1
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Kumar V, Wahane A, Gupta A, Manautou JE, Bahal R. Multivalent Lactobionic Acid and N-Acetylgalactosamine-Conjugated Peptide Nucleic Acids for Efficient In Vivo Targeting of Hepatocytes. Adv Healthc Mater 2023; 12:e2202859. [PMID: 36636995 PMCID: PMC10175146 DOI: 10.1002/adhm.202202859] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/27/2022] [Indexed: 01/14/2023]
Abstract
Peptide nucleic acids (PNAs) are used/applied in various studies to target genomic DNA and RNA to modulate gene expression. Non-specific targeting and rapid elimination always remain a challenge for PNA-based applications. Here, the synthesis, characterization, in vitro and in vivo study of di lactobionic acid (diLBA) and tris N-acetyl galactosamine (tGalNAc) conjugated PNAs for liver-targeted delivery are reported. For proof of concept, diLBA, and tGalNAc conjugated PNAs (anti-miR-122 PNAs) were synthesized to target microRNA-122 (miR-122) which is over-expressed in the hepatic tissue. Different lengths of anti-miR-122 PNAs conjugated with diLBA and tGalNAc are tested. Cell culture and in vivo analyses to determine biodistribution, efficacy, and toxicity profile are performed. This work indicates that diLBA conjugates show significant retention in hepatocytes in addition to tGalNAc conjugates after in vivo delivery. Full-length PNA conjugates show significant downregulation of miR-122 levels and subsequent de-repression of its downstream targets with no evidence of toxicity. The results provide a robust framework for ligand-conjugated delivery systems for PNAs that can be explored for broader biomedical applications.
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Affiliation(s)
- Vikas Kumar
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
| | - Aniket Wahane
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
| | - Anisha Gupta
- School of Pharmacy, University of Saint Joseph, West Hartford, CT, 06117, USA
| | - José E Manautou
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
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2
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Mueller BL, Liberman MJ, Kolpashchikov DM. OWL2: a molecular beacon-based nanostructure for highly selective detection of single-nucleotide variations in folded nucleic acids. NANOSCALE 2023; 15:5735-5742. [PMID: 36880268 DOI: 10.1039/d2nr05590b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Hybridization probes have been used in the detection of specific nucleic acids for the last 50 years. Despite the extensive efforts and the great significance, the challenges of the commonly used probes include (1) low selectivity in detecting single nucleotide variations (SNV) at low (e.g. room or 37 °C) temperatures; (2) low affinity in binding folded nucleic acids, and (3) the cost of fluorescent probes. Here we introduce a multicomponent hybridization probe, called OWL2 sensor, which addresses all three issues. The OWL2 sensor uses two analyte binding arms to tightly bind and unwind folded analytes, and two sequence-specific strands that bind both the analyte and a universal molecular beacon (UMB) probe to form fluorescent 'OWL' structure. The OWL2 sensor was able to differentiate single base mismatches in folded analytes in the temperature range of 5-38 °C. The design is cost-efficient since the same UMB probe can be used for detecting any analyte sequence.
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Affiliation(s)
- Brittany L Mueller
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA.
| | - Mark J Liberman
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA.
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA.
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
- National Center for Forensic Science, University of Central Florida, Orlando, FL, USA
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3
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Amarasekara H, Oshaben KM, Jeans KB, Sangsari PR, Morgan NY, O’Farrell B, Appella DH. Cyclopentane peptide nucleic acid: Gold nanoparticle conjugates for the detection of nucleic acids in a microfluidic format. Biopolymers 2022; 113:e23481. [PMID: 34812507 PMCID: PMC8957522 DOI: 10.1002/bip.23481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 11/06/2022]
Abstract
Routine patient testing for viral infections is critical to identify infected individuals for treatment and to prevent spreading of infections to others. Developing robust and reliable diagnostic tools to detect nucleic acids of viruses at the point-of-care could greatly assist the clinical management of viral infections. The remarkable stability and high binding affinity of peptide nucleic acids (PNAs) to target nucleic acids could make PNA-based biosensors an excellent starting point to develop new nucleic acid detection technologies. We report the application of cyclopentane-modified PNAs to capture target nucleic acids in a microfluidic channel, and the use of bioorthogonal PNAs conjugated to gold nanoparticles as probes to semi-quantitatively signal the presence of a target nucleic acid derived from HIV-1. The basic results presented could be used to develop more advanced devices to detect nucleic acids from viruses such as HIV, SARS-CoV-2, and a wide range of other human diseases.
