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Lavecchia di Tocco F, Botti V, Cannistraro S, Bizzarri AR. Detection of miR-155 Using Peptide Nucleic Acid at Physiological-like Conditions by Surface Plasmon Resonance and Bio-Field Effect Transistor. BIOSENSORS 2024; 14:79. [PMID: 38391998 PMCID: PMC10887097 DOI: 10.3390/bios14020079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/21/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
MicroRNAs are small ribonucleotides that act as key gene regulators. Their altered expression is often associated with the onset and progression of several human diseases, including cancer. Given their potential use as biomarkers, there is a need to find detection methods for microRNAs suitable for use in clinical setting. Field-effect-transistor-based biosensors (bioFETs) appear to be valid tools to detect microRNAs, since they may reliably quantitate the specific binding between the immobilized probe and free target in solution through an easily detectable electrical signal. We have investigated the detection of human microRNA 155 (miR-155) using an innovative capturing probe constituted by a synthetic peptide nucleic acid (PNA), which has the advantage to form a duplex even at ionic strengths approaching the physiological conditions. With the aim to develop an optimized BioFET setup, the interaction kinetics between miR-155 and the chosen PNA was preliminarily investigated by using surface plasmon resonance (SPR). By exploiting both these results and our custom-made bioFET system, we were able to attain a low-cost, real-time, label-free and highly specific detection of miR-155 in the nano-molar range.
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Affiliation(s)
| | | | | | - Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Largo dell’Università, 01100 Viterbo, Italy; (F.L.d.T.); (V.B.); (S.C.)
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2
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Shen YZ, Guan J, Ma C, Shu Y, Xu Q, Hu XY. Competitive Displacement Triggering DBP Photoelectrochemical Aptasensor via Cetyltrimethylammonium Bromide Bridging Aptamer and Perovskite. Anal Chem 2022; 94:1742-1751. [PMID: 35026109 DOI: 10.1021/acs.analchem.1c04348] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Here, a label-free perovskite-based photoelectrochemical (PEC) aptasensor was rationally designed for the displacement assay of dibutyl phthalate (DBP), a well-known endocrine disruptor, with the aid of cetyltrimethylammonium bromide (CTAB). In this method, CTAB significantly enhanced the PEC response and humidity resistance of the CH3NH3PbI3 perovskite by forming a protecting layer and passivating the X- and A-sites vacancies of CH3NH3PbI3. In addition, CTAB facilitated the immobilization of an aptamer through van der Waals and hydrophobicity forces, as well as the electrostatic interactions between the phosphate group of the aptamer and the cationic group of CTAB. When exposed to DBP in the affinity solution, the DBP aptamer was released from the electrode because the affinity between DBP and its aptamer competes with the interaction of the aptamer and CTAB. The displacement of the aptamer from the perovskite surface relieves the block effect and thus enhances the photoelectric signal of perovskite. By virtue of the good photoelectrochemical characters of CH3NH3PbI3 and the specific recognition ability of aptamer, the linear range of the PEC sensor was 1.0 × 10-13 to 1.0 × 10-8 M and the detection and quantification limits were down to 2.5 × 10-14 and 8.2 × 10-14 M (S/N = 3), respectively. This work offers a novel strategy for designing aptasensors for the detection of various targets and exhibits the marvelous potential of organic-inorganic perovskite in the field of PEC analysis.
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Affiliation(s)
- Ying-Zhuo Shen
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Jie Guan
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Chen Ma
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Yun Shu
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Qin Xu
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Xiao-Ya Hu
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
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3
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Swenson CS, Lackey HH, Reece EJ, Harris JM, Heemstra JM, Peterson EM. Evaluating the effect of ionic strength on PNA:DNA duplex formation kinetics. RSC Chem Biol 2021; 2:1249-1256. [PMID: 34458838 PMCID: PMC8341200 DOI: 10.1039/d1cb00025j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/07/2021] [Indexed: 11/21/2022] Open
Abstract
Peptide nucleic acid (PNA) is a unique synthetic nucleic acid analog that has been adopted for use in many biological applications. These applications rely upon the robust Franklin-Watson-Crick base pairing provided by PNA, particularly at lower ionic strengths. However, our understanding of the relationship between the kinetics of PNA:DNA hybridization and ionic strength is incomplete. Here we measured the kinetics of association and dissociation of PNA with DNA across a range of ionic strengths and temperatures at single-molecule resolution using total internal reflection fluorescence imaging. Unlike DNA:DNA duplexes, PNA:DNA duplexes are more stable at lower ionic strength, and we demonstrate that this is due to a higher association rate. While the dissociation rate of PNA:DNA duplexes is largely insensitive to ionic strength, it is significantly lower than that of DNA:DNA duplexes having the same number and sequence of base pairing interactions. The temperature dependence of PNA:DNA kinetic rate constants indicate a significant enthalpy barrier to duplex dissociation, and to a lesser extent, duplex formation. This investigation into the kinetics of PNA:DNA hybridization provides a framework towards better understanding and design of PNA sequences for future applications.
