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Bai L, Zhang H, Zhou Y, Liang H, Chen S, Pang X, Michael GM, Zhang L, Chen L. Development of a surface plasmon resonance (SPR) assay for rapid detection of Aeromonas hydrophila. Anal Biochem 2023; 670:115151. [PMID: 37028781 DOI: 10.1016/j.ab.2023.115151] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/04/2023] [Accepted: 04/03/2023] [Indexed: 04/09/2023]
Abstract
Aquaculture plays an increasingly important if not critical role in the current and future world food supply. Aeromonas hydrophila, a heterotrophic, Gram-negative, bacterium found in fresh or brackish water in warm climates poses a serious threat to the aquaculture industry in many areas, causing significant economic losses. Rapid, portable detection methods of A. hydrophila are needed for its effective control and mitigation. We have developed a surface plasmon resonance (SPR) technique to detect PCR (polymerase chain reaction) products that can replace agarose gel electrophoresis, or otherwise provide an alternative to costlier and more complicated real-time, fluorescence-based detection. The SPR method provides sensitivity comparable to gel electrophoresis, while reducing labor, cross-contamination, and test time, and employs simpler instrumentation with lower cost than real-time PCR.
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Affiliation(s)
- Linyi Bai
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, 250000, PR China
| | - Hao Zhang
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, PR China; State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, 300072, PR China
| | - Yuan Zhou
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, 250000, PR China
| | - Hongkun Liang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, 250000, PR China
| | - Shujun Chen
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, 250000, PR China
| | - Xuehui Pang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250000, PR China
| | - G Mauk Michael
- Department of Engineering Technology, Division of Engineering Management and Technology, College of Engineering, Drexel University, One Drexel Plaza, 3001 Market Street, Philadelphia, PA, 19104, USA
| | - Lulu Zhang
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, PR China.
| | - Lei Chen
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, 250000, PR China.
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2
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Label-Free Homogeneous microRNA Detection in Cell Culture Medium Based on Graphene Oxide and Specific Fluorescence Quenching. NANOMATERIALS 2021; 11:nano11020368. [PMID: 33540562 PMCID: PMC7912907 DOI: 10.3390/nano11020368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/19/2021] [Accepted: 01/28/2021] [Indexed: 02/07/2023]
Abstract
Label-free homogeneous optical detection of low concentration of oligonucleotides using graphene oxide in complex solutions containing proteins remains difficult. We used a colloidal graphene oxide (GO) as a fluorescent probe quencher to detect microRNA-21 spiked-in cell culture medium, overcoming previously reported problematic aspects of protein interference with graphene oxide. We used a "turn off" assay for specific quenching-based detection of oligo DNA-microRNA hybridization in solution. A fluorescein conjugated 30-mer single-stranded DNA (ssDNA) probe was combined with a complementary synthetic microRNA (18 nucleotides) target. The probe-target hybridization was detected by specific quenching due to photoinduced electron transfer (PET). On the next step, GO captures and quenches the unhybridized probe by fluorescence resonance energy transfer (FRET) in the presence of cell culture medium supplemented with platelet lysate, 0.1% sodium dodecyl sulfate (SDS), 0.1% Triton X-100 and 50% formamide. This resulted in sensitive measurement of the specific probe-target complexes remaining in solution. The detection is linear in the range of 1 nM and 8 nM in a single 100 μL total volume assay sample containing 25% cell culture medium supplemented with platelet lysate. We highlight a general approach that may be adopted for microRNA target detection within complex physiological media.
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3
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Indumathi K, Abiram A, Praveena G. Effect of peptidic backbone on the nucleic acid dimeric strands. Mol Phys 2020. [DOI: 10.1080/00268976.2019.1584682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- K. Indumathi
- Department of Physics, PSGR Krishnammal College for Women, Coimbatore, India
| | - A. Abiram
- Department of Physics, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - G. Praveena
- Department of Physics, PSGR Krishnammal College for Women, Coimbatore, India
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Qi Y, Wang Y, Zhao C, Ma Y, Yang W. Highly Transparent Cyclic Olefin Copolymer Film with a Nanotextured Surface Prepared by One-Step Photografting for High-Density DNA Immobilization. ACS APPLIED MATERIALS & INTERFACES 2019; 11:28690-28698. [PMID: 31322850 DOI: 10.1021/acsami.9b09662] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Compared with conventional glass slides and two-dimensional (2D) planar microarrays, polymer-based support materials and three-dimensional (3D) surface structures have attracted increasing attention in the field of biochips because of their good processability in microfabrication and low cost in mass production, as well as their improved sensitivity and specificity for the detection of biomolecules. In the present study, UV-induced emulsion graft polymerization was carried out on a cyclic olefin copolymer (COC) surface to generate 3D nanotextures composed of loosely stacked nanoparticles with a diameter of approximately 50 nm. The introduction of a hierarchical nanostructure on a COC surface only resulted in a 5% decrease in its transparency at a wavelength of 550 nm but significantly increased the surface area, which markedly improved immobilization density and efficiency of an oligonucleotide probe compared with the functional group and polymer brush-modified substrates. The highest immobilization efficiency of the probes reached 93%, and a limit of detection of 75 pM could be obtained. The hybridization experiment demonstrated that the 3D gene chip exhibited excellent sensitivity for target DNA detection and single-nucleotide polymorphism discrimination. This one-step approach to the construction of nanotextured surfaces on the COC has promising applications in the fields of biochips and immunoassays.
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Bellassai N, D'Agata R, Jungbluth V, Spoto G. Surface Plasmon Resonance for Biomarker Detection: Advances in Non-invasive Cancer Diagnosis. Front Chem 2019; 7:570. [PMID: 31448267 PMCID: PMC6695566 DOI: 10.3389/fchem.2019.00570] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/26/2019] [Indexed: 12/24/2022] Open
Abstract
Biomarker-based cancer analysis has great potential to lead to a better understanding of disease at the molecular level and to improve early diagnosis and monitoring. Unlike conventional tissue biopsy, liquid biopsy allows the detection of a large variety of circulating biomarkers, such as microRNA (miRNA), exosomes, circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and proteins, in an easily accessible and minimally invasive way. In this review, we describe and evaluate the relevance and applicability of surface plasmon resonance (SPR) and localized SPR (LSPR)-based platforms for the detection of different classes of cancer biomarkers in liquid biopsy samples. Firstly, we critically discuss unsolved problems and issues in capturing and analyzing biomarkers. Secondly, we highlight current challenges which need to be resolved in applying SPR biosensors into clinical practice. Then, we mainly focus on applications of SPR-based platforms that process a patient sample aiming to detect and quantify biomarkers as a minimally invasive liquid biopsy tool for cancer patients appearing over the last 5 years. Finally, we describe the analytical performances of selected SPR biosensor assays and their significant advantages in terms of high sensitivity and specificity as well as accuracy and workflow simplicity.