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Affiliation(s)
- Harsha Amarasekara
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Room 404, Bethesda, MD 20892, USA
| | - Kaylyn M. Oshaben
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Room 404, Bethesda, MD 20892, USA,Altratech Ltd., Forge House, Forge Hill, Cork, T12 F867, Ireland
| | - Kendra B. Jeans
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Room 404, Bethesda, MD 20892, USA
| | - Paniz Rezvan Sangsari
- Biomedical Engineering and Physical Science Shared Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Y. Morgan
- Biomedical Engineering and Physical Science Shared Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brian O’Farrell
- Altratech Ltd., Forge House, Forge Hill, Cork, T12 F867, Ireland
| | - Daniel H. Appella
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Room 404, Bethesda, MD 20892, USA
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4
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Forte G, Ventimiglia G, Pesaturo M, Petralia S. A highly sensitive PNA-microarray system for miRNA122 recognition. Biotechnol J 2022; 17:e2100587. [PMID: 35225426 DOI: 10.1002/biot.202100587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 11/09/2022]
Abstract
Surface chemistry is a fundamental aspect of the development of the sensitive biosensor based on microarray technology. Here we described an advanced PNA-microarray system for the detection of miRNA, composed by a multilayered Si/Al/Agarose component. A straightforward optical signal enhancement is achieved thanks to a combination of the Al film mirror effect and the positive interference for the emission wavelength of the Cy5 fluorescent label tuned by the agarose film. The PNA-microarray was investigated for the detection of miRNA_122, resulting in a sensitivity of about 1.75 μM-1 and Limit of Detection in the range of 0.043 nM as a function of the capture probe sequence. The contribution, in terms of H-bonds amounts at 298 and 333 K, of the agarose coating to the dsPNA-RNA interactions was demonstrated by Molecular Dynamic simulations. These results pave the way for advanced sensing strategies suitable for the environmental monitoring and the public safety. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Giuseppe Forte
- Department of Drug Science and Health, University of Catania, via S. Sofia 64, 95125, Catania, Italy
| | - Giorgio Ventimiglia
- EM Microelectronic, Rue de Sors 3, 2074, Marin (Suisse), Marin-Epagnier, Switzerland
| | | | - Salvatore Petralia
- Department of Drug Science and Health, University of Catania, via S. Sofia 64, 95125, Catania, Italy
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5
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Magni M, Dall'Angelo S, Baldoli C, Licandro E, Falciola L, Mussini PR. Metal‐free phthalimide‐labeled peptide nucleic acids for electrochemical biosensing applications. ELECTROCHEMICAL SCIENCE ADVANCES 2022. [DOI: 10.1002/elsa.202100164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Mirko Magni
- Department of Chemistry Università degli Studi di Milano ‐ Via C. Golgi 19 Milano Italy
| | - Sergio Dall'Angelo
- Department of Chemistry Università degli Studi di Milano ‐ Via C. Golgi 19 Milano Italy
- Institute of Medical Sciences University of Aberdeen Aberdeen Scotland UK
| | - Clara Baldoli
- CNR‐ Institute of Chemical Sciences and Technologies (SCITEC) Milano Italy
| | - Emanuela Licandro
- Department of Chemistry Università degli Studi di Milano ‐ Via C. Golgi 19 Milano Italy
| | - Luigi Falciola
- Department of Chemistry Università degli Studi di Milano ‐ Via C. Golgi 19 Milano Italy
| | - Patrizia R. Mussini
- Department of Chemistry Università degli Studi di Milano ‐ Via C. Golgi 19 Milano Italy
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6
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Tadimety A, Zhang Y, Molinski JH, Palinski TJ, Tsongalis GJ, Zhang JXJ. Plasmonic Nanoparticle Conjugation for Nucleic Acid Biosensing. Methods Mol Biol 2022; 2393:73-87. [PMID: 34837175 DOI: 10.1007/978-1-0716-1803-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This chapter details the use of gold nanorods conjugated with peptide nucleic acid probes for sequence-specific detection of circulating tumor DNA (ctDNA). ctDNA is gaining increased attention as a biomarker for liquid biopsy, the process of detecting molecules in the peripheral blood rather than a tissue sample. It has wide ranging applications as a diagnostic and prognostic biomarker with a similar mutational profile as the tumor. Plasmonic nanoparticles offer a relatively rapid, amplification-free method for detection of ctDNA through the use of sequence-specific peptide nucleic acid (PNA) probes. In this chapter, we discuss methods for probe design, conjugation to plasmonic particles, and ctDNA quantitation with the resulting sensor. This chapter is a resource for those looking to use plasmonic gold particles for sensing in a solution format for a range of applications.
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Affiliation(s)
- Amogha Tadimety
- Laboratory of Clinical Genomics and Advanced Technology, Department of Pathology and laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Yichen Zhang
- Laboratory of Clinical Genomics and Advanced Technology, Department of Pathology and laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - John H Molinski
- Laboratory of Clinical Genomics and Advanced Technology, Department of Pathology and laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Timothy J Palinski
- Laboratory of Clinical Genomics and Advanced Technology, Department of Pathology and laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Gregory J Tsongalis
- Laboratory of Clinical Genomics and Advanced Technology, Department of Pathology and laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - John X J Zhang
- Laboratory of Clinical Genomics and Advanced Technology, Department of Pathology and laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA.