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Affiliation(s)
- Colin S Swenson
- Department of Chemistry, Emory University Atlanta GA 30322 USA
| | - Hershel H Lackey
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| | - Eric J Reece
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| | - Joel M Harris
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| | | | - Eric M Peterson
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
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4
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Zhang X, Du P, Cui X, Chen G, Wang Y, Zhang Y, Abd El-Aty AM, Hacımüftüoğlu A, Wang J, He H, Jin M, Hammock B. A sensitive fluorometric bio-barcodes immunoassay for detection of triazophos residue in agricultural products and water samples by iterative cycles of DNA-RNA hybridization and dissociation of fluorophores by Ribonuclease H. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 717:137268. [PMID: 32084695 PMCID: PMC7938870 DOI: 10.1016/j.scitotenv.2020.137268] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 05/10/2023]
Abstract
Although the toxicity of triazophos is high and it has been pulled from the market in many countries; it is still widely used and frequently detected in agricultural products. While conventional analyses have been routinely used for the quantification and monitoring of triazophos residues, those for detecting low residual levels are deemed necessary. Therefore, we developed a novel and sensitive fluorometric signal amplification immunoassay employing bio-barcodes for the quantitative analysis of triazophos residues in foodstuffs and surface water. Herein, monoclonal antibodies (mAbs) attached to gold nanoparticles (AuNPs) were coated with DNA oligonucleotides (used as a signal generator), and a complementary fluorogenic RNA was used for signal amplification. The system generated detection signals through DNA-RNA hybridization and subsequent dissociation of fluorophores by Ribonuclease H (RNase H). It has to be noted that RNase H can only disintegrate the RNA in DNA-RNA duplex, but not cleave single or double-stranded DNA. Hence, with iterative cycles of DNA-RNA hybridization, sufficient strong signal was obtained for reliable detection of residues. Furthermore, this method enables quantitative detection of triazophos residues through fluorescence intensity measurements. The competitive immunoassay shows a wide linear range of 0.01-100 ng/mL with a limit of detection (LOD) of 0.0032 ng/mL. The assay substantially meets the demand for the low residue detection of triazophos residues in agricultural products and water samples. Accuracy (expressed as spiked recovery %) and coefficient of variation (CV) were ranged from 73.4% to 116% and 7.04% to 17.4%, respectively. The proposed bio-barcodes immunoassay has the advantages of being stable, reproducible, and reliable for residue detection. In sum, the present study provides a novel approach for detection of small molecules in various sample matrices.
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Affiliation(s)
- Xiuyuan Zhang
- College of Life Sciences, YanTai University, Yantai 264005, China; Key Laboratory of Agro-product Quality and Food Safety, Institute of Quality Standard &Testing Technology for Agro-Products, Chinses Academy of Agricultural Science, Beijing 100081, China
| | - Pengfei Du
- Key Laboratory of Agro-product Quality and Food Safety, Institute of Quality Standard &Testing Technology for Agro-Products, Chinses Academy of Agricultural Science, Beijing 100081, China
| | - Xueyan Cui
- Key Laboratory of Agro-product Quality and Food Safety, Institute of Quality Standard &Testing Technology for Agro-Products, Chinses Academy of Agricultural Science, Beijing 100081, China
| | - Ge Chen
- Key Laboratory of Agro-product Quality and Food Safety, Institute of Quality Standard &Testing Technology for Agro-Products, Chinses Academy of Agricultural Science, Beijing 100081, China
| | - Yuanshang Wang
- Key Laboratory of Agro-product Quality and Food Safety, Institute of Quality Standard &Testing Technology for Agro-Products, Chinses Academy of Agricultural Science, Beijing 100081, China
| | - Yudan Zhang
- Key Laboratory of Agro-product Quality and Food Safety, Institute of Quality Standard &Testing Technology for Agro-Products, Chinses Academy of Agricultural Science, Beijing 100081, China
| | - A M Abd El-Aty
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt; Department of Medical Pharmacology, Medical Faculty, Ataturk University, 25240 Erzurum, Turkey
| | - Ahmet Hacımüftüoğlu
- Department of Medical Pharmacology, Medical Faculty, Ataturk University, 25240 Erzurum, Turkey
| | - Jing Wang
- Key Laboratory of Agro-product Quality and Food Safety, Institute of Quality Standard &Testing Technology for Agro-Products, Chinses Academy of Agricultural Science, Beijing 100081, China
| | - Hongjun He
- College of Life Sciences, YanTai University, Yantai 264005, China.
| | - Maojun Jin
- Key Laboratory of Agro-product Quality and Food Safety, Institute of Quality Standard &Testing Technology for Agro-Products, Chinses Academy of Agricultural Science, Beijing 100081, China; Department of Entomology & Nematology and the UC Davis Comprehensive Cancer Center, Davis, CA 95616, USA.
| | - Bruce Hammock
- Department of Entomology & Nematology and the UC Davis Comprehensive Cancer Center, Davis, CA 95616, USA
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5
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Traeger JC, Schwartz DK. Interplay of electrostatic repulsion and surface grafting density on surface-mediated DNA hybridization. J Colloid Interface Sci 2020; 566:369-374. [DOI: 10.1016/j.jcis.2020.01.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 12/14/2022]
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6
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An Electrochemical DNA Biosensor for Carcinogenicity of Anticancer Compounds Based on Competition between Methylene Blue and Oligonucleotides. SENSORS 2019; 19:s19235111. [PMID: 31766637 PMCID: PMC6928940 DOI: 10.3390/s19235111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 12/15/2022]
Abstract
A toxicity electrochemical DNA biosensor has been constructed for the detection of carcinogens using 24 base guanine DNA rich single stranded DNA, and methylene blue (MB) as the electroactive indicator. This amine terminated ssDNA was immobilized onto silica nanospheres and deposited on gold nanoparticle modified carbon-paste screen printed electrodes (SPEs). The modified SPE was initially exposed to a carcinogen, followed by immersion in methylene blue for an optimized duration. The biosensor response was measured using differential pulse voltammetry. The performance of the biosensor was identified on several anti-cancer compounds. The toxicity DNA biosensor demonstrated a linear response range to the cadmium chloride from 0.0005 ppm to 0.01 ppm (R2 = 0.928) with a limit of detection at 0.0004 ppm. The biosensor also exhibited its versatility to screen the carcinogenicity of potential anti-cancer compounds.