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Affiliation(s)
- Noemi Bellassai
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy
| | - Roberta D'Agata
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy
| | - Vanessa Jungbluth
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy
| | - Giuseppe Spoto
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy
- Istituto Nazionale di Biostrutture e Biosistemi, Università degli Studi di Catania, Catania, Italy
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Duffy J, Padovani F, Brunetti G, Noy P, Certa U, Hegner M. Towards personalised rapid label free miRNA detection for cancer and liver injury diagnostics in cell lysates and blood based samples. NANOSCALE 2018; 10:12797-12804. [PMID: 29947396 DOI: 10.1039/c8nr03604g] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Advances in prevention, diagnosis and therapy are coupled to innovation and development of new medical tools, leading to improved patient prognosis. We developed an automatic biosensor platform that could provide a non-invasive, rapid and personalised diagnosis using nanomechanical cantilever sensors. miRNA are involved in gene expression and are extractable biomarkers for multiple diseases. We detected specific expression patterns of miRNA relevant to cancer and adverse drug effects directly in cell lysates or blood based samples using only a few microliters of sample within one hour. Specific miRNA hybridisation to the upper cantilever surface induces physical bending of the sensor which is detected by monitoring the position of a laser that reflects from the sensors surface. Internal reference sensors negate environmental and nonspecific effects. We showed that the sensitivity of label free cantilever nanomechanical sensing of miRNA surpasses that of surface plasmon resonance by more than three orders of magnitude. A cancer associated miRNA expression profile from cell lysates and one associated with hepatocytes derived from necrotic liver tissue in blood-based samples has been successfully detected. Our label free mechanical approach displays the capability to perform in relevant clinical samples while also obtaining comparable results to PCR based techniques. Without the need to individually extend, amplify or label each target allowing multitarget analysis from one sample.
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Affiliation(s)
- James Duffy
- Centre Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), School of Physics, Trinity College Dublin, Dublin 2, Ireland.
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Chen C, Hou X, Si J. Protein analysis by Mach-Zehnder interferometers with a hybrid plasmonic waveguide with nano-slots. OPTICS EXPRESS 2017; 25:31294-31308. [PMID: 29245806 DOI: 10.1364/oe.25.031294] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/17/2017] [Indexed: 06/07/2023]
Abstract
Optical biosensing devices for the affinity analysis of molecular binding events could offer significant advantages over current analytical methods. However, most of those excited with a single optical mode are "blind" to the conformational change of bound molecules. We succeeded in designing Mach-Zehnder interferometers (MZI) with a hybrid plasmonic (HP) waveguide with nano-slots. By addressing the structure with dual polarizations, the optogeometrical properties (density and thickness) of protein layers have been determined without ambiguity. Differences in the hybrid mode dispersion between the transverse electric (TE) and transverse magnetic (TM) modes separately allow the determination of the thickness and the density at all stages during the molecular interaction. Moreover, nano-slots can be equated with an effective optical capacitance resulting in strong field confinement and low propagation loss. A proof of concept is conducted by analyzing the conformational change of HepV, a recombinant fragment of collagen V, during complicated molecular interaction. Instead of wavelength interrogation, a cost-effective method with output intensity variation at particular wavelengths due to "resonance phenomena" was employed to monitor the biological event.
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D'Agata R, Giuffrida MC, Spoto G. Peptide Nucleic Acid-Based Biosensors for Cancer Diagnosis. Molecules 2017; 22:E1951. [PMID: 29137122 PMCID: PMC6150339 DOI: 10.3390/molecules22111951] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/06/2017] [Accepted: 11/09/2017] [Indexed: 12/18/2022] Open
Abstract
The monitoring of DNA and RNA biomarkers freely circulating in the blood constitutes the basis of innovative cancer detection methods based on liquid biopsy. Such methods are expected to provide new opportunities for a better understanding of cancer disease at the molecular level, thus contributing to improved patient outcomes. Advanced biosensors can advance possibilities for cancer-related nucleic acid biomarkers detection. In this context, peptide nucleic acids (PNAs) play an important role in the fabrication of highly sensitive biosensors. This review provides an overview of recently described PNA-based biosensors for cancer biomarker detection. One of the most striking features of the described detection approaches is represented by the possibility to detect target nucleic acids at the ultra-low concentration with the capability to identify single-base mutations.
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Affiliation(s)
- Roberta D'Agata
- Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125 Catania, Italy.
| | - Maria Chiara Giuffrida
- Consorzio Interuniversitario "Istituto Nazionale di Biostrutture e Biosistemi", c/o Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125 Catania, Italy.
| | - Giuseppe Spoto
- Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125 Catania, Italy.
- Consorzio Interuniversitario "Istituto Nazionale di Biostrutture e Biosistemi", c/o Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125 Catania, Italy.
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Huang CJ, Lin ZE, Yang YS, Chan HWH, Chen WY. Neutralized chimeric DNA probe for detection of single nucleotide polymorphism on surface plasmon resonance biosensor. Biosens Bioelectron 2017; 99:170-175. [PMID: 28755610 DOI: 10.1016/j.bios.2017.07.052] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 12/27/2022]
Abstract
An implementation of neutralized chimeric DNA oligomer as a probe for sensitive detection of single nucleotide polymorphisms (SNPs) on a surface plasmon resonance imaging sensor is investigated. The chimeric DNA oligomer was synthesized in a conventional DNA synthesizer, containing neutral nucleotides with a methylated phosphate group. The secondary structures and melting points of the chimeric DNA fragment and its complexes with perfect-matched and single-mismatched complementary DNA molecules were examined by using circular dichroism and UV-vis spectroscopy in comparison with the native probe DNA counterpart. The results indicate that the chimeric DNA complexes can form a B-form structure and exhibit high thermostability. Moreover, the hybridization and discrimination efficiency of the chimeric probe DNA for the SNP genotyping were verified by using the SPRi sensor under different experimental conditions. The data reveal the effects of the ionic strength and operation temperature on the selectivity of the chimeric probe DNA for the SNP detection. The hybridization condition with a low ionic strength and high temperature allows the chimeric probe DNA distinguishing perfect-matched and single-mismatched target DNA molecules to the best extent, likely due to the reduced electrostatic repulsive force and presence of the additional methyl group on the backbone. Consequently, the direct and label-free detection with the SPR technique and neutralized chimeric probe DNA can be realized for the SNP genotyping by optimizing the operation condition and sequence design.
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Affiliation(s)
- Chun-Jen Huang
- Department of Biomedical Sciences and Engineering, National Central University, Jhong-Li 320, Taiwan; Department of Chemical and Materials Engineering, National Central University, Jhong-Li 320, Taiwan
| | - Zhong-En Lin
- Department of Chemical and Materials Engineering, National Central University, Jhong-Li 320, Taiwan
| | - Yuh-Shyong Yang
- Institute of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
| | | | - Wen-Yih Chen
- Department of Chemical and Materials Engineering, National Central University, Jhong-Li 320, Taiwan.
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10
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Zhao X, Lin CW. Rapid label-free visual detection of KRAS mutations using peptide nucleic acid and unmodified gold nanoparticles. RSC Adv 2017. [DOI: 10.1039/c7ra09088a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Colorectal cancer (CRC) is among the most commonly diagnosed cancers worldwide.
