. Thus, there is a clinical need to improve early detection of CRC and personalize therapy for patients with this disease. In the era of precision oncology, liquid biopsy has emerged as a major approach to characterize the circulating tumor elements present in body fluids, including cell-free DNA and RNA, circulating tumor cells, and extracellular vesicles. This non-invasive tool has allowed the identification of relevant molecular alterations in CRC patients, including some indicating the disruption of epigenetic mechanisms. Epigenetic alterations found in solid and liquid biopsies have shown great utility as biomarkers for early detection, prognosis, monitoring, and evaluation of therapeutic response in CRC patients. Here, we summarize current knowledge of the most relevant epigenetic mechanisms associated with cancer development and progression, and the implications of their deregulation in cancer cells and liquid biopsy of CRC patients. In particular, we describe the methodologies used to analyze these epigenetic alterations in circulating tumor material, and we focus on the clinical utility of epigenetic marks in liquid biopsy as tumor biomarkers for CRC patients. We also discuss the great challenges and emerging opportunities of this field for the diagnosis and personalized management of CRC patients.
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Affiliation(s)
- Aitor Rodriguez-Casanova
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Nicolás Costa-Fraga
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Aida Bao-Caamano
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Rafael López-López
- Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain.,Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Laura Muinelo-Romay
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.,Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
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15
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Saini V, Dawar R, Suneja S, Gangopadhyay S, Kaur C. Can microRNA become next-generation tools in molecular diagnostics and therapeutics? A systematic review. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-020-00125-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Abstract
Background
MicroRNAs (miRNAs) represent a novel class of single-stranded RNA molecules of 18–22 nucleotides that serve as powerful tools in the regulation of gene expression. They are important regulatory molecules in several biological processes.
Main body
Alteration in the expression profiles of miRNAs have been found in several diseases. It is anticipated that miRNA expression profiling can become a novel diagnostic tool in the future.
Hence, this review evaluates the implications of miRNAs in various diseases and the recent advances in miRNA expression level detection and their target identification. A systematic approach to review existing literature available on databases such as Medline, PubMed, and EMBASE was conducted to have a better understanding of mechanisms mediating miRNA-dependent gene regulation and their role as diagnostic markers and therapeutic agents.
Conclusion
A clear understanding of the complex multilevel regulation of miRNA expression is a prerequisite to explicate the origin of a wide variety of diseases. It is understandable that miRNAs offer potential targets both in diagnostics and therapeutics of a multitude of diseases. The inclusion of specific miRNA expression profiles as biomarkers may lead to crucial advancements in facilitating disease diagnosis and classification, monitoring its prognosis, and treatment. However, standardization of methods has a pivotal role in the success of extensive use of miRNA expression profiling in routine clinical settings.
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16
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Manicardi A, Cadoni E, Madder A. Visible-light triggered templated ligation on surface using furan-modified PNAs. Chem Sci 2020; 11:11729-11739. [PMID: 34094412 PMCID: PMC8162948 DOI: 10.1039/d0sc04875e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/02/2020] [Indexed: 12/25/2022] Open
Abstract
Oligonucleotide-templated reactions are frequently exploited for target detection in biosensors and for the construction of DNA-based materials and probes in nanotechnology. However, the translation of the specifically used template chemistry from solution to surfaces, with the final aim of achieving highly selective high-throughput systems, has been difficult to reach and therefore, poorly explored. Here, we show the first example of a visible light-triggered templated ligation on a surface, employing furan-modified peptide nucleic acids (PNAs). Tailored photo-oxidation of the pro-reactive furan moiety is ensured by the simultaneous introduction of a weak photosensitizer as well as a nucleophilic moiety in the reacting PNA strand. This allows one to ensure a localized production of singlet oxygen for furan activation, which is not affected by probe dilution or reducing conditions. Simple white light irradiation in combination with target-induced proximity between reactive functionalities upon recognition of a short 22mer DNA or RNA sequence that functions as a template, allows sensitive detection of nucleic acid targets in a 96 well plate format.
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Affiliation(s)
- Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
| | - Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
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17
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Rossetti M, Bertucci A, Patiño T, Baranda L, Porchetta A. Programming DNA-Based Systems through Effective Molarity Enforced by Biomolecular Confinement. Chemistry 2020; 26:9826-9834. [PMID: 32428310 DOI: 10.1002/chem.202001660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/12/2020] [Indexed: 12/12/2022]
Abstract
The fundamental concept of effective molarity is observed in a variety of biological processes, such as protein compartmentalization within organelles, membrane localization and signaling paths. To control molecular encountering and promote effective interactions, nature places biomolecules in specific sites inside the cell in order to generate a high, localized concentration different from the bulk concentration. Inspired by this mechanism, scientists have artificially recreated in the lab the same strategy to actuate and control artificial DNA-based functional systems. Here, it is discussed how harnessing effective molarity has led to the development of a number of proximity-induced strategies, with applications ranging from DNA-templated organic chemistry and catalysis, to biosensing and protein-supported DNA assembly.
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Affiliation(s)
- Marianna Rossetti
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Bertucci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Tania Patiño
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Lorena Baranda
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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18
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Coordinated AR and microRNA regulation in prostate cancer. Asian J Urol 2020; 7:233-250. [PMID: 32742925 PMCID: PMC7385519 DOI: 10.1016/j.ajur.2020.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 03/22/2020] [Accepted: 04/17/2020] [Indexed: 12/26/2022] Open
Abstract
The androgen receptor (AR) remains a key driver of prostate cancer (PCa) progression, even in the advanced castrate-resistant stage, where testicular androgens are absent. It is therefore of critical importance to understand the molecular mechanisms governing its activity and regulation during prostate tumourigenesis. MicroRNAs (miRs) are small ∼22 nt non-coding RNAs that regulate target gene, often through association with 3′ untranslated regions (3′UTRs) of transcripts. They display dysregulation during cancer progression, can function as oncogenes or tumour suppressors, and are increasingly recognised as targets or regulators of hormonal action. Thus, understanding factors which modulate miRs synthesis is essential. There is increasing evidence for complex and dynamic bi-directional cross-talk between the multi-step miR biogenesis cascade and the AR signalling axis in PCa. This review summarises the wealth of mechanisms by which miRs are regulated by AR, and conversely, how miRs impact AR's transcriptional activity, including that of AR splice variants. In addition, we assess the implications of the convergence of these pathways on the clinical employment of miRs as PCa biomarkers and therapeutic targets.