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7
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Beh CW, Zhang Y, Zheng YL, Sun B, Wang TH. Fluorescence spectroscopic detection and measurement of single telomere molecules. Nucleic Acids Res 2019; 46:e117. [PMID: 30010842 PMCID: PMC6212783 DOI: 10.1093/nar/gky627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 06/28/2018] [Indexed: 01/26/2023] Open
Abstract
Telomeres are the end-caps of chromosomes that serve to protect the integrity of the genome. Below certain critical lengths, the telomeres can no longer fulfill their protective function, and chromosomal instability ensues. Telomeres shorten during normal cell division due to the end replication problem and are implicated in the development of various aging-associated diseases, including cancer. Telomere length has the potential to serve as a useful biomarker in the field of aging and cancer. However, existing methods of telomere measurement are either too laborious, unable to provide absolute measurement of individual telomere lengths, or limited to certain chromosomes or cell types. Here, we describe an easy single-molecule, fluorescence spectroscopic method for measuring the length of telomeres that permits the profiling of absolute telomere lengths in any DNA sample. We have demonstrated the accurate detection of telomeres as short as 100 bp using cloned telomere standards, and have profiled telomere lengths in human cancer cell lines and primary cells. Since this method allows direct comparison between samples, it could greatly improve the clinical utility of telomere biomarkers.
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Affiliation(s)
- Cyrus W Beh
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ye Zhang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yun-Ling Zheng
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Bing Sun
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
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8
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Lahiri H, Mishra S, Mukhopadhyay R. Nanoscale Nucleic Acid Recognition at the Solid-Liquid Interface Using Xeno Nucleic Acid Probes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8875-8888. [PMID: 30398876 DOI: 10.1021/acs.langmuir.8b02770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Challenges in reliable nucleic acid detection are manifold. The major ones are related to false positive or negative signals due to a lack of target specificity in detection and to low sensitivity, especially when a plethora of background sequences are present that can mask the specific recognition signal. Utilizing designed synthetic nucleic acids that are commonly called xeno nucleic acids could offer potential routes to meeting such challenges. In this article, we present the general framework of nucleic acid detection, especially for nanoscale applications, and discuss how and why the xeno nucleic acids could be truly an alternative to the DNA probes. Two specific cases, locked nucleic acid (LNA) and peptide nucleic acid (PNA), which are nuclease-resistant and can form thermally stable duplexes with DNA, are addressed. It is shown that the relative ease of the conformationally rigid LNA probe to be oriented upright on the substrate surface and of the nonionic PNA probe to result into high probe density assists in their use in nanoscale nucleic acid recognition. It is anticipated that success with these probes may lead to important developments such as PCR-independent approaches where the major aim is to detect a small number of target sequences present in the analyte medium.
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Affiliation(s)
- Hiya Lahiri
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
| | - Sourav Mishra
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
| | - Rupa Mukhopadhyay
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
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9
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Veerbeek J, Steen R, Vijselaar W, Rurup WF, Korom S, Rozzi A, Corradini R, Segerink L, Huskens J. Selective Functionalization with PNA of Silicon Nanowires on Silicon Oxide Substrates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:11395-11404. [PMID: 30179484 PMCID: PMC6158678 DOI: 10.1021/acs.langmuir.8b02401] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/29/2018] [Indexed: 06/02/2023]
Abstract
Silicon nanowire chips can function as sensors for cancer DNA detection, whereby selective functionalization of the Si sensing areas over the surrounding silicon oxide would prevent loss of analyte and thus increase the sensitivity. The thermal hydrosilylation of unsaturated carbon-carbon bonds onto H-terminated Si has been studied here to selectively functionalize the Si nanowires with a monolayer of 1,8-nonadiyne. The silicon oxide areas, however, appeared to be functionalized as well. The selectivity toward the Si-H regions was increased by introducing an extra HF treatment after the 1,8-nonadiyne monolayer formation. This step (partly) removed the monolayer from the silicon oxide regions, whereas the Si-C bonds at the Si areas remained intact. The alkyne headgroups of immobilized 1,8-nonadiyne were functionalized with PNA probes by coupling azido-PNA and thiol-PNA by click chemistry and thiol-yne chemistry, respectively. Although both functionalization routes were successful, hybridization could only be detected on the samples with thiol-PNA. No fluorescence was observed when introducing dye-labeled noncomplementary DNA, which indicates specific DNA hybridization. These results open up the possibilities for creating Si nanowire-based DNA sensors with improved selectivity and sensitivity.
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Affiliation(s)
- Janneke Veerbeek
- Molecular NanoFabrication group, MESA+ Institute for Nanotechnology, and BIOS Lab on a
Chip group, MESA+ Institute for Nanotechnology, TechMed Centre and
Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Raymond Steen
- Molecular NanoFabrication group, MESA+ Institute for Nanotechnology, and BIOS Lab on a
Chip group, MESA+ Institute for Nanotechnology, TechMed Centre and
Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Wouter Vijselaar
- Molecular NanoFabrication group, MESA+ Institute for Nanotechnology, and BIOS Lab on a
Chip group, MESA+ Institute for Nanotechnology, TechMed Centre and
Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - W. Frederik Rurup
- Molecular NanoFabrication group, MESA+ Institute for Nanotechnology, and BIOS Lab on a
Chip group, MESA+ Institute for Nanotechnology, TechMed Centre and
Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Saša Korom
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Andrea Rozzi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Roberto Corradini
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Loes Segerink
- Molecular NanoFabrication group, MESA+ Institute for Nanotechnology, and BIOS Lab on a
Chip group, MESA+ Institute for Nanotechnology, TechMed Centre and
Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Jurriaan Huskens
- Molecular NanoFabrication group, MESA+ Institute for Nanotechnology, and BIOS Lab on a
Chip group, MESA+ Institute for Nanotechnology, TechMed Centre and
Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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10
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Machnik G, Skudrzyk E, Bułdak Ł, Ruczyński J, Kozłowska A, Mucha P, Rekowski P, Szkróbka W, Basiak M, Bołdys A, Sławska H, Okopień B. Monitoring the Transcriptional Activity of Human Endogenous Retroviral HERV-W Family Using PNA Strand Invasion into Double-Stranded DNA. Mol Biotechnol 2018; 60:124-133. [PMID: 29313202 PMCID: PMC5799313 DOI: 10.1007/s12033-017-0057-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the presented assay, we elaborated a method for distinguishing sequences that are genetically closely related to each other. This is particularly important in a situation where a fine balance of the allele abundance is a point of research interest. We developed a peptide nucleic acid (PNA) strand invasion technique for the differentiation between multiple sclerosis-associated retrovirus (MSRV) and ERVWE1 sequences, both molecularly similar, belonging to the human endogenous retrovirus HERV-W family. We have found that this method may support the PCR technique in screening for minor alleles which, in certain conditions, may be undetected by the standard PCR technique. We performed the analysis of different ERVWE1 and MSRV template mixtures ranging from 0 to 100% of ERVWE1 in the studied samples, finding the linear correlation between template composition and signal intensity of final reaction products. Using the PNA strand invasion assay, we were able to estimate the relative ERVWE1 expression level in human specimens such as U-87 MG, normal human astrocytes cell lines and placental tissue. The results remained in concordance with those obtained by semi-quantitative or quantitative PCR.