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7
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Mocenigo M, Porchetta A, Rossetti M, Brass E, Tonini L, Puzzi L, Tagliabue E, Triulzi T, Marini B, Ricci F, Ippodrino R. Rapid, Cost-Effective Peptide/Nucleic Acid-Based Platform for Therapeutic Antibody Monitoring in Clinical Samples. ACS Sens 2020; 5:3109-3115. [PMID: 32909731 DOI: 10.1021/acssensors.0c01046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We demonstrate here a homogeneous assay, named NanoHybrid, for monoclonal antibody quantification directly in serum samples in a single-step format. NanoHybrid is composed of both synthetic peptide nucleic acids (PNAs) and nucleic acid strands conjugated to recognition elements and optical labels and is designed to allow fast fluorescence quantification of a therapeutic antibody. More specifically, we have characterized our analytical assay for the detection of trastuzumab (Herceptin), a monoclonal antibody (mAb) drug used for breast cancer treatment and for tumors overexpressing the HER2/neu protein. We show here that NanoHybrid is capable of performing fast drug quantification directly in blood serum. The results obtained with a pool of samples from breast cancer patients under trastuzumab treatment are compared with CE-IVD ELISA (enzyme-linked immunosorbent assay) showing a good agreement (Cohen's K = 0.729). Due to the modular nature of the NanoHybrid platform, this technology can be programmed to potentially detect and quantify any antibody for which a high-affinity recognition element has been characterized. We envision the application of NanoHybrid in a point-of-care (POC) drug monitoring system based on disposable kits for therapeutic drug management.
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Affiliation(s)
- Marco Mocenigo
- Ulisse BioMed Labs, Area Science Park, SS 14, km 163.5, 34149 Trieste, Italy
- Molecular Genetics and Biotechnology PhD Study Programme, University of Nova Gorica, Vipavska 13, 5000 Nova Gorica, Slovenia
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Marianna Rossetti
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Erik Brass
- Ulisse BioMed Labs, Area Science Park, SS 14, km 163.5, 34149 Trieste, Italy
| | - Lucia Tonini
- Ulisse BioMed Labs, Area Science Park, SS 14, km 163.5, 34149 Trieste, Italy
| | - Luca Puzzi
- Ulisse BioMed Labs, Area Science Park, SS 14, km 163.5, 34149 Trieste, Italy
| | - Elda Tagliabue
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Tiziana Triulzi
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Bruna Marini
- Ulisse BioMed Labs, Area Science Park, SS 14, km 163.5, 34149 Trieste, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Rudy Ippodrino
- Ulisse BioMed Labs, Area Science Park, SS 14, km 163.5, 34149 Trieste, Italy
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8
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PNA-Based MicroRNA Detection Methodologies. Molecules 2020; 25:molecules25061296. [PMID: 32178411 PMCID: PMC7144472 DOI: 10.3390/molecules25061296] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) are small noncoding RNAs involved in the fine regulation of post-transcriptional processes in the cell. The physiological levels of these short (20-22-mer) oligonucleotides are important for the homeostasis of the organism, and therefore dysregulation can lead to the onset of cancer and other pathologies. Their importance as biomarkers is constantly growing and, in this context, detection methods based on the hybridization to peptide nucleic acids (PNAs) are gaining their place in the spotlight. After a brief overview of their biogenesis, this review will discuss the significance of targeting miR, providing a wide range of PNA-based approaches to detect them at biologically significant concentrations, based on electrochemical, fluorescence and colorimetric assays.
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9
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Fouz MF, Appella DH. PNA Clamping in Nucleic Acid Amplification Protocols to Detect Single Nucleotide Mutations Related to Cancer. Molecules 2020; 25:molecules25040786. [PMID: 32059456 PMCID: PMC7070360 DOI: 10.3390/molecules25040786] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/30/2020] [Accepted: 02/02/2020] [Indexed: 01/02/2023] Open
Abstract
This review describes the application of peptide nucleic acids (PNAs) as clamps that prevent nucleic acid amplification of wild-type DNA so that DNA with mutations may be observed. These methods are useful to detect single-nucleotide polymorphisms (SNPs) in cases where there is a small amount of mutated DNA relative to the amount of normal (unmutated/wild-type) DNA. Detecting SNPs arising from mutated DNA can be useful to diagnose various genetic diseases, and is especially important in cancer diagnostics for early detection, proper diagnosis, and monitoring of disease progression. Most examples use PNA clamps to inhibit PCR amplification of wild-type DNA to identify the presence of mutated DNA associated with various types of cancer.
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10
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Malik YS, Verma A, Kumar N, Deol P, Kumar D, Ghosh S, Dhama K. Biotechnological innovations in farm and pet animal disease diagnosis. GENOMICS AND BIOTECHNOLOGICAL ADVANCES IN VETERINARY, POULTRY, AND FISHERIES 2020. [PMCID: PMC7150312 DOI: 10.1016/b978-0-12-816352-8.00013-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The application of innovative diagnostic technologies for the detection of animal pathogens at an early stage is essential in restricting the economic loss incurred due to emerging infectious animal diseases. The desirable characteristics of such diagnostic methods are easy to use, cost-effective, highly sensitive, and specific, coupled with the high-throughput detection capabilities. The enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) are still the most common assays used for the detection of animal pathogens across the globe. However, utilizing the principles of ELISA and PCR, several serological and molecular technologies have been developed to achieve higher sensitivity, rapid, and point-of-care (POC) detection such as lateral flow assays, biosensors, loop-mediated isothermal amplification, recombinase polymerase amplification, and molecular platforms for field-level detection of animal pathogens. Furthermore, animal disease diagnostics need to be updated regularly to capture new, emerging and divergent infectious pathogens, and biotechnological innovations are helpful in fulfilling the rising demand for such diagnostics for the welfare of the society. Therefore, this chapter primarily describes and discusses in detail the serological, molecular, novel high-throughput, and POC assays to detect pathogens affecting farm and companion animals.
