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Feng C, Liu X, Sun YF, Ren CL. Double-Stranded DNA Immobilized in Lying-Flat and Upright Orientation on a PNIPAm-Coated Surface: A Theoretical Study. ACS Macro Lett 2024:105-111. [PMID: 38190547 DOI: 10.1021/acsmacrolett.3c00647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Surface-immobilized double-stranded DNA (dsDNA) in upright orientation plays an important role in optimizing and understanding DNA-based nanosensors and nanodevices. However, it is difficult to regulate the surface density of upright DNA due to the fact that DNA usually stands vertically at a high packing density but may lie down at a low packing density. We herein report dsDNA immobilized in upright orientation on a poly(N-isopropylacrylamide) (PNIPAm)-coated surface in theory. The theoretical results reveal that the angle of upright DNA relative to the surface is larger than that of DNA immobilized on the bare surface caused by the lying-flat DNA under proper PNIPAm surface coverage at 45 °C. The surface density of upright DNA is significantly influenced by DNA concentration and DNA length. It is envisioned that the density-regulated DNA molecules immobilized in upright orientation in the present work are well suited to bottom-up construction of complex DNA-based nanostructures and nanodevices.
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Affiliation(s)
- Chao Feng
- State Key Laboratory of Metastable Materials Science & Technology and Hebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University, Qinhuangdao 066004, China
| | - Xiao Liu
- State Key Laboratory of Metastable Materials Science & Technology and Hebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University, Qinhuangdao 066004, China
| | - Yang-Feng Sun
- Industrial Technology Center, Chengde Petroleum College, Chengde 067000, China
| | - Chun-Lai Ren
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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2
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Ansari MH, Hassan S, Qurashi A, Khanday FA. Microfluidic-integrated DNA nanobiosensors. Biosens Bioelectron 2016; 85:247-260. [DOI: 10.1016/j.bios.2016.05.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/02/2016] [Accepted: 05/02/2016] [Indexed: 11/28/2022]
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3
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Su Q, Nöll G. A sandwich-like strategy for the label-free detection of oligonucleotides by surface plasmon fluorescence spectroscopy (SPFS). Analyst 2016; 141:5784-5791. [PMID: 27484040 PMCID: PMC5166564 DOI: 10.1039/c6an01129b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cutting surface-bound optical molecular beacons results in a sandwich-like detection strategy with lower background fluorescence.
For the detection of oligonucleotides a sandwich-like detection strategy has been developed by which the background fluorescence is significantly lowered in comparison with surface-bound molecular beacons. Surface bound optical molecular beacons are DNA hairpin structures comprising a stem and a loop. The end of the stem is modified with a fluorophore and a thiol anchor for chemisorption on gold surfaces. In the closed state the fluorophore is in close proximity to the gold surface, and most of the fluorescence is quenched. After hybridization with a target the hairpin opens, the fluorophore and surface become separated, and the fluorescence drastically increases. Using this detection method the sensitivity is limited by the difference in the fluorescence intensity in the closed and open state. As the background fluorescence is mainly caused by non-quenched fluorophores, a strategy to reduce the background fluorescence is to cut the beacon in two halves. First a thiolated ssDNA capture probe strand (first half) is chemisorbed to a gold surface together with relatively short thiol spacers. Next the target is hybridized by one end to the surface-anchored capture probe and by the other to a fluorophore-labeled reporter probe DNA (second half). The signal readout is done by surface plasmon fluorescence spectroscopy (SPFS). Using this detection strategy the background fluorescence can be significantly lowered, and the detection limit is lowered by more than one order of magnitude. The detection of a target takes only a few minutes and the sensor chips can be used for multiple detection steps without a significant decrease in performance.
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Affiliation(s)
- Qiang Su
- Nöll Junior Research Group, Organic Chemistry, Chem. Biol. Dept., Faculty IV, Siegen University, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
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4
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Flaender M, Costa G, Nonglaton G, Saint-Pierre C, Gasparutto D. A DNA array based on clickable lesion-containing hairpin probes for multiplexed detection of base excision repair activities. Analyst 2016; 141:6208-6216. [DOI: 10.1039/c6an01165a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An electrophoresis-free fluorescent functional assay has been developed to measure DNA repair activities in a miniaturized and parallelized manner.