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Affiliation(s)
- Grzegorz Machnik
- Department of Internal Medicine and Clinical Pharmacology, School of Medicine in Katowice, Medical University of Silesia, Medyków 18, 40-752, Katowice, Poland.
| | - Estera Skudrzyk
- Department of Internal Medicine and Clinical Pharmacology, School of Medicine in Katowice, Medical University of Silesia, Medyków 18, 40-752, Katowice, Poland
| | - Łukasz Bułdak
- Department of Internal Medicine and Clinical Pharmacology, School of Medicine in Katowice, Medical University of Silesia, Medyków 18, 40-752, Katowice, Poland
| | - Jarosław Ruczyński
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Agnieszka Kozłowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Piotr Mucha
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Piotr Rekowski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Witold Szkróbka
- Department of Internal Medicine and Clinical Pharmacology, School of Medicine in Katowice, Medical University of Silesia, Medyków 18, 40-752, Katowice, Poland
| | - Marcin Basiak
- Department of Internal Medicine and Clinical Pharmacology, School of Medicine in Katowice, Medical University of Silesia, Medyków 18, 40-752, Katowice, Poland
| | - Aleksandra Bołdys
- Department of Internal Medicine and Clinical Pharmacology, School of Medicine in Katowice, Medical University of Silesia, Medyków 18, 40-752, Katowice, Poland
| | - Helena Sławska
- Department of Gynaecology, Obstetrics and Oncological Gynaecology, Medical University of Silesia, Batorego 15, 41-902, Bytom, Poland
| | - Bogusław Okopień
- Department of Internal Medicine and Clinical Pharmacology, School of Medicine in Katowice, Medical University of Silesia, Medyków 18, 40-752, Katowice, Poland
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11
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Nicol A, Knoll W. Characteristics of Fluorescence Emission Excited by Grating-Coupled Surface Plasmons. PLASMONICS (NORWELL, MASS.) 2018; 13:2337-2343. [PMID: 30595677 PMCID: PMC6280977 DOI: 10.1007/s11468-018-0757-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 04/11/2018] [Indexed: 06/09/2023]
Abstract
Dye molecules placed on metallic gratings can experience an enhanced electromagnetic field if illuminated under surface plasmon excitation conditions, a situation that can be employed for sensor applications. The fluorescence emission in this situation exhibits a characteristic emission polarization and geometry given by the fluorophore/grating interaction. We present experiments visualizing the full shape of the emission profiles and demonstrate how they can be manipulated by means of the grating constant. The excitation and emission processes taking place on the grating surface are characterized by polarization sensitive measurements.
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Affiliation(s)
- Andreas Nicol
- Bayer AG, Engineering and Technology, Building E 41, 51368 Leverkusen, Germany
| | - Wolfgang Knoll
- AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- University of Natural Resources and Life Sciences, Vienna,(BOKU), Vienna, Austria
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12
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Kaisti M, Kerko A, Aarikka E, Saviranta P, Boeva Z, Soukka T, Lehmusvuori A. Real-time wash-free detection of unlabeled PNA-DNA hybridization using discrete FET sensor. Sci Rep 2017; 7:15734. [PMID: 29147003 PMCID: PMC5691077 DOI: 10.1038/s41598-017-16028-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/06/2017] [Indexed: 11/25/2022] Open
Abstract
We demonstrate an electrochemical sensor for detection of unlabeled single-stranded DNA using peptide nucleic acid (PNA) probes coupled to the field-effect transistor (FET) gate. The label-free detection relies on the intrinsic charge of the DNA backbone. Similar detection schemes have mainly concentrated on sensitivity improvement with an emphasis on new sensor structures. Our approach focuses on using an extended-gate that separates the FET and the sensing electrode yielding a simple and mass fabricable device. We used PNA probes for efficient hybridization in low salt conditions that is required to avoid the counter ion screening. As a result, significant part of the target DNA lies within the screening length of the sensor. With this, we achieved a wash-free detection where typical gate potential shifts are more than 70 mV with 1 µM target DNA. We routinely obtained a real-time, label- and wash-free specific detection of target DNA in nanomolar concentration with low-cost electronics and the responses were achieved within minutes after introducing targets to the solution. Furthermore, the results suggest that the sensor performance is limited by specificity rather than by sensitivity and using low-cost electronics does not limit the sensor performance in the presented sensor configuration.
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Affiliation(s)
- Matti Kaisti
- University of Turku, Department of Future Technologies, 20500, Turku, Finland.
| | - Anssi Kerko
- University of Turku, Department of Biotechnology, 20520, Turku, Finland
| | - Eero Aarikka
- University of Turku, Department of Biotechnology, 20520, Turku, Finland
| | - Petri Saviranta
- Medical Biotechnology Centre, VTT Technical Research Centre of Finland, Espoo FI-02044, VTT, Finland
| | - Zhanna Boeva
- Åbo Akademi University, Department of Science and Engineering, 20500, Turku, Finland
| | - Tero Soukka
- University of Turku, Department of Biotechnology, 20520, Turku, Finland
| | - Ari Lehmusvuori
- University of Turku, Department of Biotechnology, 20520, Turku, Finland.