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11
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Karunakaran I, Angamuthu A, Gopalan P. Impact of N-(2-aminoethyl) Glycine Unit on Watson-Crick Base Pairs. Z PHYS CHEM 2019. [DOI: 10.1515/zpch-2017-1095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Abstract
We aim to understand the structure and stability of the backbone tailored Watson-Crick base pairs, Guanine-Cytosine (GC), Adenine-Thymine (AT) and Adenine-Uracil (AU) by incorporating N-(2-aminoethyl) glycine units (linked by amide bonds) at the purine and pyrimidine sites of the nucleobases. Density functional theory (DFT) is employed in which B3LYP/6-311++G∗
∗ level of theory has been used to optimize all the structures. The peptide attached base pairs are compared with the natural deoxyribose nucleic acid (DNA)/ribonucleic acid (RNA) base pairs and the calculations are carried out in both the gas and solution phases. The structural propensities of the optimized base pairs are analyzed using base pair geometries, hydrogen bond distances and stabilization energies and, compared with the standard reference data. The structural parameters were found to correlate well with the available data. The addition of peptide chain at the back bone of the DNA/RNA base pairs results only with a minimal distortion and hence does not alter the structural configuration of the base pairs. Also enhanced stability of the base pairs is spotted while adding peptidic chain at the purine site rather than the pyrimidine site of the nucleobases. The stability of the complexes is further interpreted by considering the hydrogen bonded N–H stretching frequencies of the respective base pairs. The discrimination in the interaction energies observed in both gas and solution phases are resulted due to the existence of distinct lowest unoccupied molecular orbitals (LUMO) in the solution phase. The reactivity of the base pairs is also analyzed through the in-depth examinations on the highest occupied molecular orbital (HOMO)-LUMO orbitals.
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Affiliation(s)
- Indumathi Karunakaran
- Department of Physics , PSGR Krishnammal College for Women , Coimbatore 641004, Tamilnadu , India
| | - Abiram Angamuthu
- Department of Physics , Karunya Institute of Technology and Sciences , Coimbatore 641114, Tamilnadu , India
| | - Praveena Gopalan
- Department of Physics , PSGR Krishnammal College for Women , Coimbatore 641004, Tamilnadu , India , Tel.: +91-7812844344
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12
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Tadimety A, Zhang Y, Kready KM, Palinski TJ, Tsongalis GJ, Zhang JXJ. Design of peptide nucleic acid probes on plasmonic gold nanorods for detection of circulating tumor DNA point mutations. Biosens Bioelectron 2019; 130:236-244. [PMID: 30769288 DOI: 10.1016/j.bios.2019.01.045] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/06/2019] [Accepted: 01/19/2019] [Indexed: 01/06/2023]
Abstract
Here we present a gold nanorod-based platform for the sequence-specific detection of circulating tumor DNA (ctDNA) point mutations without the need for amplification or fluorescence labeling. Peptide nucleic acid probes complimentary to the G12V mutation in the KRAS gene were conjugated to gold nanorods, and the localized surface plasmon resonance absorbance through the sample was measured after exposure to synthetic ctDNA at various concentrations. Each step of the reaction was thoroughly controlled, starting from reagent concentrations and including conjugation, sonication, and incubation time. The platform was evaluated in both buffer and spiked healthy patient serum, demonstrating a linear working range below 125 nanograms of ctDNA per milliliter solution, and an effective limit of detection of 2 nanograms of ctDNA per milliliter. A clear distinction between mutant and wild type synthetic ctDNA was also found using this platform. In order to improve upon the selectivity of the sensor, a DNA hybridization simulation was performed to understand how the addition of mutations to the peptide nucleic acid probe could enhance the selectivity for capture of mutant over wild type sequences. The top candidate from the simulations, which had an additional mutation two base pairs away from the mutation of interest, had a significant impact on the selectivity between mutant and wild type capture. This paper provides a framework for sequence-specific capture of ctDNA, and a method of improving selectivity for desired point mutations through careful probe design.
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Affiliation(s)
- Amogha Tadimety
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755, USA
| | - Yichen Zhang
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755, USA
| | - Kasia M Kready
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755, USA
| | - Timothy J Palinski
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755, USA
| | - Gregory J Tsongalis
- Laboratory of Clinical Genomics and Advanced Technology, Department of Pathology and laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH 03766, USA; Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, NH 03766, USA
| | - John X J Zhang
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755, USA; Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, NH 03766, USA.