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19
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Zhou QY, Zhong XY, Zhao LL, Wang LJ, Zhou YL, Zhang XX. High-throughput ultra-sensitive discrimination of single nucleotide polymorphism via click chemical ligation. Analyst 2020; 145:172-176. [PMID: 31724655 DOI: 10.1039/c9an01672d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single nucleotide polymorphisms (SNPs) have been proven to be important biomarkers for disease diagnosis, prognosis and disease pathogenesis. Here, taking the advantages of a self-assembled oligonucleotide sandwich structure and robust chemical reactions, we have developed a simple, high-throughput and effective colorimetric analytical technique termed CuAAC-based ligation-assisted assays (CuAAC-LA) for SNP detection using a DNA-BIND 96-well plate. With the 5'-azide and 3'-alkyne groups labelled on two oligonucleotide probes, the target DNA can direct a Cu(i)-catalyzed alkyne-azide cycloaddition (CuAAC) click reaction. Since the small difference in duplex stability caused by a single-nucleotide mismatch was amplified by the steric effects of these reactive groups for the ligation reaction of an unstable duplex, CuAAC-LA exhibited an ultra-sensitive discrimination ability for a mutant type target in the presence of large amounts of wild type targets. As low as 0.05% SNP could be clearly detected, which was better than most previously reported methods by various DNA ligases, indicating that a simple and rapid synthetic method i.e., the DNA template-directed click reaction held the potential to replace the ligase for SNP detection.
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Affiliation(s)
- Qian-Yu Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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20
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Stoica SC, Dorobantu DM, Vardeu A, Biglino G, Ford KL, Bruno DV, Zakkar M, Mumford A, Angelini GD, Caputo M, Emanueli C. MicroRNAs as potential biomarkers in congenital heart surgery. J Thorac Cardiovasc Surg 2020; 159:1532-1540.e7. [PMID: 31043318 DOI: 10.1016/j.jtcvs.2019.03.062] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 03/10/2019] [Accepted: 03/26/2019] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Pediatric congenital heart surgery (CHS) involves intracardiac, valvular, and vascular repairs. Accurate tools to aid short-term outcome prediction in pediatric CHS are lacking. Clinical scores, such as the vasoactive-inotrope score and ventilation index, are used to define outcome in clinical studies. MicroRNA-1-3p (miR-1) is expressed by both cardiomyocytes and vascular cells and is regulated by hypoxia. In adult patients, miR-1 increases in the circulation after open-heart cardiac surgery, suggesting its potential as a clinical biomarker. Thus, we investigated whether perioperative circulating miR-1 measurements can help predict post-CHS short-term outcomes in pediatric patients. METHODS Plasma miR-1 was retrospectively measured in a cohort of 199 consecutive pediatric CHS patients (median age 1.2 years). Samples were taken before surgery and at the end of the operation. Plasma miR-1 concentration was measured by reverse transcription-quantitative polymerase chain reaction and expressed as miR-1 copies/μL and as relative expression to spiked-in exogenous cel-miR-39. RESULTS Baseline plasma miR-1 did not vary across different diagnoses, increased during surgery (204-fold median relative increase, P < .001), and was associated with aortic crossclamp duration postoperatively (P < .001). Importantly, miR-1 levels at the end of the operation positively correlated with intensive care stay (P < .001), early severe cardiovascular events (P = .01), and with high vasoactive-inotrope score (P = .001) and ventilation index (P < .001), suggesting that miR-1 could accelerate the identification of patients with cardiopulmonary bypass-related ischemic complications, requiring more intensive support. CONCLUSIONS Our study suggests miR-1 as a novel potential circulating biomarker to predict early postoperative outcome and inform clinical management in pediatric heart surgery.
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Affiliation(s)
- Serban C Stoica
- Bristol Heart Institute, University of Bristol, Bristol, United Kingdom; Royal Hospital for Children, University Hospitals Bristol National Health System Trust, Department of Cardiac Surgery and Cardiology, Bristol, United Kingdom
| | - Dan M Dorobantu
- Royal Hospital for Children, University Hospitals Bristol National Health System Trust, Department of Cardiac Surgery and Cardiology, Bristol, United Kingdom; "Professor C.C. Iliescu" Emergency Institute for Cardiovascular Diseases, Cardiology Department, Bucharest, Romania
| | - Antonella Vardeu
- Bristol Heart Institute, University of Bristol, Bristol, United Kingdom
| | - Giovanni Biglino
- Bristol Heart Institute, University of Bristol, Bristol, United Kingdom
| | - Kerrie L Ford
- Bristol Heart Institute, University of Bristol, Bristol, United Kingdom
| | - Domenico V Bruno
- Bristol Heart Institute, University of Bristol, Bristol, United Kingdom; Royal Hospital for Children, University Hospitals Bristol National Health System Trust, Department of Cardiac Surgery and Cardiology, Bristol, United Kingdom
| | - Mustafa Zakkar
- Royal Hospital for Children, University Hospitals Bristol National Health System Trust, Department of Cardiac Surgery and Cardiology, Bristol, United Kingdom
| | - Andrew Mumford
- Bristol Heart Institute, University of Bristol, Bristol, United Kingdom
| | - Gianni D Angelini
- Bristol Heart Institute, University of Bristol, Bristol, United Kingdom; Royal Hospital for Children, University Hospitals Bristol National Health System Trust, Department of Cardiac Surgery and Cardiology, Bristol, United Kingdom
| | - Massimo Caputo
- Bristol Heart Institute, University of Bristol, Bristol, United Kingdom; Royal Hospital for Children, University Hospitals Bristol National Health System Trust, Department of Cardiac Surgery and Cardiology, Bristol, United Kingdom; Rush Medical Center, Chicago, Ill
| | - Costanza Emanueli
- Bristol Heart Institute, University of Bristol, Bristol, United Kingdom; National Heart and Lung Institute, Imperial College London, London, United Kingdom.