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13
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Makra I, Brajnovits A, Jágerszki G, Fürjes P, Gyurcsányi RE. Potentiometric sensing of nucleic acids using chemically modified nanopores. NANOSCALE 2017; 9:739-747. [PMID: 27973633 DOI: 10.1039/c6nr05886h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Unlike the overwhelming majority of nanopore sensors that are based on the measurement of a transpore ionic current, here we introduce a potentiometric sensing scheme and demonstrate its application for the selective detection of nucleic acids. The sensing concept uses the charge inversion that occurs in the sensing zone of a nanopore upon binding of negatively charged microRNA strands to positively charged peptide-nucleic acid (PNA) modified nanopores. The initial anionic permselectivity of PNA-modified nanopores is thus gradually changed to cationic permselectivity, which can be detected simply by measuring the nanoporous membrane potential. A quantitative theoretical treatment of the potentiometric microRNA response is provided based on the Nernst-Planck/Poisson model for the nanopore system assuming first order kinetics for the nucleic acid hybridization. An excellent correlation between the theoretical and experimental results was observed, which revealed that the binding process is focused at the nanopore entrance with contributions from both in pore and out of pore sections of the nanoporous membrane. The theoretical treatment is able to give clear guidelines for further optimization of potentiometric nanopore-based nucleic acid sensors by predicting the effect of the most important experimental parameters on the potential response.
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Affiliation(s)
- István Makra
- MTA-BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellért tér 4, 1111 Budapest, Hungary.
| | - Alexandra Brajnovits
- MTA-BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellért tér 4, 1111 Budapest, Hungary.
| | - Gyula Jágerszki
- MTA-BME Research Group of Technical Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellért tér 4, 1111 Budapest, Hungary
| | - Péter Fürjes
- MTA Centre for Energy Research - Institute of Technical Physics and Materials Science, Konkoly-Thege str. 29-33, H-1121 Budapest, Hungary
| | - Róbert E Gyurcsányi
- MTA-BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellért tér 4, 1111 Budapest, Hungary.
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14
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Jang K, Park C, You J, Choi J, Park H, Park J, Lee H, Choi CH, Na S. Highly sensitive, direct and real-time detection of silver nanowires by using a quartz crystal microbalance. NANOTECHNOLOGY 2016; 27:475506. [PMID: 27779116 DOI: 10.1088/0957-4484/27/47/475506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
For several decades, silver nanomaterials (AgNMs) have been used in various research areas and commercial products. Among the many AgNMs, silver nanowires (AgNWs) are one of the mostly widely used nanomaterials due to their high electrical and thermal conductivity. However, recent studies have investigated the toxicity of AgNWs. For this reason, it is necessary to develop a successful detection method of AgNWs for protecting human health. In this study, label-free, highly sensitive, direct, and real-time detection of AgNWs is performed for the first time. The detection mechanism is based on the resonance frequency shift upon the mass change from the hybridization between the probe DNA on the electrode and the linker DNA attached on AgNWs. The frequency shift is measured by using a quartz crystal microbalance. We are able to detect 1 ng ml-1 of AgNWs in deionized water in real-time. Moreover, our detection method can selectively detect AgNWs among other types of one-dimensional nanomaterials and can also be applied to detection in drinking water.
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Affiliation(s)
- Kuewhan Jang
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Korea
| | - Chanho Park
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Korea
| | - Juneseok You
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Korea
| | - Jaeyeong Choi
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Korea
| | - Hyunjun Park
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Korea
| | - Jinsung Park
- Department of Control and Instrumentation Engineering, Korea University, Sejong 339-700, Korea
| | - Howon Lee
- Department of Mechanical and Aerospace Engineering, Rutgers University, 98 Brett Rd, Piscataway, NJ 08854, USA
| | - Chang-Hwan Choi
- Department of Mechanical Engineering, Stevens Institute of Technology, Hoboken, New Jersey 07030, USA
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Korea
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15
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Qiao W, Chiang HC, Xie H, Levicky R. Surface vs. solution hybridization: effects of salt, temperature, and probe type. Chem Commun (Camb) 2016; 51:17245-8. [PMID: 26459915 DOI: 10.1039/c5cc06674c] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hybridization thermodynamics on solid supports are compared with those in solution for two types of hybridization probe, DNA and uncharged morpholino oligonucleotides of identical sequences. Trends in hybridization affinity are discussed with respect to ionic strength, temperature, and surface behavior.
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Affiliation(s)
- Wanqiong Qiao
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Hao-Chun Chiang
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Hui Xie
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Rastislav Levicky
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
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16
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Toren P, Ozgur E, Bayindir M. Real-Time and Selective Detection of Single Nucleotide DNA Mutations Using Surface Engineered Microtoroids. Anal Chem 2015; 87:10920-6. [DOI: 10.1021/acs.analchem.5b02664] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Pelin Toren
- Institute
of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
- UNAM-National
Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
| | - Erol Ozgur
- Institute
of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
- UNAM-National
Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
| | - Mehmet Bayindir
- Institute
of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
- UNAM-National
Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
- Department
of Physics, Bilkent University, 06800 Ankara, Turkey
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17
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Yang F, Dong B, Nie K, Shi H, Wu Y, Wang H, Liu Z. Light-Directed Synthesis of High-Density Peptide Nucleic Acid Microarrays. ACS COMBINATORIAL SCIENCE 2015; 17:608-14. [PMID: 26339951 DOI: 10.1021/acscombsci.5b00074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptide nucleic acids (PNAs) are a class of nucleic acid mimics that can bind to the complementary DNA or RNA with high specificity and sensitivity. PNA-based microarrays have distinct characteristics and have improved performance in many aspects compared to DNA microarrays. A new set of PNA monomers has been synthesized and used as the building blocks for the preparation of high density PNA microarrays. These monomers have their backbones protected by the photolabile group 2-(2-nitrophenyl)propyloxy carbonyl (NPPOC), and their exocyclic amino groups protected by amide carbonyl groups. A light-directed synthesis system was designed and applied to the in situ synthesis of a PNA microarray with a density of over 10,000 probes per square centimeter. This PNA microarray was able to detect single and multiple base-mismatches correctly with a high discrimination ratio.