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Affiliation(s)
- Xihong Zhao
- Key Laboratory for Green Chemical Process of Ministry of Education
- Key Laboratory for Hubei Novel Reactor & Green Chemical Technology
- Research Center for Environmental Ecology and Engineering
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
| | - Chii-Wann Lin
- Institute of Biomedical Engineering
- National Taiwan University
- Taipei 10617
- Taiwan
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11
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Matsishin MJ, Ushenin IV, Rachkov AE, Solatkin AP. SPR Detection and Discrimination of the Oligonucleotides Related to the Normal and the Hybrid bcr-abl Genes by Two Stringency Control Strategies. NANOSCALE RESEARCH LETTERS 2016; 11:19. [PMID: 26759355 PMCID: PMC4710624 DOI: 10.1186/s11671-016-1226-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/05/2016] [Indexed: 05/29/2023]
Abstract
In this study, we applied two stringency control strategies for surface plasmon resonance (SPR) detection of DNA hybridization and discrimination of completely and partially complementary 24-mer sequences. These sequences are specific to the human normal bcr and the hybrid bcr-abl genes, protein products of which are responsible for some leukemia. SPR sensors based on resonance phenomena in nanoscale gold films are well suited for label-free, real-time investigations of the macromolecule interactions. Thermodynamic parameters obtained using the web server DINAMelt allowed supposing the possibility for realization (a) stringency control based on the ionic strength of the hybridization buffer and (b) stringency control based on the temperature elevation. The first one resulted in that the discrimination index of completely complementary and partially complementary oligonucleotides depending on the target concentration varied from 1.3 to 1.8 in 2 × SSC and from 2.0 to 2.9 in 0.5 × SSC. For implementation of the second stringency control strategy, SPR spectrometer measuring flow cell with built-in high-precision temperature control and regulation as well as corresponding software was created. It is shown that the duplexes formed by the immobilized probes mod-Ph and completely complementary oligonucleotides P1 remained without significant changes until ~50 °C, while the duplexes formed with partially complementary oligonucleotide Bcrex14 almost entirely disrupted at 40 °C. Thus, the absolutely effective thermodiscrimination of this pair of oligonucleotides was achieved in this temperature range (40-50 °C).
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Affiliation(s)
- M J Matsishin
- Institute of High Technologies, Taras Shevchenko Kyiv National University, 64 Volodymyrska Str., 01003, Kyiv, Ukraine.
- Laboratory of Biomolecular Electronics, Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., 03680, Kyiv, Ukraine.
| | - Iu V Ushenin
- V. Ye. Lashkaryov Institute of Semiconductor Physics, NAS of Ukraine, 41, Prospect Nauki, Kyiv, 03028, Ukraine
| | - A E Rachkov
- Laboratory of Biomolecular Electronics, Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., 03680, Kyiv, Ukraine
| | - A P Solatkin
- Institute of High Technologies, Taras Shevchenko Kyiv National University, 64 Volodymyrska Str., 01003, Kyiv, Ukraine
- Laboratory of Biomolecular Electronics, Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., 03680, Kyiv, Ukraine
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12
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Obaje EA, Cummins G, Schulze H, Mahmood S, Desmulliez MP, Bachmann TT. Carbon screen-printed electrodes on ceramic substrates for label-free molecular detection of antibiotic resistance. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/jin2.16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Eleojo A. Obaje
- Division of Infection and Pathway Medicine, Edinburgh Medical School, College of Medicine and Veterinary Medicine; The University of Edinburgh; Chancellor's Building, 49 Little France Crescent Edinburgh EH16 4SB Scotland UK
| | - Gerard Cummins
- School of Engineering and Physical Sciences, MIcroSystems Engineering Centre; Heriot-Watt University; Edinburgh EH14 4AS Scotland UK
| | - Holger Schulze
- Division of Infection and Pathway Medicine, Edinburgh Medical School, College of Medicine and Veterinary Medicine; The University of Edinburgh; Chancellor's Building, 49 Little France Crescent Edinburgh EH16 4SB Scotland UK
| | - Salman Mahmood
- School of Engineering and Physical Sciences, MIcroSystems Engineering Centre; Heriot-Watt University; Edinburgh EH14 4AS Scotland UK
| | - Marc P.Y. Desmulliez
- School of Engineering and Physical Sciences, MIcroSystems Engineering Centre; Heriot-Watt University; Edinburgh EH14 4AS Scotland UK
| | - Till T. Bachmann
- Division of Infection and Pathway Medicine, Edinburgh Medical School, College of Medicine and Veterinary Medicine; The University of Edinburgh; Chancellor's Building, 49 Little France Crescent Edinburgh EH16 4SB Scotland UK
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Thipmanee O, Numnuam A, Limbut W, Buranachai C, Kanatharana P, Vilaivan T, Hirankarn N, Thavarungkul P. Enhancing capacitive DNA biosensor performance by target overhang with application on screening test of HLA-B*58:01 and HLA-B*57:01 genes. Biosens Bioelectron 2016; 82:99-104. [PMID: 27054813 DOI: 10.1016/j.bios.2016.03.065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/12/2016] [Accepted: 03/24/2016] [Indexed: 10/22/2022]
Abstract
A highly sensitive label-free DNA biosensor based on PNA probes immobilized on a gold electrode was used to detect a hybridization event. The effect of a target DNA overhang on the hybridization efficiency was shown to enhance the detected signal and allowed detection at a very low concentration. The sensors performances were investigated with a complementary target that had the same length as the probe, and the signal was compared to the target DNAs with different lengths and overhangs. A longer target DNA overhang was found to provide a better response. When the overhang was on the electrode side the signal enhancement was greater than when the overhang was on the solution side due to the increased thickness of the sensing surface, hence produced a larger capacitance change. Using conformationally constrained acpcPNA probes, double stranded DNA was detected sensitively and specifically without any denaturing step. When two acpcPNA probes were applied for the screening test for the double stranded HLA-B*58:01 and HLA-B*57:01 genes that are highly similar, the method differentiated the two genes in all samples. Both purified and unpurified PCR products gave comparable results. This method would be potentially useful as a rapid screening test without the need for purification and denaturation of the PCR products.