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21
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PNA-Based MicroRNA Detection Methodologies. Molecules 2020; 25:molecules25061296. [PMID: 32178411 PMCID: PMC7144472 DOI: 10.3390/molecules25061296] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) are small noncoding RNAs involved in the fine regulation of post-transcriptional processes in the cell. The physiological levels of these short (20-22-mer) oligonucleotides are important for the homeostasis of the organism, and therefore dysregulation can lead to the onset of cancer and other pathologies. Their importance as biomarkers is constantly growing and, in this context, detection methods based on the hybridization to peptide nucleic acids (PNAs) are gaining their place in the spotlight. After a brief overview of their biogenesis, this review will discuss the significance of targeting miR, providing a wide range of PNA-based approaches to detect them at biologically significant concentrations, based on electrochemical, fluorescence and colorimetric assays.
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22
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Pavagada S, Channon RB, Chang JYH, Kim SH, MacIntyre D, Bennett PR, Terzidou V, Ladame S. Oligonucleotide-templated lateral flow assays for amplification-free sensing of circulating microRNAs. Chem Commun (Camb) 2019; 55:12451-12454. [PMID: 31556888 DOI: 10.1039/c9cc05607f] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Herein we demonstrate the first example of oligonucleotide-templated reaction (OTR) performed on paper, using lateral flow to capture and concentrate specific nucleic acid biomarkers on a test line. Quantitative analysis, using a low-cost benchtop fluorescence reader showed very high specificity down to the single nucleotide level and proved sensitive enough for amplification-free, on-chip, detection of endogenous concentrations of miR-150-5p, a recently identified predictive blood biomarker for preterm birth.
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Affiliation(s)
- Suraj Pavagada
- Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
| | - Robert B Channon
- Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
| | - Jason Y H Chang
- Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
| | - Sung Hye Kim
- Parturition Research Group, Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK
| | - David MacIntyre
- Parturition Research Group, Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK and March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK and Queen Charlotte's Hospital, Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - Phillip R Bennett
- Parturition Research Group, Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK and March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK and Queen Charlotte's Hospital, Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - Vasso Terzidou
- Parturition Research Group, Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK and March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK and Chelsea & Westminster Hospital, Imperial College Healthcare NHS Trust, London, SW10 9NH, UK
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. and March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK
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23
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Saarbach J, Sabale PM, Winssinger N. Peptide nucleic acid (PNA) and its applications in chemical biology, diagnostics, and therapeutics. Curr Opin Chem Biol 2019; 52:112-124. [PMID: 31541865 DOI: 10.1016/j.cbpa.2019.06.006] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/07/2019] [Accepted: 06/06/2019] [Indexed: 12/11/2022]
Abstract
Peptide nucleic acid (PNA) stands as one of the most successful artificial oligonucleotide mimetics. Salient features include the stability of hybridization complexes (either as duplexes or triplexes), metabolic stability, and ease of chemical modifications. These features have enabled important applications such as antisense agents, gene editing, nucleic acid sensing and as a platform to program the assembly of PNA-tagged molecules. Here, we review recent advances in these areas.
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Affiliation(s)
- Jacques Saarbach
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Pramod M Sabale
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland.
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24
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Sulaiman DA, Chang JYH, Bennett NR, Topouzi H, Higgins CA, Irvine DJ, Ladame S. Hydrogel-Coated Microneedle Arrays for Minimally Invasive Sampling and Sensing of Specific Circulating Nucleic Acids from Skin Interstitial Fluid. ACS NANO 2019; 13:9620-9628. [PMID: 31411871 PMCID: PMC6746174 DOI: 10.1021/acsnano.9b04783] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Minimally invasive technologies that can sample and detect cell-free nucleic acid biomarkers from liquid biopsies have recently emerged as clinically useful for early diagnosis of a broad range of pathologies, including cancer. Although blood has so far been the most commonly interrogated bodily fluid, skin interstitial fluid has been mostly overlooked despite containing the same broad variety of molecular biomarkers originating from cells and surrounding blood capillaries. Emerging technologies to sample this fluid in a pain-free and minimally-invasive manner often take the form of microneedle patches. Herein, we developed microneedles that are coated with an alginate-peptide nucleic acid hybrid material for sequence-specific sampling, isolation, and detection of nucleic acid biomarkers from skin interstitial fluid. Characterized by fast sampling kinetics and large sampling capacity (∼6.5 μL in 2 min), this platform technology also enables the detection of specific nucleic acid biomarkers either on the patch itself or in solution after light-triggered release from the hydrogel. Considering the emergence of cell-free nucleic acids in bodily fluids as clinically informative biomarkers, platform technologies that can detect them in an automated and minimally invasive fashion have great potential for personalized diagnosis and longitudinal monitoring of patient-specific disease progression.