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Affiliation(s)
- Mélanie Flaender
- Université Grenoble Alpes
- INAC – SyMMES/CEA
- F-38000 Grenoble
- France
| | - Guillaume Costa
- Université Grenoble Alpes
- LETI/DTBS-SBSC/CEA
- F-38000 Grenoble
- France
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5
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Zhang X, Daaboul GG, Spuhler PS, Freedman DS, Yurt A, Ahn S, Avci O, Ünlü MS. Nanoscale characterization of DNA conformation using dual-color fluorescence axial localization and label-free biosensing. Analyst 2015; 139:6440-9. [PMID: 25340741 DOI: 10.1039/c4an01425a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantitative determination of the density and conformation of DNA molecules tethered to the surface can help optimize and understand DNA nanosensors and nanodevices, which use conformational or motional changes of surface-immobilized DNA for detection or actuation. We present an interferometric sensing platform that combines (i) dual-color fluorescence spectroscopy for precise axial co-localization of two fluorophores attached at different nucleotides of surface-immobilized DNA molecules and (ii) independent label-free quantification of biomolecule surface density at the same site. Using this platform, we examined the conformation of DNA molecules immobilized on a three-dimensional polymeric surface and demonstrated simultaneous detection of DNA conformational change and binding in real-time. These results demonstrate that independent quantification of both surface density and molecular nanoscale conformation constitutes a versatile approach for nanoscale solid-biochemical interface investigations and molecular binding assays.
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Affiliation(s)
- Xirui Zhang
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA.
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6
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Nöll G, Su Q, Heidel B, Yu Y. A reusable sensor for the label-free detection of specific oligonucleotides by surface plasmon fluorescence spectroscopy. Adv Healthc Mater 2014; 3:42-6. [PMID: 23788367 DOI: 10.1002/adhm.201300056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 03/19/2013] [Indexed: 01/07/2023]
Abstract
The development of a reusable molecular beacon (MB)-based sensor for the label-free detection of specific oligonucleotides using surface plasmon fluorescence spectroscopy (SPFS) as the readout method is described. The MBs are chemisorbed at planar gold surfaces serving as fluorescence quenching units. Target oligonucleotides of 24 bases can be detected within a few minutes at high single-mismatch discrimination rates.
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Affiliation(s)
- Gilbert Nöll
- Nöll Junior Research Group for Nanotechnology, Siegen University, Faculty IV, Department of Chemistry-Biology, Organic Chemistry, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
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7
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Abi A, Ferapontova EE. Electroanalysis of single-nucleotide polymorphism by hairpin DNA architectures. Anal Bioanal Chem 2012; 405:3693-703. [PMID: 23263518 DOI: 10.1007/s00216-012-6633-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/27/2012] [Accepted: 12/06/2012] [Indexed: 12/21/2022]
Abstract
Genetic analysis of infectious and genetic diseases and cancer diagnostics require the development of efficient tools for fast and reliable analysis of single-nucleotide polymorphism (SNP) in targeted DNA and RNA sequences often responsible for signalling disease onset. Here, we highlight the main trends in the development of electrochemical genosensors for sensitive and selective detection of SNP that are based on hairpin DNA architectures exhibiting better SNP recognition properties compared with linear DNA probes. SNP detection by electrochemical hairpin DNA beacons is discussed, and comparative analysis of the existing SNP sensing strategies based on enzymatic and nanoparticle signal amplification schemes is presented.
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Affiliation(s)
- Alireza Abi
- Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 1590-14, 8000 Aarhus C, Denmark
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8
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Peng HI, Strohsahl CM, Miller BL. Microfluidic nanoplasmonic-enabled device for multiplex DNA detection. LAB ON A CHIP 2012; 12:1089-1093. [PMID: 22301735 DOI: 10.1039/c2lc21114a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We describe a rapid, quantitative, multiplex, self-labelled, and real-time DNA biosensor employing Ag nanoparticle-bound DNA hairpin probes immobilized in a microfluidic channel. Capture of complementary target DNAs by the microarrayed DNA hairpin probes results in a positive fluorescence signal via a conformational change of the probe molecules, signalling the presence of target DNAs. The device's capability for quantitative analyses was evaluated and a detection time as low as 6 min (with a target flow rate of 0.5 μl min(-1)) was sufficient to generate significant detection signals. This detection time translates to merely 3 μl of target solution consumption. An unoptimized sensitivity of 500 pM was demonstrated for this device.