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Affiliation(s)
- Orawan Thipmanee
- 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
| | - Chittanon Buranachai
- Trace Analysis and Biosensor Research Center, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Department of Physics, 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
| | - Nattiya Hirankarn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence in Immunology and Immune-Mediated Diseases, 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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14
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Kongpeth J, Jampasa S, Chaumpluk P, Chailapakul O, Vilaivan T. Immobilization-free electrochemical DNA detection with anthraquinone-labeled pyrrolidinyl peptide nucleic acid probe. Talanta 2015; 146:318-25. [PMID: 26695270 DOI: 10.1016/j.talanta.2015.08.059] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/25/2015] [Accepted: 08/26/2015] [Indexed: 01/04/2023]
Abstract
Electrochemical detection provides a simple, rapid, sensitive and inexpensive method for DNA detection. In traditional electrochemical DNA biosensors, the probe is immobilized onto the electrode. Hybridization with the DNA target causes a change in electrochemical signal, either from the intrinsic signal of the probe/target or through a label or a redox indicator. The major drawback of this approach is the requirement for probe immobilization in a controlled fashion. In this research, we take the advantage of different electrostatic properties between PNA and DNA to develop an immobilization-free approach for highly sequence-specific electrochemical DNA sensing on a screen-printed carbon electrode (SPCE) using a square-wave voltammetric (SWV) technique. Anthraquinone-labeled pyrrolidinyl peptide nucleic acid (AQ-PNA) was employed as a probe together with an SPCE that was modified with a positively-charged polymer (poly quaternized-(dimethylamino-ethyl)methacrylate, PQDMAEMA). The electrostatic attraction between the negatively-charged PNA-DNA duplex and the positively-charged modified SPCE attributes to the higher signal of PNA-DNA duplex than that of the electrostatically neutral PNA probe, resulting in a signal change. The calibration curve of this proposed method exhibited a linear range between 0.35 and 50 nM of DNA target with a limit of detection of 0.13 nM (3SD(blank)/Slope). The sub-nanomolar detection limit together with a small sample volume required (20 μL) allowed detection of <10 fmol (<1 ng) of DNA. With the high specificity of the pyrrolidinyl PNA probe used, excellent discrimination between complementary and various single-mismatched DNA targets was obtained. An application of this new platform for a sensitive and specific detection of isothermally-amplified shrimp's white spot syndrome virus (WSSV) DNA was successfully demonstrated.
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Affiliation(s)
- Jutatip Kongpeth
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Sakda Jampasa
- Program in Petrochemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Piyasak Chaumpluk
- Laboratory of Plant Transgenic Technology and Biosensor, Department of Botany, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Orawon Chailapakul
- Electrochemistry and Optical Spectroscopy Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
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Surface plasmon resonance: a versatile technique for biosensor applications. SENSORS 2015; 15:10481-510. [PMID: 25951336 PMCID: PMC4481982 DOI: 10.3390/s150510481] [Citation(s) in RCA: 587] [Impact Index Per Article: 65.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/24/2015] [Accepted: 04/28/2015] [Indexed: 02/07/2023]
Abstract
Surface plasmon resonance (SPR) is a label-free detection method which has emerged during the last two decades as a suitable and reliable platform in clinical analysis for biomolecular interactions. The technique makes it possible to measure interactions in real-time with high sensitivity and without the need of labels. This review article discusses a wide range of applications in optical-based sensors using either surface plasmon resonance (SPR) or surface plasmon resonance imaging (SPRI). Here we summarize the principles, provide examples, and illustrate the utility of SPR and SPRI through example applications from the biomedical, proteomics, genomics and bioengineering fields. In addition, SPR signal amplification strategies and surface functionalization are covered in the review.
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16
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Diware MS, Cho HM, Chegal W, Cho YJ, Jo JH, O SW, Paek SH, Yoon YH, Kim D. Solution immersed silicon (SIS)-based biosensors: a new approach in biosensing. Analyst 2015; 140:706-9. [DOI: 10.1039/c4an01584c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The non-reflecting condition for p-polarized waves is effectively utilized for biomolecular detection through the measurement of thickness change.
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Affiliation(s)
- M. S. Diware
- Center for Nanometrology
- Korea Research Institute of Standards and Science
- Daejeon 305-340
- Republic of Korea
| | - H. M. Cho
- Center for Nanometrology
- Korea Research Institute of Standards and Science
- Daejeon 305-340
- Republic of Korea
| | - W. Chegal
- Center for Nanometrology
- Korea Research Institute of Standards and Science
- Daejeon 305-340
- Republic of Korea
| | - Y. J. Cho
- Center for Nanometrology
- Korea Research Institute of Standards and Science
- Daejeon 305-340
- Republic of Korea
| | - J. H. Jo
- Department of Applied Optics and Electromagnetic
- Hannam University
- Daejeon 306-791
- Republic of Korea
| | - S. W. O
- Department of Bio-Microsystem Technology
- Korea University
- Seoul 136-701
- Republic of Korea
| | - S. H. Paek
- Department of Bio-Microsystem Technology
- Korea University
- Seoul 136-701
- Republic of Korea
| | - Y. H. Yoon
- Division of Mechanical System Engineering
- Chonbuk National University
- Jeonju 561-756
- Republic of Korea
| | - D. Kim
- Division of Mechanical System Engineering
- Chonbuk National University
- Jeonju 561-756
- Republic of Korea
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17
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Armitage BA. Analysis of PNA hybridization by surface plasmon resonance. Methods Mol Biol 2014; 1050:159-65. [PMID: 24297358 DOI: 10.1007/978-1-62703-553-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Reactions templated by a specific nucleic acid sequence have emerged as an attractive strategy for nucleic acid sensing. The Staudinger reaction using an azide-quenched fluorophore and a phosphine is particularly well suited by virtue of its bioorthogonality and biocompatibility. The reaction is promoted by a complementary nucleic acid that aligns the phosphine with the azide-quenched fluorophore. Cellular RNAs can catalyze the Staudinger reaction, and signal amplification can be achieved through multiple turnover of the template. Peptide nucleic acids (PNAs) provide a convenient platform for the preparation of specific probes as they combine desirable hybridization properties, robust synthesis, ease of fluorophore conjugation, and high biochemical stability. Herein, we describe protocols for fast fluorescent detection of miRNAs in human cells with PNA-based probes via reductive unquenching of bis-azidorhodamine by trialkylphosphine.
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Affiliation(s)
- Bruce A Armitage
- Department of Chemistry, Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, USA
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18
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Ermini ML, Mariani S, Scarano S, Minunni M. Bioanalytical approaches for the detection of single nucleotide polymorphisms by Surface Plasmon Resonance biosensors. Biosens Bioelectron 2014; 61:28-37. [PMID: 24841091 DOI: 10.1016/j.bios.2014.04.052] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 04/23/2014] [Indexed: 11/16/2022]
Abstract
The mapping of specific single nucleotide polymorphisms (SNPs) in patients' genome is a main goal in theranostics, aiming to the development of therapies based on personalized medicine. In this review, Surface Plasmon Resonance (SPR) and Surface Plasmon Resonance imaging (SPRi) biosensors applied to the recognition of SNPs were reviewed, since these technologies are emerging in clinical diagnosis as powerful tools thanks to their analytical features, mainly the real-time and label-free monitoring based on array format for parallel analysis. Since the literature is heterogeneous, a critical classification and a systemic comparison of the analytical performances of published methods were here reviewed on the basis of the analytical strategy and the assay design. In particular, the use of helping agents (i.e. proteins, nanoparticles (NPs), intercalating agents) or artificial DNAs, often coupled to SPR to achieve allele discrimination and/or enhanced sensitivity, were here revised and classified. Finally, the real suitability of SPR biosensors to clinical diagnostics for SNPs detection was addressed by comparing their features and performances with those of other biosensors based on other techniques (e.g. electrochemical biosensors).