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13
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Karadeema RJ, Stancescu M, Steidl TP, Bertot SC, Kolpashchikov DM. The owl sensor: a 'fragile' DNA nanostructure for the analysis of single nucleotide variations. NANOSCALE 2018; 10:10116-10122. [PMID: 29781024 DOI: 10.1039/c8nr01107a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Analysis of single nucleotide variations (SNVs) in DNA and RNA sequences is instrumental in healthcare for the detection of genetic and infectious diseases and drug-resistant pathogens. Here we took advantage of the developments in DNA nanotechnology to design a hybridization sensor, named the 'owl sensor', which produces a fluorescence signal only when it complexes with fully complementary DNA or RNA analytes. The novelty of the owl sensor operation is that the selectivity of analyte recognition is, at least in part, determined by the structural rigidity and stability of the entire DNA nanostructure rather than exclusively by the stability of the analyte-probe duplex, as is the case for conventional hybridization probes. Using two DNA and two RNA analytes we demonstrated that owl sensors differentiate SNVs in a wide temperature range of 5 °C-32 °C, a performance unachievable by conventional hybridization probes including the molecular beacon probe. The owl sensor reliably detects cognate analytes even in the presence of 100 times excess of single base mismatched sequences. The approach, therefore, promises to add to the toolbox for the diagnosis of SNVs at ambient temperatures.
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Affiliation(s)
- Rebekah J Karadeema
- Chemistry Department, University of Central Florida, Orlando, FL 32816, USA.
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14
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Askaravi M, Rezatofighi SE, Rastegarzadeh S, Seifi Abad Shapouri MR. Development of a new method based on unmodified gold nanoparticles and peptide nucleic acids for detecting bovine viral diarrhea virus-RNA. AMB Express 2017; 7:137. [PMID: 28655215 PMCID: PMC5484653 DOI: 10.1186/s13568-017-0432-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 06/16/2017] [Indexed: 11/21/2022] Open
Abstract
A simple colorimetric assay is presented for detecting bovine viral diarrhea virus (BVDV)-RNA based on aggregation of gold nanoparticles (AuNPs) in the presence of charge-neutral peptide nucleic acids (PNA). Free charge-neutral PNA oligomers tended to be adsorbed onto AuNPs and act as a coagulant, whereas hybridizing complementary RNA with PNA disrupted PNA-induced AuNP aggregation, and the NPs remained stable. However, non-complementary RNA did not have this effect, and PNA induced aggregation of the AuNPs that resulted in a color change of the reaction from red to blue. The label-free colorimetric assay developed was estimated to have a 10.48 ng/reaction BVDV-RNA detection limit for the visual assay and 1.05 ng/reaction BVDV-RNA using a spectrophotometer. Diagnostic sensitivity and specificity for the assay was in accordance with real-time reverse transcriptase–polymerase chain reaction (RT-PCR) and nested RT-PCR results were 98 and 100%, respectively. Absorption of the 520/620 nm ratio was linear, along with an increase in the target RNA concentration of 1.64–52.4 ng/reaction (R2 = 0.992), which showed a linear correlation for the quantitative assay. This study established a rapid visual label and enzyme-free diagnostic assay for detecting BVDV that is applicable in any clinical laboratory.
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15
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Coarsey CT, Esiobu N, Narayanan R, Pavlovic M, Shafiee H, Asghar W. Strategies in Ebola virus disease (EVD) diagnostics at the point of care. Crit Rev Microbiol 2017; 43:779-798. [PMID: 28440096 PMCID: PMC5653233 DOI: 10.1080/1040841x.2017.1313814] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/21/2016] [Accepted: 03/25/2017] [Indexed: 12/13/2022]
Abstract
Ebola virus disease (EVD) is a devastating, highly infectious illness with a high mortality rate. The disease is endemic to regions of Central and West Africa, where there is limited laboratory infrastructure and trained staff. The recent 2014 West African EVD outbreak has been unprecedented in case numbers and fatalities, and has proven that such regional outbreaks can become a potential threat to global public health, as it became the source for the subsequent transmission events in Spain and the USA. The urgent need for rapid and affordable means of detecting Ebola is crucial to control the spread of EVD and prevent devastating fatalities. Current diagnostic techniques include molecular diagnostics and other serological and antigen detection assays; which can be time-consuming, laboratory-based, often require trained personnel and specialized equipment. In this review, we discuss the various Ebola detection techniques currently in use, and highlight the potential future directions pertinent to the development and adoption of novel point-of-care diagnostic tools. Finally, a case is made for the need to develop novel microfluidic technologies and versatile rapid detection platforms for early detection of EVD.