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Affiliation(s)
- Feipeng Yang
- Department
of Biomedical
Engineering, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
| | - Bo Dong
- Department
of Biomedical
Engineering, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
| | - Kaixuan Nie
- Department
of Biomedical
Engineering, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
| | - Huanhuan Shi
- Department
of Biomedical
Engineering, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
| | - Yanqi Wu
- Department
of Biomedical
Engineering, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
| | - Hongyin Wang
- Department
of Biomedical
Engineering, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
| | - Zhengchun Liu
- Department
of Biomedical
Engineering, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
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18
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Xiang Y, Zhu X, Huang Q, Zheng J, Fu W. Real-time monitoring of mycobacterium genomic DNA with target-primed rolling circle amplification by a Au nanoparticle-embedded SPR biosensor. Biosens Bioelectron 2015; 66:512-9. [DOI: 10.1016/j.bios.2014.11.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/13/2014] [Accepted: 11/14/2014] [Indexed: 10/24/2022]
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19
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Silicon nanowires as field-effect transducers for biosensor development: A review. Anal Chim Acta 2014; 825:1-25. [DOI: 10.1016/j.aca.2014.03.016] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 03/11/2014] [Accepted: 03/13/2014] [Indexed: 12/28/2022]
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20
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De Costa NTS, Heemstra JM. Differential DNA and RNA sequence discrimination by PNA having charged side chains. Bioorg Med Chem Lett 2014; 24:2360-3. [PMID: 24731279 DOI: 10.1016/j.bmcl.2014.03.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 12/14/2022]
Abstract
PNA sequences modified with charged side chains were evaluated for base-pairing sequence selectivity under physiological conditions. PNA having negatively charged aspartic acid side chains shows higher selectivity with RNA, while PNA having positively charged lysine side chains shows higher selectivity with DNA. These observations provide insight into the binding selectivity of modified PNA in antisense and antigene applications.
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Affiliation(s)
- N Tilani S De Costa
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112, USA; Center for Cell and Genome Science, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Jennifer M Heemstra
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112, USA; Center for Cell and Genome Science, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA.
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21
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De A, van Nieuwkasteele J, Carlen ET, van den Berg A. Integrated label-free silicon nanowire sensor arrays for (bio)chemical analysis. Analyst 2013; 138:3221-9. [PMID: 23608895 DOI: 10.1039/c3an36586g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a label-free (bio)chemical analysis platform that uses all-electrical silicon nanowire sensor arrays integrated with a small volume microfluidic flow-cell for real-time (bio)chemical analysis and detection. The integrated sensing platform contains an automated multi-sample injection system that eliminates erroneous sensor responses from sample switching due to flow rate fluctuations and provides precise sample volumes down to 10 nl. Biochemical sensing is demonstrated with real-time 15-mer DNA-PNA (peptide nucleic acid) duplex hybridization measurements from different sample concentrations in a low ionic strength, and the equilibrium dissociation constant KD ≈ 140 nM has been extracted from the experimental data using the first order Langmuir binding model. Chemical sensing is demonstrated with pH measurements from different injected samples in flow that have sensitivities consistent with the gate-oxide materials. A differential sensor measurement configuration results in a 30× reduction in sensor drift. The integrated label-free analysis platform is suitable for a wide range of small volume chemical and biochemical analyses.
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Affiliation(s)
- Arpita De
- BIOS/Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente, Postbus 217, 7500 AE Enschede, The Netherlands
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22
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Ou Q, He J, Liu C, Shi L, Zhao C, Xu Y, Gu D. Preparation and evaluation of a peptide nucleic acid gene chip system associated with surface plasmon resonance. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-012-0844-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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De A, Souchelnytskyi S, van den Berg A, Carlen ET. Peptide nucleic acid (PNA)-DNA duplexes: comparison of hybridization affinity between vertically and horizontally tethered PNA probes. ACS APPLIED MATERIALS & INTERFACES 2013; 5:4607-4612. [PMID: 23668364 DOI: 10.1021/am4011429] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We compare the PNA-DNA duplex hybridization characteristics of vertically tethered and new horizontally tethered PNA probes on solid surfaces. The horizontal 15-mer PNA probe has been synthesized with linker molecules attached at three locations (γ-points) positioned along the PNA backbone that provides covalent attachment of the probe with the backbone aligned parallel to the surface, which is important for DNA hybridization assays that use electric field effect sensors for detection. A radioactive labeled assay and real-time surface plasmon resonance (SPR) biosensor are used to assess the probe surface density, nonspecific binding, and DNA hybridization affinity, respectively, of the new PNA probe configuration. The estimated equilibrium dissociation constants of the horizontally tethered duplex and the vertically tethered duplex are of the same order of magnitude (KD ≈ 5 nM), which indicates a sufficient hybridization affinity for many electronic biosensors that benefit from the horizontal alignment, which minimizes the effects of counterion screening.