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Affiliation(s)
- Maria Laura Ermini
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, via della Lastruccia 3-13, 50019 Sesto Fiorentino, FI, Italy
| | - Stefano Mariani
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, via della Lastruccia 3-13, 50019 Sesto Fiorentino, FI, Italy
| | - Simona Scarano
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, via della Lastruccia 3-13, 50019 Sesto Fiorentino, FI, Italy
| | - Maria Minunni
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, via della Lastruccia 3-13, 50019 Sesto Fiorentino, FI, Italy; Consorzio Sistemi a Grande Interfase, Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, FI, Italy.
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19
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Murphy NM, Pouton CW, Irving HR. Human leukocyte antigen haplotype phasing by allele-specific enrichment with peptide nucleic acid probes. Mol Genet Genomic Med 2014; 2:245-53. [PMID: 24936514 PMCID: PMC4049365 DOI: 10.1002/mgg3.65] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/10/2013] [Accepted: 12/17/2013] [Indexed: 12/22/2022] Open
Abstract
Targeted capture of large fragments of genomic DNA that enrich for human leukocyte antigen (HLA) system haplotypes has utility in haematopoietic stem cell transplantation. Current methods of HLA matching are based on inference or familial studies of inheritance; and each approach has its own inherent limitations. We have designed and tested a probe–target-extraction method for capturing specific HLA haplotypes by hybridization of peptide nucleic acid (PNA) probes to alleles of the HLA-DRB1 gene. Short target fragments contained in plasmids were initially used to optimize the method followed by testing samples of genomic DNA from human subjects with preselected HLA haplotypes and obtained approximately 10% enrichment for the specific haplotype. When performed with high-molecular-weight genomic DNA, 99.0% versus 84.0% alignment match was obtained for the specific haplotype probed. The allele-specific target enrichment that we obtained can facilitate the elucidation of haplotypes between the 65 kb separating the HLA-DRB1 and the HLA-DQA1 genes, potentially spanning a total distance of at least 130 kb. Allele-specific target enrichment with PNA probes is a straightforward technique that has the capability to improve the resolution of DNA and whole genome sequencing technologies by allowing haplotyping of enriched DNA and crucially, retaining the DNA methylation profile.
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Affiliation(s)
- Nicholas M Murphy
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus) Melbourne, Victoria, 3052, Australia ; Department of Preimplantation Genetic Diagnosis, Melbourne IVF 344 Victoria Parade, East Melbourne, Australia
| | - Colin W Pouton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus) Melbourne, Victoria, 3052, Australia
| | - Helen R Irving
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus) Melbourne, Victoria, 3052, Australia
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20
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Gambari R. Peptide nucleic acids: a review on recent patents and technology transfer. Expert Opin Ther Pat 2014; 24:267-94. [PMID: 24405414 DOI: 10.1517/13543776.2014.863874] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION DNA/RNA-based drugs are considered of major interest in molecular diagnosis and nonviral gene therapy. In this field, peptide nucleic acids (PNAs, DNA analogs in which the sugar-phosphate backbone is replaced by N-(2-aminoethyl)glycine units or similar building blocks) have been demonstrated to be excellent candidates as diagnostic reagents and biodrugs. AREAS COVERED Recent (2002 - 2013) patents based on studies on development of PNA analogs, delivery systems for PNAs, applications of PNAs in molecular diagnosis, and use of PNA for innovative therapeutic protocols. EXPERT OPINION PNAs are unique reagents in molecular diagnosis and have been proven to be very active and specific for alteration of gene expression, despite the fact that solubility and uptake by target cells can be limiting factors. Accordingly, patents on PNAs have taken in great consideration delivery strategies. PNAs have been proven stable and effective in vivo, despite the fact that possible long-term toxicity should be considered. For possible clinical applications, the use of PNA molecules in combination with drugs already employed in therapy has been suggested. Considering the patents available and the results on in vivo testing on animal models, we expect in the near future relevant PNA-based clinical trials.
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Affiliation(s)
- Roberto Gambari
- University of Ferrara, Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section , Via Fossato di Mortara n.74, 44100 Ferrara , Italy +39 532 974443 ; +39 532 974500 ;
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21
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Rachkov A, Patskovsky S, Soldatkin A, Meunier M. Discrimination of single base mismatched oligonucleotides related to the rpoB gene of Mycobacterium tuberculosis using a surface plasmon resonance biosensor. Biotechnol Appl Biochem 2013; 60:453-8. [PMID: 23654350 DOI: 10.1002/bab.1101] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 01/14/2013] [Indexed: 01/27/2023]
Abstract
Single base mismatched oligonucleotides related to the rpoB gene of Mycobacterium tuberculosis, the mutations of which cause drug resistance of the infectious agent, were detected and discriminated using a surface plasmon resonance biosensor system. Thiol-modified oligonucleotides of the selected sequence (the probe) and 1-mercapto-6-hexanol were immobilized on a gold sensor surface. Hybridization between immobilized probe P2 and perfectly matched target T2 as well as a single base mismatched target TN was investigated in buffer solutions of various stringencies. Discrimination of perfectly matched and single base mismatched targets is achieved due to a difference in the level of their hybridization with the immobilized probe depending on stringency of the buffer solution. In 0.5×SSC buffer solution (7.5 mM sodium citrate, pH 7, containing 75 mM NaCl), sensor response at T2 injection into the measuring sensor cell was 16 times that at TN injection. The experimental results on surface hybridization between the studied oligonucleotides demonstrated a good correlation with theoretical calculations of thermodynamic parameters of these interactions in the solution. The described approach could be proposed as a basis for creating a biosensor for real-time label-free diagnostics of drug-resistant tuberculosis.
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Affiliation(s)
- A Rachkov
- Laser Processing and Plasmonics Laboratory, École Polytechnique de Montréal, Montréal, Canada
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22
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Wang Q, Chen L, Long Y, Tian H, Wu J. Molecular beacons of xeno-nucleic acid for detecting nucleic acid. Theranostics 2013; 3:395-408. [PMID: 23781286 PMCID: PMC3677410 DOI: 10.7150/thno.5935] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/10/2013] [Indexed: 12/24/2022] Open
Abstract
Molecular beacons (MBs) of DNA and RNA have aroused increasing interest because they allow a continuous readout, excellent spatial and temporal resolution to observe in real time. This kind of dual-labeled oligonucleotide probes can differentiate between bound and unbound DNA/RNA in homogenous hybridization with a high signal-to-background ratio in living cells. This review briefly summarizes the different unnatural sugar backbones of oligonucleotides combined with fluorophores that have been employed to sense DNA/RNA. With different probes, we epitomize the fundamental understanding of driving forces and these recognition processes. Moreover, we will introduce a few novel and attractive emerging applications and discuss their advantages and disadvantages. We also highlight several perspective probes in the application of cancer therapeutics.