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Affiliation(s)
- Chad T. Coarsey
- Department of Computer and Electrical Engineering & Computer Science, Florida Atlantic University, Boca Raton, FL, United States
- Asghar-Lab: Micro and Nanotechnology in Medicine, Florida Atlantic University, Boca Raton, FL, United States
| | - Nwadiuto Esiobu
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, United States
| | - Ramswamy Narayanan
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, United States
| | - Mirjana Pavlovic
- Department of Computer and Electrical Engineering & Computer Science, Florida Atlantic University, Boca Raton, FL, United States
| | - Hadi Shafiee
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Waseem Asghar
- Department of Computer and Electrical Engineering & Computer Science, Florida Atlantic University, Boca Raton, FL, United States
- Asghar-Lab: Micro and Nanotechnology in Medicine, Florida Atlantic University, Boca Raton, FL, United States
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, United States
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16
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Nanoelectronic three-dimensional (3D) nanotip sensing array for real-time, sensitive, label-free sequence specific detection of nucleic acids. Biomed Microdevices 2016; 18:7. [PMID: 26780442 DOI: 10.1007/s10544-016-0032-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The improvements in our ability to sequence and genotype DNA have opened up numerous avenues in the understanding of human biology and medicine with various applications, especially in medical diagnostics. But the realization of a label free, real time, high-throughput and low cost biosensing platforms to detect molecular interactions with a high level of sensitivity has been yet stunted due to two factors: one, slow binding kinetics caused by the lack of probe molecules on the sensors and two, limited mass transport due to the planar structure (two-dimensional) of the current biosensors. Here we present a novel three-dimensional (3D), highly sensitive, real-time, inexpensive and label-free nanotip array as a rapid and direct platform to sequence-specific DNA screening. Our nanotip sensors are designed to have a nano sized thin film as their sensing area (~ 20 nm), sandwiched between two sensing electrodes. The tip is then conjugated to a DNA oligonucleotide complementary to the sequence of interest, which is electrochemically detected in real-time via impedance changes upon the formation of a double-stranded helix at the sensor interface. This 3D configuration is specifically designed to improve the biomolecular hit rate and the detection speed. We demonstrate that our nanotip array effectively detects oligonucleotides in a sequence-specific and highly sensitive manner, yielding concentration-dependent impedance change measurements with a target concentration as low as 10 pM and discrimination against even a single mismatch. Notably, our nanotip sensors achieve this accurate, sensitive detection without relying on signal indicators or enhancing molecules like fluorophores. It can also easily be scaled for highly multiplxed detection with up to 5000 sensors/square centimeter, and integrated into microfluidic devices. The versatile, rapid, and sensitive performance of the nanotip array makes it an excellent candidate for point-of-care diagnostics, and high-throughput DNA analysis applications.
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17
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Startsev MA, Ostrowski M, Goldys EM, Inglis DW. A mobility shift assay for DNA detection using nanochannel gradient electrophoresis. Electrophoresis 2016; 38:335-341. [PMID: 27515373 DOI: 10.1002/elps.201600358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 08/02/2016] [Accepted: 08/03/2016] [Indexed: 12/18/2022]
Abstract
Conventional detection of pathogenic or other biological contamination relies on amplification of DNA using sequence-specific primers. Recent work in nanofluidics has shown very high concentration enhancement of biomolecules with some degree of simultaneous separation. This work demonstrates the combination of these two approaches by selectively concentrating a mobility-shifted hybridization product, potentially enabling rapid detection of rare DNA fragments such as highly specific 16S ribosomal DNA. We have performed conductivity gradient electrofocusing within nanofluidic channels and have shown concentration of hybridized peptide nucleic acids and DNA oligomers. We also show selectivity to single base-pair mismatch on 18-mer oligos. This approach may enable sensitive optical detection of small amounts of DNA.
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Affiliation(s)
- Michael A Startsev
- Department of Physics and Astronomy, Macquarie University, Sydney, Australia
| | - Martin Ostrowski
- Department of Chemistry and Bimolecular Sciences, Macquarie University, Sydney, Australia
| | - Ewa M Goldys
- Department of Physics and Astronomy, Macquarie University, Sydney, Australia
| | - David W Inglis
- Department of Engineering, Macquarie University, Sydney, Australia
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18
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Manukyan AK. Development of force field parameters for cyclopentane-modified peptide nucleic acids. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1671-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Silva RM, Pratas D, Castro L, Pinho AJ, Ferreira PJSG. Three minimal sequences found in Ebola virus genomes and absent from human DNA. Bioinformatics 2015; 31:2421-5. [PMID: 25840045 PMCID: PMC4514932 DOI: 10.1093/bioinformatics/btv189] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/27/2015] [Indexed: 01/03/2023] Open
Abstract
Motivation: Ebola virus causes high mortality hemorrhagic fevers, with more than 25 000 cases and 10 000 deaths in the current outbreak. Only experimental therapies are available, thus, novel diagnosis tools and druggable targets are needed. Results: Analysis of Ebola virus genomes from the current outbreak reveals the presence of short DNA sequences that appear nowhere in the human genome. We identify the shortest such sequences with lengths between 12 and 14. Only three absent sequences of length 12 exist and they consistently appear at the same location on two of the Ebola virus proteins, in all Ebola virus genomes, but nowhere in the human genome. The alignment-free method used is able to identify pathogen-specific signatures for quick and precise action against infectious agents, of which the current Ebola virus outbreak provides a compelling example. Availability and Implementation: EAGLE is freely available for non-commercial purposes at http://bioinformatics.ua.pt/software/eagle. Contact:raquelsilva@ua.pt; pratas@ua.pt Supplementary Information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Diogo Pratas
- IEETA and DETI, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | | | - Armando J Pinho
- IEETA and DETI, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Paulo J S G Ferreira
- IEETA and DETI, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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20
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Moccia M, Adamo MFA, Saviano M. Insights on chiral, backbone modified peptide nucleic acids: Properties and biological activity. ARTIFICIAL DNA, PNA & XNA 2014; 5:e1107176. [PMID: 26752710 PMCID: PMC5329900 DOI: 10.1080/1949095x.2015.1107176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 10/02/2015] [Accepted: 10/07/2015] [Indexed: 12/14/2022]
Abstract
PNAs are emerging as useful synthetic devices targeting natural miRNAs. In particular 3 classes of structurally modified PNAs analogs are herein described, namely α, β and γ, which differ by their backbone modification. Their mode and binding affinity for natural nucleic acids and their use in medicinal chemistry as potential miRNA binders is discussed.