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Affiliation(s)
- Dana Al Sulaiman
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Jason Y. H. Chang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, U.S.A
| | - Nitasha R. Bennett
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, U.S.A
| | - Helena Topouzi
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Claire A. Higgins
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Darrell J. Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, U.S.A
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, U.S.A
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, U.S.A
- Ragon Institute of MIT, MGH, and Harvard, Boston MA 02139
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd., Chevy Chase, MD
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
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25
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Wang YM, Trinh MP, Zheng Y, Guo K, Jimenez LA, Zhong W. Analysis of circulating non-coding RNAs in a non-invasive and cost-effective manner. Trends Analyt Chem 2019; 117:242-262. [PMID: 32292220 PMCID: PMC7156030 DOI: 10.1016/j.trac.2019.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Non-coding RNAs (ncRNAs) participate in regulation of gene expression, and are highly relevant to pathological development. They are found to be stably present in diverse body fluids, including those in the circulatory system, which can be sampled non-invasively for clinical tests. Thus, circulating ncRNAs have great potential to be disease biomarkers. However, tremendous efforts are desired to discover and utilize ncRNAs as biomarkers in clinical diagnosis, calling for technological advancement in analysis of circulating ncRNAs in biospecimens. Hence, this review summarizes the recent developments in this area, highlighting the works devoted to cancer diagnosis and prognosis. Three main directions are focused: 1) Extraction and purification of ncRNAs from body fluids; 2) Quantification of the purified circulating ncRNAs; and 3) Microfluidic platforms for integration of both steps to enable point-of-care diagnostics. These technologies have laid a solid foundation to move forward the applications of circulating ncRNAs in disease diagnosis and cure.
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Affiliation(s)
- Yu-Min Wang
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
- Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry and Environment, South China Normal University, Guangzhou, Guangdong 510006, P. R. China
| | - Michael Patrick Trinh
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Yongzan Zheng
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Kaizhu Guo
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Luis A. Jimenez
- Program in Biomedical Sciences, University of California at Riverside, Riverside, California 92521, United States
| | - Wenwan Zhong
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
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26
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Abstract
Bioorthogonal reactions that proceed readily under physiological conditions without interference from biomolecules have found widespread application in the life sciences. Complementary to the bioorthogonal reactions that ligate two molecules, reactions that release a molecule or cleave a linker are increasingly attracting interest. Such dissociative bioorthogonal reactions have a broad spectrum of uses, for example, in controlling bio-macromolecule activity, in drug delivery, and in diagnostic assays. This review article summarizes the developed bioorthogonal reactions linked to a release step, outlines representative areas of the applications of such reactions, and discusses aspects that require further improvement.
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Affiliation(s)
- Julian Tu
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah, 84112, USA
| | - Minghao Xu
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah, 84112, USA
| | - Raphael M Franzini
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah, 84112, USA
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27
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MicroRNA amplification and detection technologies: opportunities and challenges for point of care diagnostics. J Transl Med 2019; 99:452-469. [PMID: 30542067 DOI: 10.1038/s41374-018-0143-3] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/03/2018] [Accepted: 08/30/2018] [Indexed: 12/13/2022] Open
Abstract
The volume of point of care (POC) testing continues to grow steadily due to the increased availability of easy-to-use devices, thus making it possible to deliver less costly care closer to the patient site in a shorter time relative to the central laboratory services. A novel class of molecules called microRNAs have recently gained attention in healthcare management for their potential as biomarkers for human diseases. The increasing interest of miRNAs in clinical practice has led to an unmet need for assays that can rapidly and accurately measure miRNAs at the POC. However, the most widely used methods for analyzing miRNAs, including Northern blot-based platforms, in situ hybridization, reverse transcription qPCR, microarray, and next-generation sequencing, are still far from being used as ideal POC diagnostic tools, due to considerable time, expertize required for sample preparation, and in terms of miniaturizations making them suitable platforms for centralized labs. In this review, we highlight various existing and upcoming technologies for miRNA amplification and detection with a particular emphasis on the POC testing industries. The review summarizes different miRNA targets and signals amplification-based assays, from conventional methods to alternative technologies, such as isothermal amplification, paper-based, oligonucleotide-templated reaction, nanobead-based, electrochemical signaling- based, and microfluidic chip-based strategies. Based on critical analysis of these technologies, the possibilities and feasibilities for further development of POC testing for miRNA diagnostics are addressed and discussed.
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28
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Choi Y, Schmidt C, Tinnefeld P, Bald I, Rödiger S. A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads. Sci Rep 2019; 9:4769. [PMID: 30886341 PMCID: PMC6423227 DOI: 10.1038/s41598-019-41136-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/28/2019] [Indexed: 01/05/2023] Open
Abstract
The DNA origami technique has great potential for the development of brighter and more sensitive reporters for fluorescence based detection schemes such as a microbead-based assay in diagnostic applications. The nanostructures can be programmed to include multiple dye molecules to enhance the measured signal as well as multiple probe strands to increase the binding strength of the target oligonucleotide to these nanostructures. Here we present a proof-of-concept study to quantify short oligonucleotides by developing a novel DNA origami based reporter system, combined with planar microbead assays. Analysis of the assays using the VideoScan digital imaging platform showed DNA origami to be a more suitable reporter candidate for quantification of the target oligonucleotides at lower concentrations than a conventional reporter that consists of one dye molecule attached to a single stranded DNA. Efforts have been made to conduct multiplexed analysis of different targets as well as to enhance fluorescence signals obtained from the reporters. We therefore believe that the quantification of short oligonucleotides that exist in low copy numbers is achieved in a better way with the DNA origami nanostructures as reporters.
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Affiliation(s)
- Youngeun Choi
- University of Potsdam, Department of Chemistry, Physical Chemistry, 14476, Potsdam, Germany.,BAM Federal Institute for Materials Research and Testing, 12489, Berlin, Germany
| | - Carsten Schmidt
- Brandenbrug University of Technology Cottbus-Senftenberg, Institute of Biotechnology, 01968, Senftenberg, Germany
| | - Philip Tinnefeld
- Department Chemie and Center for NanoScience, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstr, 5-13 Haus E, 81377, Muenchen, Germany
| | - Ilko Bald
- University of Potsdam, Department of Chemistry, Physical Chemistry, 14476, Potsdam, Germany. .,BAM Federal Institute for Materials Research and Testing, 12489, Berlin, Germany.
| | - Stefan Rödiger
- Brandenbrug University of Technology Cottbus-Senftenberg, Institute of Biotechnology, 01968, Senftenberg, Germany.