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23
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Šípová H, Homola J. Surface plasmon resonance sensing of nucleic acids: a review. Anal Chim Acta 2013; 773:9-23. [PMID: 23561902 DOI: 10.1016/j.aca.2012.12.040] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 12/19/2012] [Accepted: 12/21/2012] [Indexed: 12/12/2022]
Abstract
Biosensors based on surface plasmon resonance (SPR) have become a central tool for the investigation and quantification of biomolecules and their interactions. Nucleic acids (NAs) play a vital role in numerous biological processes and therefore have been one of the major groups of biomolecules targeted by the SPR biosensors. This paper discusses the advances of NA SPR biosensor technology and reviews its applications both in the research of molecular interactions involving NAs (NA-NA, NA-protein, NA-small molecule), as well as for the field of bioanalytics in the areas of food safety, medical diagnosis and environmental monitoring.
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Affiliation(s)
- Hana Šípová
- Institute of Photonics and Electronics, Academy of Sciences of the Czech Republic, Chaberská 57, Prague, Czech Republic
| | - Jiří Homola
- Institute of Photonics and Electronics, Academy of Sciences of the Czech Republic, Chaberská 57, Prague, Czech Republic.
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24
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Josephs EA, Ye T. Electric-field dependent conformations of single DNA molecules on a model biosensor surface. NANO LETTERS 2012; 12:5255-5261. [PMID: 22963660 DOI: 10.1021/nl3024356] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Despite the variety of nucleic acid sensors developed, we still do not have definite answers to some questions that are important to the molecular binding and, ultimately, the sensitivity and reliability of the sensors. How do the DNA probes distribute on the surface at the nanoscale? As the functionalized surfaces are highly heterogeneous, how are the conformations affected when the probe molecules interact with defects? How do DNA molecules respond to electric fields on the surface, which are applied in a variety of detection methods? With in situ electrochemical atomic force microscopy and careful tailoring of nanoscale surface interactions, we are able to observe the nanoscale conformations of individual DNA molecules on a model biosensor surface: thiolated DNA on a gold surface passivated with a hydroxyl-terminated alkanethiol self-assembled monolayer. We find that under applied electric fields, the conformations are highly sensitive to the choice of the alkanethiol molecule. Depending on the monolayer and the nature of the defects, the DNA molecules may either adopt a highly linear or a highly curved conformation. These unusual structures are difficult to observe through existing "ensemble" characterizations of nucleic acid sensors. These findings provide a step toward correlating target-binding affinity, selectivity, and kinetics to the nanoscale chemical structure of and around the probe molecules in practical nucleic acid devices.
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Affiliation(s)
- Eric A Josephs
- School of Engineering, University of California, Merced, California 95343, USA
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25
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A microfluidic-based electrochemical biochip for label-free diffusion-restricted DNA hybridization analysis. Biosens Bioelectron 2012; 38:114-20. [DOI: 10.1016/j.bios.2012.05.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 04/20/2012] [Accepted: 05/08/2012] [Indexed: 11/22/2022]
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26
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Escorihuela J, Bañuls MJ, Puchades R, Maquieira Á. Development of Oligonucleotide Microarrays onto Si-Based Surfaces via Thioether Linkage Mediated by UV Irradiation. Bioconjug Chem 2012; 23:2121-8. [DOI: 10.1021/bc300333a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jorge Escorihuela
- Centro de Reconocimiento
Molecular y Desarrollo Tecnológico,
Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia,
Spain
| | - María-José Bañuls
- Centro de Reconocimiento
Molecular y Desarrollo Tecnológico,
Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia,
Spain
| | - Rosa Puchades
- Centro de Reconocimiento
Molecular y Desarrollo Tecnológico,
Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia,
Spain
| | - Ángel Maquieira
- Centro de Reconocimiento
Molecular y Desarrollo Tecnológico,
Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia,
Spain
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27
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Dettin M, Silvestri D, Danesin R, Cretaio E, Picariello G, Casarin E, Sonato A, Romanato F, Morpurgo M. Synthesis and chromatography-free purification of PNA-PEO conjugates for the functionalisation of gold sensors. Molecules 2012; 17:11026-45. [PMID: 22976467 PMCID: PMC6268724 DOI: 10.3390/molecules170911026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/30/2012] [Accepted: 08/31/2012] [Indexed: 01/06/2023] Open
Abstract
Peptide Nucleic Acids (PNAs) linked to high molecular weight (MW) poly(ethylene oxide) (PEO) derivatives could be useful conjugates for the direct functionalisation of gold surfaces dedicated to Surface Plasmon Resonance (SPR)-based DNA sensing. However their use is hampered by the difficulty to obtain them through a convenient and economical route. In this work we compared three synthetic strategies to obtain PNA-high MW PEO conjugates composed of (a) a 15-mer PNA sequence as the probe complementary to genomic DNA of Mycobacterium tuberculosis, (b) a PEO moiety (2 or 5 KDa MW) and (c) a terminal trityl-protected thiol necessary (after acidic deprotection) for grafting to gold surfaces. The 15-mer PNA was obtained by solid-phase synthesis. Its amino terminal group was later condensed to bi-functional PEO derivatives (2 and 5 KDa MW) carrying a Trt-cysteine at one end and a carboxyl group at the other end. The reaction was carried out either in solution, using HATU or PyOxim as coupling agents, or through the solid-phase approach, with 49.6%, 100% and 5.2% yield, respectively. A differential solvent extraction strategy for product purification without the need for chromatography is described. The ability of the 5 KDa PEO conjugate to function as a probe for complementary DNA detection was demonstrated using a Grating-Coupling Surface Plasmon Resonance (GC-SPR) system. The optimized PEO conjugation and purification protocols are economical and simple enough to be reproduced also within laboratories that are not highly equipped for chemical synthesis.
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Affiliation(s)
- Monica Dettin
- Department of Industrial Engineering, University of Padova, via Marzolo, 9, 35131 Padova, Italy; (M.D.); (R.D.)
| | - Davide Silvestri
- Department of Pharmaceutical Chemistry and Pharmacology, University of Padova, via Marzolo, 5, 35131 Padova, Italy; (D.S.); (E.C.)
| | - Roberta Danesin
- Department of Industrial Engineering, University of Padova, via Marzolo, 9, 35131 Padova, Italy; (M.D.); (R.D.)
| | - Erica Cretaio
- Inter-University Consortium of Veneto for Nanotechnology (CIVEN), via delle Industrie, 5, 30174 Venezia, Italy;
| | | | - Elisabetta Casarin
- Department of Pharmaceutical Chemistry and Pharmacology, University of Padova, via Marzolo, 5, 35131 Padova, Italy; (D.S.); (E.C.)
| | - Agnese Sonato
- Physics Department, University of Padova, via Marzolo, 8, 35131 Padova, Italy; (A.S.); (F.R.)
| | - Filippo Romanato
- Physics Department, University of Padova, via Marzolo, 8, 35131 Padova, Italy; (A.S.); (F.R.)
| | - Margherita Morpurgo
- Department of Pharmaceutical Chemistry and Pharmacology, University of Padova, via Marzolo, 5, 35131 Padova, Italy; (D.S.); (E.C.)