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24
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Ghosh S, Mishra S, Banerjee T, Mukhopadhyay R. Facilitating mismatch discrimination by surface-affixed PNA probes via ionic regulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:3370-3379. [PMID: 23414328 DOI: 10.1021/la400125x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
There has been a search for alternative nucleic acids that can be more effectively used in nucleic acid detection technologies compared to the DNA probes. Peptide nucleic acid (PNA), which contains a non-ionic peptidic backbone, offers such possibilities since it is nuclease-resistant, it binds to DNA with high affinity, and it can be readily self-assembled onto solid substrates, e.g., gold(111), with a molecular backbone orientation away from the substrate. Although application of PNA as a sensor probe has been exemplified, so far there is little or no account of the ionic modulation of single base mismatch discrimination capacity of surface-tethered PNA probes. Herein, we report "on-surface" melting temperatures of PNA-DNA duplexes formed on gold(111) surface, as obtained from fluorescence measurements. We show that surface-tethered PNA forms a stabler duplex than DNA, and is more effective in single base mismatch discrimination than DNA. Importantly, although PNA backbone is non-ionic, variation in the ionic components in hybridization buffer, i.e., varying concentration of monovalent sodium ion, and the nature of anion and the cation, exhibits clear effects on the mismatch discrimination capacity of PNA probes. In general, with decreasing cation concentration, PNA-DNA duplexes are stabilized and mismatch discrimination capacity of the PNA probes is enhanced. The stabilizing/destabilizing effects of anions are found to follow the Hofmeister series, emphasizing the importance of hydrophobic interaction between nucleobases for stability of the PNA-DNA duplexes. Interestingly, the nature of ionic dependence of "on-surface" mismatch detection ability of PNA probes differs significantly from the "solution" behavior of these probes.
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Affiliation(s)
- Srabani Ghosh
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India
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25
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Wu J, Coradin T, Aimé C. Reversible bioresponsive aptamer-based nanocomposites: ATP binding and removal from DNA-grafted silica nanoparticles. J Mater Chem B 2013; 1:5353-5359. [DOI: 10.1039/c3tb20499e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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26
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D'Agata R, Breveglieri G, Zanoli LM, Borgatti M, Spoto G, Gambari R. Direct detection of point mutations in nonamplified human genomic DNA. Anal Chem 2011; 83:8711-7. [PMID: 21978174 DOI: 10.1021/ac2021932] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultrasensitive detection protocols not requiring polymerase chain reaction (PCR)-mediated target DNA amplification are expected to significantly improve our possibilities in several research and diagnostic applications for which minute cell quantities are available. For this reason we have tested a nanoparticle-enhanced surface plasmon resonance imaging (SPRI) sensing strategy to detect point mutations in nonamplified genomic DNA. We have used genomic DNAs, not subject to costly, time-consuming, and prone to contamination PCR-based amplification procedures, obtained from both healthy individuals and homozygous or heterozygous patients affected by β-thalassemia, in order to demonstrate the specificity and the sensitivity of the described sensing strategy. The assay we describe is ultrasensitive and convenient. Attomolar concentrations of target genomic DNA are detected, DNAs from healthy individuals and homozygous or heterozygous patients affected by β-thalassemia are discriminated, and only simple manipulations of the genetic samples are required before the analysis. The proposed ultrasensitive detection of DNA point mutations involved in genomic disorders possibly represents an important advantage in several biomedical applications.
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Affiliation(s)
- Roberta D'Agata
- Dipartimento di Scienze Chimiche, Università di Catania, Catania, Italy
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27
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Liu Y, Irving D, Qiao W, Ge D, Levicky R. Kinetic mechanisms in morpholino-DNA surface hybridization. J Am Chem Soc 2011; 133:11588-96. [PMID: 21699181 PMCID: PMC3148943 DOI: 10.1021/ja202631b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Morpholinos (MOs) are DNA analogues whose uncharged nature can bring fundamental advantages to surface hybridization technologies such as DNA microarrays, by using MOs as the immobilized, or "probe", species. Advancement of MO-based diagnostics, however, is challenged by limited understanding of the surface organization of MO molecules and of how this organization impacts hybridization kinetics and thermodynamics. The present study focuses on hybridization kinetics between monolayers of MO probes and DNA targets as a function of the instantaneous extent of hybridization (i.e., duplex coverage), total probe coverage, and ionic strength. Intriguingly, these experiments reveal distinct kinetic stages, none of which are consistent with Langmuir kinetics. The initial stage, in which duplex coverage remains relatively sparse, indicates confluence of two effects: blockage of target access to unhybridized probes by previously formed duplexes and deactivation of the solid support due to consumption of probe molecules. This interpretation is consistent with a surface organization in which unhybridized MO probes localize near the solid support, underneath a layer of MO-DNA duplexes. As duplex coverage builds, provided saturation is not reached first, the initial stage can transition to an unusual regime characterized by near independence of hybridization rate on duplex coverage, followed by a prolonged approach to equilibrium. The possible origins of these more complex latter behaviors are discussed. Comparison with published data for DNA and peptide nucleic acid (PNA) probes is carried out to look for universal trends in kinetics. This comparison reveals qualitative similarities when comparable surface organization of probes is expected. In addition, MO monolayers are found capable of a broad range of reactivities that span reported values for PNA and DNA probes.
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Affiliation(s)
- Yatao Liu
- Department of Chemical and Biological Engineering, Polytechnic Institute of New York University, 6 MetroTech Center, Brooklyn, New York 11201, USA
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28
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Sforza S, Corradini R, Tedeschi T, Marchelli R. Food analysis and food authentication by peptide nucleic acid (PNA)-based technologies. Chem Soc Rev 2010; 40:221-32. [PMID: 20882238 DOI: 10.1039/b907695f] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
This tutorial review will address the issue of DNA determination in food by using Peptide Nucleic Acid (PNA) probes with different technological platforms, with a particular emphasis on the applications devoted to food authentication. After an introduction aimed at describing PNAs structure, binding properties and their use as genetic probes, the review will then focus specifically on the use of PNAs in the field of food analysis. In particular, the following issues will be considered: detection of genetically modified organisms (GMOs), of hidden allergens, of microbial pathogens and determination of ingredient authenticity. Finally, the future perspectives for the use of PNAs in food analysis will be briefly discussed according to the most recent developments.
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Affiliation(s)
- Stefano Sforza
- Department of Organic and Industrial Chemistry, University of Parma, Parco Area delle Scienze 17a, University Campus, I-43124, Parma, Italy.