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29
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Zhang X, Chen L, Lim KH, Gonuguntla S, Lim KW, Pranantyo D, Yong WP, Yam WJT, Low Z, Teo WJ, Nien HP, Loh QW, Soh S. The Pathway to Intelligence: Using Stimuli-Responsive Materials as Building Blocks for Constructing Smart and Functional Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1804540. [PMID: 30624820 DOI: 10.1002/adma.201804540] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/09/2018] [Indexed: 05/22/2023]
Abstract
Systems that are intelligent have the ability to sense their surroundings, analyze, and respond accordingly. In nature, many biological systems are considered intelligent (e.g., humans, animals, and cells). For man-made systems, artificial intelligence is achieved by massively sophisticated electronic machines (e.g., computers and robots operated by advanced algorithms). On the other hand, freestanding materials (i.e., not tethered to a power supply) are usually passive and static. Hence, herein, the question is asked: can materials be fabricated so that they are intelligent? One promising approach is to use stimuli-responsive materials; these "smart" materials use the energy supplied by a stimulus available from the surrounding for performing a corresponding action. After decades of research, many interesting stimuli-responsive materials that can sense and perform smart functions have been developed. Classes of functions discussed include practical functions (e.g., targeting and motion), regulatory functions (e.g., self-regulation and amplification), and analytical processing functions (e.g., memory and computing). The pathway toward creating truly intelligent materials can involve incorporating a combination of these different types of functions into a single integrated system by using stimuli-responsive materials as the basic building blocks.
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Affiliation(s)
- Xuan Zhang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Linfeng Chen
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Kang Hui Lim
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Spandhana Gonuguntla
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Kang Wen Lim
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Dicky Pranantyo
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Wai Pong Yong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Wei Jian Tyler Yam
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Zhida Low
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Wee Joon Teo
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Hao Ping Nien
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Qiao Wen Loh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Siowling Soh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
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30
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Boriachek K, Umer M, Islam MN, Gopalan V, Lam AK, Nguyen NT, Shiddiky MJA. An amplification-free electrochemical detection of exosomal miRNA-21 in serum samples. Analyst 2019; 143:1662-1669. [PMID: 29512659 DOI: 10.1039/c7an01843f] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Recent evidence suggests that small non-coding RNAs such as microRNA (miRNA) encapsulated in exosomes represent an important mechanism of communication between the cells. Exosomal miRNAs play an important role in carcinogenesis via enhancing the cell to cell communication and targeting the cell growth molecular pathways which in turn facilitate metastasis in cancers. Despite progressive advances, the current methods for the exosomal miRNA detection mostly rely on labor-intensive sequencing approaches which are often prone to amplification bias and require costly and bulky equipment. Herein, we report an electrochemical approach for the detection of cancer-derived exosomal miRNAs in human serum samples by selectively isolating the target miRNA using magnetic beads pre-functionalized with capture probes and then directly adsorbing the targets onto a gold electrode surface. The level of adsorbed miRNA is detected electrochemically in the presence of an [Fe(CN)6]4-/3- redox system. This method enabled an excellent detection sensitivity of 1.0 pM with a relative standard deviation (%RSD) of <5.5% in cancer cells and serum samples (n = 8) collected from patients with colorectal adenocarcinoma (CRC). We believe that our approach could be useful in clinical settings for the quantification of exosomal miRNA in cancer patients.
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Affiliation(s)
- Kseniia Boriachek
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia.
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31
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Abstract
Nucleic acid analysis plays an important role in diagnosing diseases as well as understanding biology. Despite advances in technology, there is still a need to develop a rapid and simple method to detect specific nucleic acids, especially in remote locations and low-resource cases. Here, we proposed a proximity proteolysis reaction in which the reaction between protease and zymogen is enhanced in the presence of a target molecule. The pair of proteins was site-specifically modified with oligonucleotides, and the conjugates were used to develop a method of detecting nucleic acids. Target DNA and RNA could be detected in less than 1 h at sub-nanomolar concentrations based on an absorbance signal. The assay method was resistant to interference by biological matrixes, and its sensitivity could be improved when combined with an isothermal nucleic acid amplification method. The results demonstrated the feasibility of this proximity proteolysis reaction as a new platform technology for detecting specific nucleic acid sequences.
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Affiliation(s)
- Hyeon Ji Park
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon 16499, Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon 16499, Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon 16499, Korea
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32
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Rani D, Pachauri V, Madaboosi N, Jolly P, Vu XT, Estrela P, Chu V, Conde JP, Ingebrandt S. Top-Down Fabricated Silicon Nanowire Arrays for Field-Effect Detection of Prostate-Specific Antigen. ACS OMEGA 2018; 3:8471-8482. [PMID: 31458975 PMCID: PMC6644640 DOI: 10.1021/acsomega.8b00990] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/18/2018] [Indexed: 05/16/2023]
Abstract
Highly sensitive electrical detection of biomarkers for the early stage screening of cancer is desired for future, ultrafast diagnostic platforms. In the case of prostate cancer (PCa), the prostate-specific antigen (PSA) is of prime interest and its detection in combination with other PCa-relevant biomarkers in a multiplex approach is advised. Toward this goal, we demonstrate the label-free, potentiometric detection of PSA with silicon nanowire ion-sensitive field-effect transistor (Si NW-ISFET) arrays. To realize the field-effect detection, we utilized the DNA aptamer-receptors specific for PSA, which were covalently and site-specifically immobilized on Si NW-ISFETs. The platform was used for quantitative detection of PSA and the change in threshold voltage of the Si NW-ISEFTs was correlated with the concentration of PSA. Concentration-dependent measurements were done in a wide range of 1 pg/mL to 1 μg/mL, which covers the clinical range of interest. To confirm the PSA-DNA aptamer binding on the Si NW surfaces, a sandwich-immunoassay based on chemiluminescence was implemented. The electrical approach using the Si NW-ISFET platform shows a lower limit of detection and a wide dynamic range of the assay. In future, our platform should be utilized to detect multiple biomarkers in one assay to obtain more reliable information about cancer-related diseases.