- Author to whom correspondence should be addressed; ; Tel.: +39-049-827-5330; Fax: +39-049-827-5366
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28
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Ermini ML, Mariani S, Scarano S, Campa D, Barale R, Minunni M. Single nucleotide polymorphism detection by optical DNA-based sensing coupled with whole genomic amplification. Anal Bioanal Chem 2012; 405:985-93. [PMID: 22955671 DOI: 10.1007/s00216-012-6345-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 08/01/2012] [Accepted: 08/08/2012] [Indexed: 12/11/2022]
Abstract
The work presented here deals with the optimization of a strategy for detection of single nucleotide polymorphisms based on surface plasmon resonance imaging. First, a sandwich-like assay was designed, and oligonucleotide sequences were computationally selected in order to study optimized conditions for the detection of the rs1045642 single nucleotide polymorphism in the gene ABCB1. Then the strategy was optimized on a surface plasmon resonance imaging biosensor using synthetic DNA sequences in order to evaluate the best conditions for the detection of a single mismatching base. Finally, the assay was tested on DNA extracted from human blood which was subsequently amplified using a whole genome amplification kit. The direct detection of the polymorphism was successfully achieved. The biochip was highly regenerable and reusable for up to 20 measurements. Furthermore, coupling these promising results with the multiarray assay, we can foresee applying this biosensor in clinical research extended to concurrent analysis of different polymorphisms.
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Affiliation(s)
- M L Ermini
- Dipartimento di Chimica, Università di Firenze, Sesto Fiorentino, Italy
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29
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Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development. Anal Bioanal Chem 2012; 402:3071-89. [PMID: 22297860 DOI: 10.1007/s00216-012-5742-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 01/12/2012] [Indexed: 01/06/2023]
Abstract
Nucleic acid biosensors have a growing number of applications in genetics and biomedicine. This contribution is a critical review of the current state of the art concerning the use of nucleic acid analogues, in particular peptide nucleic acids (PNA) and locked nucleic acids (LNA), for the development of high-performance affinity biosensors. Both PNA and LNA have outstanding affinity for natural nucleic acids, and the destabilizing effect of base mismatches in PNA- or LNA-containing heterodimers is much higher than in double-stranded DNA or RNA. Therefore, PNA- and LNA-based biosensors have unprecedented sensitivity and specificity, with special applicability in DNA genotyping. Herein, the most relevant PNA- and LNA-based biosensors are presented, and their advantages and their current limitations are discussed. Some of the reviewed technology, while promising, still needs to bridge the gap between experimental status and the harder reality of biotechnological or biomedical applications.
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30
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Ultrathin and smooth poly(methyl methacrylate) (PMMA) films for label-free biomolecule detection with total internal reflection ellipsometry (TIRE). Biosens Bioelectron 2012; 36:250-6. [DOI: 10.1016/j.bios.2012.04.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 04/17/2012] [Accepted: 04/17/2012] [Indexed: 02/07/2023]
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31
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Sahu B, Sacui I, Rapireddy S, Zanotti KJ, Bahal R, Armitage BA, Ly DH. Synthesis and characterization of conformationally preorganized, (R)-diethylene glycol-containing γ-peptide nucleic acids with superior hybridization properties and water solubility. J Org Chem 2011; 76:5614-27. [PMID: 21619025 PMCID: PMC3175361 DOI: 10.1021/jo200482d] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Developed in the early 1990s, peptide nucleic acid (PNA) has emerged as a promising class of nucleic acid mimic because of its strong binding affinity and sequence selectivity toward DNA and RNA and resistance to enzymatic degradation by proteases and nucleases; however, the main drawbacks, as compared to other classes of oligonucleotides, are water solubility and biocompatibility. Herein we show that installation of a relatively small, hydrophilic (R)-diethylene glycol ("miniPEG", R-MP) unit at the γ-backbone transforms a randomly folded PNA into a right-handed helix. Synthesis of optically pure (R-MP)γPNA monomers is described, which can be accomplished in a few simple steps from a commercially available and relatively cheap Boc-l-serine. Once synthesized, (R-MP)γPNA oligomers are preorganized into a right-handed helix, hybridize to DNA and RNA with greater affinity and sequence selectivity, and are more water soluble and less aggregating than the parental PNA oligomers. The results presented herein have important implications for the future design and application of PNA in biology, biotechnology, and medicine, as well as in other disciplines, including drug discovery and molecular engineering.
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Affiliation(s)
- Bichismita Sahu
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Iulia Sacui
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Srinivas Rapireddy
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Kimberly J. Zanotti
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Raman Bahal
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Bruce A. Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Danith H. Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
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32
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Mir M, Martínez-Rodríguez S, Castillo-Fernández O, Homs-Corbera A, Samitier J. Electrokinetic techniques applied to electrochemical DNA biosensors. Electrophoresis 2011; 32:811-21. [DOI: 10.1002/elps.201000487] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 11/05/2010] [Accepted: 11/07/2010] [Indexed: 11/10/2022]
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Kim JS, Cho JB, Park BG, Lee W, Lee KB, Oh MK. Size-controllable quartz nanostructure for signal enhancement of DNA chip. Biosens Bioelectron 2011; 26:2085-9. [DOI: 10.1016/j.bios.2010.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 09/05/2010] [Accepted: 09/06/2010] [Indexed: 11/27/2022]
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Huang C, Stakenborg T, Cheng Y, Colle F, Steylaerts T, Jans K, Van Dorpe P, Lagae L. Label-free genosensor based on immobilized DNA hairpins on gold surface. Biosens Bioelectron 2010; 26:3121-6. [PMID: 21208795 DOI: 10.1016/j.bios.2010.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 11/18/2010] [Accepted: 12/03/2010] [Indexed: 10/18/2022]
Abstract
In this report, we demonstrate a label-free genosensor based on DNA hairpins coupled to gold coated sensor surfaces. The hairpin probes were labeled with a thiolated moiety for immobilization at the 5' end and with a fluorophore for signal transduction at the 3' end. In the absence of the complement, the fluorophore is quenched by energy transfer to the gold surface. Addition of the target sequence leads to the hairpin unfolding, and releases the fluorescent signal. This built-in property, using a gold film as both the immobilizing substrate and quenching agent, has the advantage of simplicity in design and ease of further integration. Our results showed that lengths of both the stem and the loop structures have significant effects on the sensor performance. Hybridization kinetics was investigated for various probe/target lengths and concentrations. An optimized hairpin probe gave a fluorescent signal increase of 39 folds after hybridization, which is much higher than the earlier reported results. A limit of detection (LOD) down to 0.3 nM for the complementary target DNA detection has been achieved. The developed sensor was further successfully applied for the detection of single-base mismatch targets, as well as for the direct detection of PCR products.