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Affiliation(s)
- Maria Moccia
- Consiglio Nazionale delle Ricerche-Institute of Cristallography; Bari, Italy
| | - Mauro F A Adamo
- Centre for Synthesis and Chemical Biology (CSCB); Department of Pharmaceutical & Medicinal Chemistry; Royal College of Surgeons in Ireland; Dublin, Ireland
| | - Michele Saviano
- Consiglio Nazionale delle Ricerche-Institute of Cristallography; Bari, Italy
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21
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Bertucci A, Manicardi A, Candiani A, Giannetti S, Cucinotta A, Spoto G, Konstantaki M, Pissadakis S, Selleri S, Corradini R. Detection of unamplified genomic DNA by a PNA-based microstructured optical fiber (MOF) Bragg-grating optofluidic system. Biosens Bioelectron 2014; 63:248-254. [PMID: 25104434 DOI: 10.1016/j.bios.2014.07.047] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 07/16/2014] [Indexed: 12/22/2022]
Abstract
Microstructured optical fibers containing microchannels and Bragg grating inscribed were internally functionalized with a peptide nucleic acid (PNA) probe specific for a gene tract of the genetically modified Roundup Ready soy. These fibers were used as an optofluidic device for the detection of DNA by measuring the shift in the wavelength of the reflected IR light. Enhancement of optical read-out was obtained using streptavidin coated gold-nanoparticles interacting with the genomic DNA captured in the fiber channels (0%, 0.1%, 1% and 10% RR-Soy), enabling to achieve statistically significant, label-free, and amplification-free detection of target DNA in low concentrations, low percentages, and very low sample volumes. Computer simulations of the fiber optics based on the finite element method (FEM) were consistent with the formation of a layer of organic material with an average thickness of 39 nm for the highest percentage (10% RR soy) analysed.
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Affiliation(s)
- Alessandro Bertucci
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Alex Manicardi
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Alessandro Candiani
- Dipartimento di Ingegneria dell'Informazione, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Sara Giannetti
- Dipartimento di Ingegneria dell'Informazione, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Annamaria Cucinotta
- Dipartimento di Ingegneria dell'Informazione, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Giuseppe Spoto
- Dipartimento di Chimica, Università di Catania, Via Andrea Doria 6, 95125 Catania, Italy
| | - Maria Konstantaki
- Foundation for Research and Technology Hellas (FORTH), Institute of Electronic Structure and Laser (IESL), P.O. Box 1385, Heraklion 71 110, Greece
| | - Stavros Pissadakis
- Foundation for Research and Technology Hellas (FORTH), Institute of Electronic Structure and Laser (IESL), P.O. Box 1385, Heraklion 71 110, Greece
| | - Stefano Selleri
- Dipartimento di Ingegneria dell'Informazione, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Roberto Corradini
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
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22
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Abstract
Nuclear acid testing is more and more used for the diagnosis of infectious diseases. This paper focuses on the use of molecular tools for HIV screening. The term 'screening' will be used under the meaning of first-line HIV molecular techniques performed on a routine basis, which excludes HIV molecular tests designed to confirm or infirm a newly discovered HIV-seropositive patient or other molecular tests performed for the follow-up of HIV-infected patients. The following items are developed successively: i) presentation of the variety of molecular tools used for molecular HIV screening, ii) use of HIV molecular tools for the screening of blood products, iii) use of HIV molecular tools for the screening of organs and tissue from human origin, iv) use of HIV molecular tools in medically assisted procreation and v) use of HIV molecular tools in neonates from HIV-infected mothers.
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Affiliation(s)
- Thomas Bourlet
- Groupe Immunité des Muqueuses et Agents Pathogènes (GIMAP) - EA3064, Faculty of Medicine of Saint-Etienne, 42023, University of Lyon, France
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23
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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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24
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Micklitsch CM, Oquare BY, Zhao C, Appella DH. Cyclopentane-peptide nucleic acids for qualitative, quantitative, and repetitive detection of nucleic acids. Anal Chem 2013; 85:251-7. [PMID: 23214925 PMCID: PMC3535555 DOI: 10.1021/ac3026459] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the development of chemically modified peptide nucleic acids (PNAs) as probes for qualitative and quantitative detection of DNA. The remarkable stability of PNAs toward enzymatic degradation makes this class of molecules ideal to develop as part of a diagnostic device that can be used outside of a laboratory setting. Using an enzyme-linked reporter assay, we demonstrate that excellent levels of detection and accuracy for anthrax DNA can be achieved using PNA probes with suitable chemical components designed into the probe. In addition, we report on DNA-templated cross-linking of PNA probes as a way to preserve genetic information for repetitive and subsequent analysis. This report is the first detailed examination of the qualitative and quantitative properties of chemically modified PNA for nucleic acid detection and provides a platform for studying and optimizing PNA probes prior to incorporation into new technological platforms.