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Affiliation(s)
- Dipti Rani
- Department
of Informatics and Microsystem Technology, University of Applied Sciences Kaiserslautern, Amerikastrasse 1, 66482 Zweibrücken, Germany
| | - Vivek Pachauri
- Department
of Informatics and Microsystem Technology, University of Applied Sciences Kaiserslautern, Amerikastrasse 1, 66482 Zweibrücken, Germany
| | - Narayanan Madaboosi
- INESC
Microsistemas e Nanotecnologias, Rua Alves Redol, 91000-029 Lisbon, Portugal
| | - Pawan Jolly
- Department
of Electronic and Electrical Engineering, University of Bath, BA2 7AY Bath, United Kingdom
| | - Xuan-Thang Vu
- Department
of Informatics and Microsystem Technology, University of Applied Sciences Kaiserslautern, Amerikastrasse 1, 66482 Zweibrücken, Germany
- Institute
of Physics I, RWTH Aachen University, Sommerfeldstr. 14, 52074 Aachen, Germany
| | - Pedro Estrela
- Department
of Electronic and Electrical Engineering, University of Bath, BA2 7AY Bath, United Kingdom
| | - Virginia Chu
- INESC
Microsistemas e Nanotecnologias, Rua Alves Redol, 91000-029 Lisbon, Portugal
| | - João Pedro Conde
- INESC
Microsistemas e Nanotecnologias, Rua Alves Redol, 91000-029 Lisbon, Portugal
| | - Sven Ingebrandt
- Department
of Informatics and Microsystem Technology, University of Applied Sciences Kaiserslautern, Amerikastrasse 1, 66482 Zweibrücken, Germany
- E-mail:
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33
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Li JH, Sun SS, Fu CJ, Zhang AQ, Wang C, Xu R, Xie SY, Wang PY. Diagnostic and prognostic value of microRNA-628 for cancers. J Cancer 2018; 9:1623-1634. [PMID: 29760801 PMCID: PMC5950592 DOI: 10.7150/jca.24193] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/24/2018] [Indexed: 12/21/2022] Open
Abstract
Background: Many studies manifested miRNA-628 (miR-628) was deregulated in various cancers, indicating that miR-628 might serve as a novel biomarker of cancer diagnosis and prognosis, but it's role was still uncertain. This study aimed to evaluate the value of miR-628 in various cancers for diagnosis and prognosis, as well as its predictive power in combination biomarkers. Materials and Methods: A literature search was performed using Medline (via PubMed), Embase, Web of Science databases, and Ovid platform up to November 2017. Meta-analysis was performed to provide summative outcomes. Quality assessment of each included study was performed. Results: Twelve articles with 20 studies were included in our meta-analysis, including 8 articles with 15 studies for diagnostic meta-analysis and 4 articles with 5 studies for prognostic meta-analysis. For the diagnostic meta-analysis of miR-628 alone, the overall pooled results for sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and the area under the summary receiver operating characteristic (SROC) curve (AUC) were 0.81 (95% CI: 0.62-0.91), 0.72 (95% CI: 0.48-0.88), 2.90 (95% CI: 1.50-5.40), 0.27 (95% CI: 0.14-0.50), 11.0 (95% CI: 4.00-25.00), and 0.84 (95% CI: 0.80-0.87), respectively. For the diagnostic meta-analysis of miR-628-related combination biomarkers, the above six parameters were 0.89 (95% CI: 0.84-0.92), 0.93 (95% CI: 0.82-0.97), 12.30 (95% CI: 4.70-32.50), 0.12 (95% CI: 0.08-0.19), and 100.00 (95% CI: 28.00-354.00), 0.93 (95% CI: 0.90-0.95), respectively. For the prognostic meta-analysis, patients with lower miR-628 had significant shorter overall survival than high expression of miR-628 (HR = 1.553, 95% CI: 1.041-2.318, z = 2.16, P = 0.031). Conclusions: This study confirms that miR-628 may be a promising biomarker for cancer diagnosis and prognosis. Expertly, microRNAs combination biomarkers could be a new alternative for clinical application.
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Affiliation(s)
- Jing-Hua Li
- Department of Epidemiology, Binzhou Medical University, YanTai, ShanDong, 264003, P.R.China
| | - Shan-Shan Sun
- Department of Epidemiology, Binzhou Medical University, YanTai, ShanDong, 264003, P.R.China
| | - Chang-Jin Fu
- Department of Epidemiology, Binzhou Medical University, YanTai, ShanDong, 264003, P.R.China
| | - An-Qi Zhang
- Department of Epidemiology, Binzhou Medical University, YanTai, ShanDong, 264003, P.R.China
| | - Chen Wang
- Department of Epidemiology, Binzhou Medical University, YanTai, ShanDong, 264003, P.R.China
| | - Rong Xu
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, YanTai, ShanDong, 264003, P.R.China
| | - Shu-Yang Xie
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, YanTai, ShanDong, 264003, P.R.China
| | - Ping-Yu Wang
- Department of Epidemiology, Binzhou Medical University, YanTai, ShanDong, 264003, P.R.China.,Department of Biochemistry and Molecular Biology, Binzhou Medical University, YanTai, ShanDong, 264003, P.R.China
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34
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Abstract
Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.