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Kanjanawarut R, Su X. Colorimetric detection of DNA using unmodified metallic nanoparticles and peptide nucleic acid probes. Anal Chem 2010; 81:6122-9. [PMID: 20337394 DOI: 10.1021/ac900525k] [Citation(s) in RCA: 182] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have developed a colorimetric assay for DNA detection based on the aggregation of unmodified metallic nanoparticles. Charge neutral peptide nucleic acids (PNA) are used as a "coagulant" of citrate anion-coated particles and as hybridization probe. In the absence of a complementary target DNA, free PNA molecules in solution induce aggressive particle aggregation because of the removal of charge repulsion as a result of PNA coating on nanoparticles. When a complementary DNA is present and PNA-DNA complexes are formed, the particles remain stable because the negative charges of the DNA strands in the complexes adsorbed on the particle surface ensure sufficient charge repulsions. In this method, no probe immobilization is needed and PNA-DNA hybridization occurs in a homogeneous phase. The assay results are displayed as rapidly as the changes in color and/or in UV-vis adsorption spectra of the colloidal solutions. We have validated the assay principle using gold- and silver-nanoparticles (AuNPs and AgNPs), with the involvement of a shorter (13 mer) and a longer (22 mer) probe sequences. A specific DNA can be detected in the presence of at least 10 times of interference DNA, and the detection limit is at a DNA/PNA ratio of 0.05. When NaCl is added to accelerate the particle aggregation, the selectivity is further improved, and single-base-mismatch discrimination is achieved. A two-component assay using a mixture of AuNPs and AgNPs has also been constituted, aiming to improve the result accuracy by making use of the multiple aggregation signatures from the two types of particles. For single-base-mismatch discrimination, the AgNPs offer a higher sensitivity than AuNPs by showing more obvious spectra and color alternation, and the two-component assay offers three parameters in the UV-vis adsorption spectra.
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Affiliation(s)
- Roejarek Kanjanawarut
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602
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Ananthanawat C, Hoven VP, Vilaivan T, Su X. Surface plasmon resonance study of PNA interactions with double-stranded DNA. Biosens Bioelectron 2010; 26:1918-23. [PMID: 20580217 DOI: 10.1016/j.bios.2010.05.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 05/19/2010] [Accepted: 05/21/2010] [Indexed: 12/19/2022]
Abstract
Peptide nucleic acid (PNA) is a well known DNA analogue bearing a N-(2-aminoethyl)glycine backbone (aegPNA). This molecule is able to not only form a duplex with single stranded (ss) nucleic acids but also higher-order (i.e., three- and four-stranded) complexes with double-stranded (ds) DNA in a sequence specific manner. Here, the application of surface plasmon resonance (SPR) to study the binding of PNA to dsDNA is reported for the first time. SPR protocols were developed to verify the sequence rules and conditions for binding (pH and ionic strength) of homopyrimidine and homopurine aegPNAs to dsDNA, for which the solution phase behaviors are known, allowing a direct comparison. Then, using real-time SPR measurements, the hybridization efficiency, binding direction (antiparallel and parallel direction), sequence-dependent binding modes of the PNA to dsDNA (triplex formation and duplex invasion) and the binding kinetics associated with the binding mode were all ascertained. These SPR protocols were then further applied to study the dsDNA binding properties of a new conformationally rigid PNA bearing a D-prolyl-2-aminocyclopentanecarboxylic acid (ACPC) backbone (acpcPNA), which revealed that acpcPNA cannot form higher-order complexes with dsDNA through either triplex formation or duplex invasion. The SPR technique is thus shown to be a powerful technique for studying higher-order nucleic acid complexes. The binding behaviors of aegPNA obtained from the SPR analysis in the solid-liquid phase measurement correlate well with those in the literature derived from solution phase measurements.
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Affiliation(s)
- Cheeraporn Ananthanawat
- Program of Macromolecular Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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Su X, Kanjanawarut R. Control of metal nanoparticles aggregation and dispersion by PNA and PNA-DNA complexes, and its application for colorimetric DNA detection. ACS NANO 2009; 3:2751-9. [PMID: 19708641 DOI: 10.1021/nn9005768] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We have demonstrated that mixed-base PNA oligomers are effective coagulants of citrate ion-coated gold and silver nanoparticles (AuNPs and AgNPs), and PNA-induced particle aggregation can be disrupted by hybridization of PNA with a specific DNA. Using particles' aggregation/dispersion as a measure, we have investigated how PNA and PNA-DNA complexes bind to AuNPs and AgNPs and modulate particles' stability differently relative to their DNA counterparts. We have made the following original discoveries: (1) mix-base PNA oligomers can induce immediate particle aggregation in a concentration- and chain-length-dependent manner; (2) PNA oligomers have a higher affinity to AuNPs and AgNPs than its ssDNA counterpart; (3) PNA-DNA complexes, although having a stable double helix structure similar to dsDNA, can effectively protect the particles from salt induced aggregation, and the protection effect of different nucleic acids are in the order of PNA-DNA complex > ssDNA > dsDNA; (4) all the characteristics are identical for AuNPs and AgNPs; and (5) AgNPs is more sensitive in response to destabilization effect and is proven a more sensitive platform for colorimetric assays. The control of particle aggregation and dispersion by PNA and PNA-DNA complexes has been used to detect a specific DNA sequence with single-base-mismatch resolution. zeta potential measurements have been conducted to reveal how distinct backbone properties of PNA and PNA-DNA complexes relative to their DNA counterparts contribute to the distinct binding characteristics.
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Affiliation(s)
- Xiaodi Su
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602.
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Ananthanawat C, Vilaivan T, Mekboonsonglarp W, Hoven VP. Thiolated pyrrolidinyl peptide nucleic acids for the detection of DNA hybridization using surface plasmon resonance. Biosens Bioelectron 2009; 24:3544-9. [PMID: 19515551 DOI: 10.1016/j.bios.2009.05.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Revised: 04/23/2009] [Accepted: 05/11/2009] [Indexed: 11/25/2022]
Abstract
Thiolated pyrrolidinyl peptide nucleic acids (HS-PNAs) bearing d-prolyl-2-aminocyclopentanecarboxylic acid (ACPC) backbones with different lengths and types of thiol modifiers were synthesized and then characterized by MALDI-TOF mass spectrometry. These HS-PNAs were immobilized on gold-coated glass by self-assembled monolayer (SAM) formation via S atom linkage for the detection of DNA hybridization using surface plasmon resonance (SPR). The amount and the stability of the immobilized HS-PNAs, as well as the effects of spacer and blocking thiol on DNA hybridization efficiency, were determined. SPR results indicated that the hybridization efficiency was enhanced when the distance between the PNA portion and the thiol terminal was increased and/or when blocking thiol was used following the HS-PNA immobilization. The immobilized HS-PNA could discriminate between fully complementary DNA from one or two base mismatched DNA with a relatively high degree of mismatch discrimination (>45%) in PBS buffer at 25 degrees C. The lowest DNA concentration at which reliable discrimination between fully complementary and single mismatched DNA could still occur was at about 0.2 microM, which is equivalent to 10 pmol of DNA. This research demonstrates that using these novel thiolated PNAs in combination with the SPR technique offers a direct, rapid and non-label based method that could potentially be applied for the analysis of genomic or PCR-amplified DNA in the future.
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Affiliation(s)
- Cheeraporn Ananthanawat
- Program of Macromolecular Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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