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25
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Atas E, Singer A, Meller A. DNA sequencing and bar-coding using solid-state nanopores. Electrophoresis 2012; 33:3437-47. [PMID: 23109189 DOI: 10.1002/elps.201200266] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 06/29/2012] [Accepted: 06/29/2012] [Indexed: 12/28/2022]
Abstract
Nanopores have emerged as a prominent single-molecule analytic tool with particular promise for genomic applications. In this review, we discuss two potential applications of the nanopore sensors: First, we present a nanopore-based single-molecule DNA sequencing method that utilizes optical detection for massively parallel throughput. Second, we describe a method by which nanopores can be used as single-molecule genotyping tools. For DNA sequencing, the distinction among the four types of DNA nucleobases is achieved by employing a biochemical procedure for DNA expansion. In this approach, each nucleobase in each DNA strand is converted into one of four predefined unique 16-mers in a process that preserves the nucleobase sequence. The resulting converted strands are then hybridized to a library of four molecular beacons, each carrying a unique fluorophore tag, that are perfect complements to the 16-mers used for conversion. Solid-state nanopores are then used to sequentially remove these beacons, one after the other, leading to a series of photon bursts in four colors that can be optically detected. Single-molecule genotyping is achieved by tagging the DNA fragments with γ-modified synthetic peptide nucleic acid probes coupled to an electronic characterization of the complexes using solid-state nanopores. This method can be used to identify and differentiate genes with a high level of sequence similarity at the single-molecule level, but different pathology or response to treatment. We will illustrate this method by differentiating the pol gene for two highly similar human immunodeficiency virus subtypes, paving the way for a novel diagnostics platform for viral classification.
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Affiliation(s)
- Evrim Atas
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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26
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Manicardi A, Accetta A, Tedeschi T, Sforza S, Marchelli R, Corradini R. PNA bearing 5-azidomethyluracil: a novel approach for solid and solution phase modification. ARTIFICIAL DNA, PNA & XNA 2012; 3:53-62. [PMID: 22772040 PMCID: PMC3429531 DOI: 10.4161/adna.20158] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Fmoc- and Boc-protected modified monomers bearing 5-azidomethyluracil nucleobase were synthesized. Four different solid-phase synthetic strategies were tested in order to evaluate the application of this series of monomers for the solid-phase synthesis of modified PNA. The azide was used as masked amine for the introduction of amide-linked functional groups, allowing the production of a library of compounds starting from a single modified monomer. The azide function was also exploited as reactive group for the modification of PNA in solution via azide-alkyne click cycloaddition.
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Affiliation(s)
- Alex Manicardi
- Dipartimento di Chimica Organica e Industriale, Università di Parma, Parma, Italy.
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27
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Singer A, Rapireddy S, Ly DH, Meller A. Electronic barcoding of a viral gene at the single-molecule level. NANO LETTERS 2012; 12:1722-8. [PMID: 22352964 PMCID: PMC3572535 DOI: 10.1021/nl300372a] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
A new single-molecule approach for rapid and purely electronic discrimination among similar genes is presented. Combining solid-state nanopores and γ-modified synthetic peptide nucleic acid probes, we accurately barcode genes by counting the number of probes attached to each gene and measuring their relative spacing. We illustrate our method by sensing individual genes from two highly similar human immunodeficiency virus subtypes, demonstrating feasibility of a novel, single-molecule diagnostic platform for rapid pathogen classification.
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Affiliation(s)
- Alon Singer
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215
| | - Srinivas Rapireddy
- Department of Chemistry, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213
| | - Danith H. Ly
- Department of Chemistry, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213
| | - Amit Meller
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215
- Corresponding author.
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28
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Toth PP. Antisense therapy and emerging applications for the management of dyslipidemia. J Clin Lipidol 2011; 5:441-9. [PMID: 22108147 DOI: 10.1016/j.jacl.2011.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 08/10/2011] [Accepted: 08/17/2011] [Indexed: 10/17/2022]
Abstract
BACKGROUND Because a significant percentage of patients who require high-dose statin therapy for dyslipidemia experience treatment-related muscle symptoms and an inconsistent clinical response, alternative or adjunctive approaches to the management of dyslipidemia are needed. One alternative approach, antisense therapy, may offer an effective and well-tolerated option for patients not satisfactorily responsive to or intolerant to standard pharmacologic dyslipidemia therapies. OBJECTIVE This review provides an overview of antisense technology and its potential role in the management of dyslipidemia. METHODS Source material was obtained primarily from the published literature identified through a search of the PubMed database. RESULTS Antisense technology is an evolving approach to therapy that has gone through a series of refinements to enhance molecular stability, potency, and tolerability. Mipomersen is an antisense molecule capable of producing clinically meaningful reductions in low-density lipoprotein cholesterol in patients with severe familial hypercholesterolemia. Further long-term clinical studies are required to more clearly quantify its impact on risk for cardiovascular events and establish whether it increases risk for hepatosteatosis. CONCLUSION Antisense therapy represents a potentially effective and well-tolerated emerging treatment modality for numerous diseases. In the treatment of hypercholesterolemia, the antisense therapy mipomersen may provide a possible treatment option for patients with treatment-resistant dyslipidemia.
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Affiliation(s)
- Peter P Toth
- Department of Preventive Cardiology, CGH Medical Center, Sterling, IL, USA.
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