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Affiliation(s)
- Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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35
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Filella X, Foj L. Novel Biomarkers for Prostate Cancer Detection and Prognosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1095:15-39. [PMID: 30229547 DOI: 10.1007/978-3-319-95693-0_2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Prostate cancer (PCa) remains as one of the most controversial issues in health care because of the dilemmas related to screening using Prostate Specific Antigen (PSA). A high number of false positive biopsies and an elevated rate of overdiagnosis are the main problems associated with PSA. New PCa biomarkers have been recently proposed to increase the predictive value of PSA. The published results showed that PCA3 score, Prostate Health Index and 4Kscore can reduce the number of unnecessary biopsies, outperforming better than PSA and the percentage of free PSA. Furthermore, 4Kscore provides with high accuracy an individual risk for high-grade PCa. High values of PHI are also associated with tumor aggressiveness. In contrast, the relationship of PCA3 score with aggressiveness remains controversial, with studies showing opposite conclusions. Finally, the development of molecular biology has opened the study of genes, among them TMPRSS2:ERG fusion gene and miRNAs, in PCa detection and prognosis.
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Affiliation(s)
- Xavier Filella
- Department of Biochemistry and Molecular Genetics (CDB), Hospital Clínic, IDIBAPS, Barcelona, Catalonia, Spain.
| | - Laura Foj
- Department of Biochemistry and Molecular Genetics (CDB), Hospital Clínic, IDIBAPS, Barcelona, Catalonia, Spain
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36
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Kangkamano T, Numnuam A, Limbut W, Kanatharana P, Vilaivan T, Thavarungkul P. Pyrrolidinyl PNA polypyrrole/silver nanofoam electrode as a novel label-free electrochemical miRNA-21 biosensor. Biosens Bioelectron 2017; 102:217-225. [PMID: 29149687 DOI: 10.1016/j.bios.2017.11.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/22/2017] [Accepted: 11/05/2017] [Indexed: 12/20/2022]
Abstract
A label-free electrochemical miRNA biosensor was developed based on a pyrrolidinyl peptide nucleic acid (acpcPNA)/polypyrrole (PPy)/silver nanofoam (AgNF) modified electrode. The AgNF was electrodeposited as redox indicator on a gold electrode, which was then functionalized with an electropolymerized layer of PPy, a conducting polymer, to immobilize the PNA probes. The fabrication process was investigated by electrochemical impedance spectroscopy. The biosensor was used to detect miRNA-21, a biomarker abnormally expressed in most cancers. The signal was monitored by the change in current of the AgNF redox reaction before and after hybridization using cyclic voltammetry. Two PNA probe lengths were investigated and the longer probe exhibited a better performance. Nucleotide overhangs on the electrode side affected the signal more than overhangs on the solution side due to the greater insulation of the sensing surface. Under optimal conditions, the electrochemical signal was proportional to miRNA-21 concentrations between 0.20fM and 1.0nM, with a very low detection limit of 0.20fM. The biosensor showed a high specificity which could discriminate between complementary, single-, doubled-base mismatched, and non-complementary targets. Three out of the seven tested plasma samples provided detectable concentrations (63 ± 4, 111 ± 4 and 164 ± 7fM). The sensor also showed good recoveries (81-119%). The results indicated the possibilities of this biosensor for analysis without RNA extraction and/or amplification, making the sensor potentially useful for both the prognosis and diagnosis of cancer in clinical application.
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Affiliation(s)
- Tawatchai Kangkamano
- Trace Analysis and Biosensor Research Center, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Department of Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Apon Numnuam
- Trace Analysis and Biosensor Research Center, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Department of Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Warakorn Limbut
- Trace Analysis and Biosensor Research Center, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Department of Applied Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Proespichaya Kanatharana
- Trace Analysis and Biosensor Research Center, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Department of Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panote Thavarungkul
- Trace Analysis and Biosensor Research Center, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Department of Physics, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand.
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37
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Ge L, Wang W, Li F. Electro-Grafted Electrode with Graphene-Oxide-Like DNA Affinity for Ratiometric Homogeneous Electrochemical Biosensing of MicroRNA. Anal Chem 2017; 89:11560-11567. [PMID: 28994278 DOI: 10.1021/acs.analchem.7b02896] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This work demonstrated for the first time a simple and rapid approach to endow the electrode with the excellent discrimination ability over single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) through the robust electrochemical grafting of in situ generated 1-naphthalenesulfonate (NS-) diazonium salt onto the surface of indium tin oxide (ITO) electrode. On the basis of understanding the influence of sequence and length on the binding affinity of ssDNA and dsDNA toward NS- grafted ITO (NS--ITO) electrode, these interesting findings were successfully employed to rationally develop a ratiometric homogeneous electrochemical biosensing platform for microRNA based on the affinity-mediated signal transduction. The achievement of ultrasensitive detection of microRNA lies in a compatibly designed T7 exonuclease-assisted isothermal amplification strategy, in which the presence of target microRNA initiated the continual and opposite affinity inversion of two rationally engineered electrochemical signal reporters, methylene blue (MB) labeled hairpin reporter and ferrocene (Fc) labeled dsDNA reporter, toward NS--ITO electrode, thereby providing the ratiometric transduction and amplification of the homogeneous electrochemical output signal. By measuring the distinct variation in the peak current intensity ratios of Fc and MB tags, this ratiometric homogeneous electrochemical microRNA biosensing platform showed a detection limit of 25 aM, which is much lower than that of the reported homogeneous electrochemical biosensors. Therefore, we envision that the proposed approach will find useful applications in disease molecular diagnoses and biomedicine.