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29
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Gong P, Wang K, Liu Y, Shepard K, Levicky R. Molecular mechanisms in morpholino-DNA surface hybridization. J Am Chem Soc 2010; 132:9663-71. [PMID: 20572663 PMCID: PMC2920048 DOI: 10.1021/ja100881a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic nucleic acid mimics provide opportunity for redesigning the specificity and affinity of hybridization with natural DNA or RNA. Such redesign is of great interest for diagnostic applications where it can enhance the desired signal against a background of competing interactions. This report compares hybridization of DNA analyte strands with morpholinos (MOs), which are uncharged nucleic acid mimics, to the corresponding DNA-DNA case in solution and on surfaces. In solution, MO-DNA hybridization is found to be independent of counterion concentration, in contrast to DNA-DNA hybridization. On surfaces, when immobilized MO or DNA "probe" strands hybridize with complementary DNA "targets" from solution, both the MO-DNA and DNA-DNA processes depend on ionic strength but exhibit qualitatively different behaviors. At lower ionic strengths, MO-DNA surface hybridization exhibits hallmarks of kinetic limitations when separation between hybridized probe sites becomes comparable to target dimensions, whereas extents of DNA-DNA surface hybridization are instead consistent with limits imposed by buildup of surface (Donnan) potential. The two processes also fundamentally differ at high ionic strength, under conditions when electrostatic effects are weak. Here, variations in probe coverage have a much diminished impact on MO-DNA than on DNA-DNA hybridization for similarly crowded surface conditions. These various observations agree with a structural model of MO monolayers in which MO-DNA duplexes segregate to the buffer interface while unhybridized probes localize near the solid support. A general perspective is presented on using uncharged DNA analogues, which also include compounds such as peptide nucleic acids (PNA), in surface hybridization applications.
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Affiliation(s)
- Ping Gong
- Seventh Sense Biosystems Inc., 101 Binney Street, Cambridge, Massachusetts 02142, USA
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30
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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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31
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Critical factors for the performance of chip array-based electrical detection of DNA for analysis of pathogenic bacteria. Anal Biochem 2008; 382:77-86. [DOI: 10.1016/j.ab.2008.05.057] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Revised: 05/15/2008] [Accepted: 05/16/2008] [Indexed: 11/19/2022]
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32
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Lao AIK, Su X, Aung KMM. SPR study of DNA hybridization with DNA and PNA probes under stringent conditions. Biosens Bioelectron 2008; 24:1717-22. [PMID: 19010658 DOI: 10.1016/j.bios.2008.08.054] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 08/09/2008] [Accepted: 08/29/2008] [Indexed: 10/21/2022]
Abstract
Surface plasmon resonance (SPR) spectroscopy has been used for studying on-chip DNA hybridization to a PNA probe and its counterpart DNA probe of a 22-mer sequence. Two stringency control strategies are used for single base mismatch discrimination, namely (1) adding a denaturant, i.e. formamide (FA), into hybridization buffer and (2) coupling negative potentials for selective dehybridization of mismatch DNA. These two strategies have either not been used before or been less-well studied in SPR detection. An end-point SPR measurement protocol (no real-time hybridization profile recorded) is developed for detecting DNA hybridization in the presence of FA, to circumvent the problem that the refractive index of FA is out of the detectable range of the SPR equipment. The missing of real-time measurement of hybridization profile is compensated with QCM measurement. Under optimal conditions, i.e. 10mM PBS with 30% FA and 1mM PBS with 50% FA, single base mismatch DNA is detected with 1.7 and 2.8 times less hybridization signals compared with the perfect match DNA, with the DNA probe and PNA probe, respectively. Under negative potential of -0.2 to -0.4V (vs. Ag/AgCl), mismatch DNA dissociates more than perfect match DNA by 1.7-2.5 times from the DNA probe and 2.1-3.5 times from the PNA probe. The higher mismatch discrimination efficiency of the PNA probe under stringent conditions would be attributable to its higher intrinsic sequence selectivity.
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Affiliation(s)
- Alex Ieng Kin Lao
- Institute of Microelectronics, Agency for Science, Technology and Research, Singapore Science Park II, Singapore
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Zhang GJ, Chua JH, Chee RE, Agarwal A, Wong SM, Buddharaju KD, Balasubramanian N. Highly sensitive measurements of PNA-DNA hybridization using oxide-etched silicon nanowire biosensors. Biosens Bioelectron 2008; 23:1701-7. [PMID: 18356037 DOI: 10.1016/j.bios.2008.02.006] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 01/02/2008] [Accepted: 02/06/2008] [Indexed: 10/22/2022]
Abstract
The highly sensitive and sequence-specific detection of single-stranded oligonucleotides using nonoxidized silicon nanowires (SiNWs) is demonstrated. To maximize device sensitivity, the surface of the SiNWs was functionalized with a densely packed organic monolayer via hydrosilylation, subsequently immobilized with peptide nucleic acid (PNA) capable of recognizing the label-free complementary target DNA. Because of the selective functionalization of the SiNWs, binding competition between the nanowire and the underlying oxide is avoided. Transmission electron microscopy was conducted to clearly differentiate the SiNW surface before and after removal of SiO(2). Fluorescence microscopy was used to further realize the selectivity of the oxide-etched chemistry on the SiNWs and sequence specificity of PNA-DNA hybridization. The concentration-dependent resistance change measurements upon hybridization of PNA-DNA show that detection limit down to 10fM can be obtained. The SiNW devices also reveal the capability of an obvious discrimination against mismatched sequences. Among several efforts being made to improve detection sensitivity, this work addresses one significant issue regarding surface functionalization which enables highly sensitive biomolecular sensing with SiNWs.
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Affiliation(s)
- Guo-Jun Zhang
- Institute of Microelectronics, A*STAR (Agency for Science, Technology and Research), Singapore 117685, Singapore.
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