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Affiliation(s)
- Lei Ge
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University , Qingdao, Shandong 266109, People's Republic of China
| | - Wenxiao Wang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University , Qingdao, Shandong 266109, People's Republic of China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University , Qingdao, Shandong 266109, People's Republic of China
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Kalogianni DP, Kalligosfyri PM, Kyriakou IK, Christopoulos TK. Advances in microRNA analysis. Anal Bioanal Chem 2017; 410:695-713. [DOI: 10.1007/s00216-017-0632-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 08/28/2017] [Accepted: 09/11/2017] [Indexed: 12/14/2022]
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39
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Affiliation(s)
- Haim H Bau
- a Department of Mechanical Engineering and Applied Mechanics , University of Pennsylvania , Philadelphia , PA , USA
| | - Changchun Liu
- a Department of Mechanical Engineering and Applied Mechanics , University of Pennsylvania , Philadelphia , PA , USA
| | - Michael Mauk
- a Department of Mechanical Engineering and Applied Mechanics , University of Pennsylvania , Philadelphia , PA , USA
| | - Jinzhao Song
- a Department of Mechanical Engineering and Applied Mechanics , University of Pennsylvania , Philadelphia , PA , USA
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40
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Abstract
Nucleic acid directed bioorthogonal reactions offer the fascinating opportunity to unveil and redirect a plethora of intracellular mechanisms. Nano- to picomolar amounts of specific RNA molecules serve as templates and catalyze the selective formation of molecules that 1) exert biological effects, or 2) provide measurable signals for RNA detection. Turnover of reactants on the template is a valuable asset when concentrations of RNA templates are low. The idea is to use RNA-templated reactions to fully control the biodistribution of drugs and to push the detection limits of DNA or RNA analytes to extraordinary sensitivities. Herein we review recent and instructive examples of conditional synthesis or release of compounds for in cellulo protein interference and intracellular nucleic acid imaging.
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Affiliation(s)
- Margherita Di Pisa
- Department of ChemistryHumboldt University BerlinBrook-Taylor Strasse 212489BerlinGermany
| | - Oliver Seitz
- Department of ChemistryHumboldt University BerlinBrook-Taylor Strasse 212489BerlinGermany
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41
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Astakhova K, Golovin AV, Prokhorenko IA, Ustinov AV, Stepanova IA, Zatsepin TS, Korshun VA. Design of 2′-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.04.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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42
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Al Sulaiman D, Chang JYH, Ladame S. Subnanomolar Detection of Oligonucleotides through Templated Fluorogenic Reaction in Hydrogels: Controlling Diffusion to Improve Sensitivity. Angew Chem Int Ed Engl 2017; 56:5247-5251. [PMID: 28382640 PMCID: PMC5502887 DOI: 10.1002/anie.201701356] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/02/2017] [Indexed: 02/06/2023]
Abstract
Oligonucleotide-templated reactions are valuable tools for nucleic acid sensing both in vitro and in vivo. They are typically carried out under conditions that make any reaction in the absence of template highly unfavorable (most commonly by using a low concentration of reactants), which has a negative impact on the detection sensitivity. Herein, we report a novel platform for fluorogenic oligonucleotide-templated reactions between peptide nucleic acid probes embedded within permeable agarose and alginate hydrogels. We demonstrate that under conditions of restricted mobility (that is, limited diffusion), non-specific interactions between probes are prevented, thus leading to lower background signals. When applied to nucleic acid sensing, this accounts for a significant increase in sensitivity (that is, lower limit of detection). Optical nucleic acid sensors based on fluorogenic peptide nucleic acid probes embedded in permeable, physically crosslinked, alginate beads were also engineered and proved capable of detecting DNA concentrations as low as 100 pm.
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Affiliation(s)
- Dana Al Sulaiman
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Jason Y H Chang
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
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43
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Al Sulaiman D, Chang JYH, Ladame S. Subnanomolar Detection of Oligonucleotides through Templated Fluorogenic Reaction in Hydrogels: Controlling Diffusion to Improve Sensitivity. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dana Al Sulaiman
- Department of Bioengineering; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Jason Y. H. Chang
- Department of Bioengineering; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Sylvain Ladame
- Department of Bioengineering; Imperial College London; South Kensington Campus London SW7 2AZ UK
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44
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Liu Y, Wei M, Li Y, Liu A, Wei W, Zhang Y, Liu S. Application of Spectral Crosstalk Correction for Improving Multiplexed MicroRNA Detection Using a Single Excitation Wavelength. Anal Chem 2017; 89:3430-3436. [DOI: 10.1021/acs.analchem.6b04176] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yuanjian Liu
- Jiangsu
Engineering Laboratory of Smart Carbon-Rich Materials and Device,
Laboratory of Environmental Medicine Engineering, Ministry of Education,
School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Min Wei
- College
of Food Science and Technology, Henan University of Technology, Zhengzhou, 450001, China
| | - Ying Li
- Jiangsu
Engineering Laboratory of Smart Carbon-Rich Materials and Device,
Laboratory of Environmental Medicine Engineering, Ministry of Education,
School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Anran Liu
- Jiangsu
Engineering Laboratory of Smart Carbon-Rich Materials and Device,
Laboratory of Environmental Medicine Engineering, Ministry of Education,
School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Wei Wei
- Jiangsu
Engineering Laboratory of Smart Carbon-Rich Materials and Device,
Laboratory of Environmental Medicine Engineering, Ministry of Education,
School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Yuanjian Zhang
- Jiangsu
Engineering Laboratory of Smart Carbon-Rich Materials and Device,
Laboratory of Environmental Medicine Engineering, Ministry of Education,
School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Songqin Liu
- Jiangsu
Engineering Laboratory of Smart Carbon-Rich Materials and Device,
Laboratory of Environmental Medicine Engineering, Ministry of Education,
School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
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45
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Al Sulaiman D, Metcalf GAD, Ladame S. Engineering innovative solutions to screen for prostate cancer. CONVERGENT SCIENCE PHYSICAL ONCOLOGY 2017. [DOI: 10.1088/2057-1739/aa5ebe] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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