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Affiliation(s)
- Hsin-I Peng
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14627, USA
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9
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Adams NM, Jackson SR, Haselton FR, Wright DW. Design, synthesis, and characterization of nucleic-acid-functionalized gold surfaces for biomarker detection. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:1068-82. [PMID: 21905721 PMCID: PMC4211628 DOI: 10.1021/la2028862] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nucleic-acid-functionalized gold surfaces have been used extensively for the development of biological sensors. The development of an effective biomarker detection assay requires careful design, synthesis, and characterization of probe components. In this Feature Article, we describe fundamental probe development constraints and provide a critical appraisal of the current methodologies and applications in the field. We discuss critical issues and obstacles that impede the sensitivity and reliability of the sensors to underscore the challenges that must be met to advance the field of biomarker detection.
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Affiliation(s)
- Nicholas M. Adams
- VU Station B 351822, Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA. VU Station B 351631, Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Stephen R. Jackson
- VU Station B 351822, Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Frederick R. Haselton
- VU Station B 351631, Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
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10
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Huang K, Martí AA. Recent trends in molecular beacon design and applications. Anal Bioanal Chem 2011; 402:3091-102. [PMID: 22159461 DOI: 10.1007/s00216-011-5570-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 12/26/2022]
Abstract
A molecular beacon (MB) is a hairpin-structured oligonucleotide probe containing a photoluminescent species (PLS) and a quencher at different ends of the strand. In a recognition and detection process, the hybridization of MBs with target DNA sequences restores the strong photoluminescence, which is quenched before hybridization. Making better MBs involves reducing the background photoluminescence and increasing the brightness of the PLS, which therefore involves the development of new PLS and quenchers, as well as innovative PLS-quencher systems. Heavy-metal complexes, nanocrystals, pyrene compounds, and other materials with excellent photophysical properties have been applied as PLS of MBs. Nanoparticles, nanowires, graphene, metal films, and many other media have also been introduced to quench photoluminescence. On the basis of their high specificity, selectivity, and sensitivity, MBs are developed as a general platform for sensing, producing, and carrying molecules other than oligonucleotides.
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Affiliation(s)
- Kewei Huang
- Department of Chemistry, Rice University, 6100 South Main Street, Houston, TX 77005, USA
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11
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Pei H, Lu N, Wen Y, Song S, Liu Y, Yan H, Fan C. A DNA nanostructure-based biomolecular probe carrier platform for electrochemical biosensing. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2010; 22:4754-8. [PMID: 20839255 PMCID: PMC3071359 DOI: 10.1002/adma.201002767] [Citation(s) in RCA: 410] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Affiliation(s)
- Hao Pei
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 (P. R. China)
| | - Na Lu
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 (P. R. China)
| | - Yanli Wen
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 (P. R. China)
| | - Shiping Song
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 (P. R. China)
| | - Yan Liu
- Department of Chemistry and Biochemistry & The Biodesign Institute, Arizona State University, Tempe, AZ (USA)
| | - Hao Yan
- Department of Chemistry and Biochemistry & The Biodesign Institute, Arizona State University, Tempe, AZ (USA)
| | - Chunhai Fan
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 (P. R. China)
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12
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Peng HI, Krauss TD, Miller BL. Aging induced Ag nanoparticle rearrangement under ambient atmosphere and consequences for nanoparticle-enhanced DNA biosensing. Anal Chem 2010; 82:8664-70. [PMID: 20857925 PMCID: PMC3021774 DOI: 10.1021/ac101919h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Localized surface plasmons of metallic nanoparticles can strongly amplify the magnitude of the surrounding electric field. This in turn enhances fluorescence from nearby fluorophores. However, little is known regarding how time-dependent changes in nanoparticle structure due to exposure to the ambient environment affect their behavior in plasmonic devices. Here, we report the interesting finding that the aging of a nanostructured Ag substrate in ambient atmosphere markedly improves the fluorescence signal of a plasmonic-based DNA detection system. The effect can be observed with an exposure time as short as two days, and a nearly 17-fold signal enhancement can be achieved with 30 days of aging. Analysis of substrate surface topography by atomic force microscopy (AFM) reveals a substantial change in nanoparticle morphology as the substrates age despite being covalently attached to a solid dry substrate. Nanoparticle morphological changes also manifest in extinction spectra. This process can be further accelerated by light. Together, our findings address the important question of Ag nanoparticle stability over time and its potential ramifications for plasmon-enabled sensors. They also imply that nanoparticle aging may be used strategically to tune nanoparticle size and geometry and plasmon spectrum, which may be beneficial for studies on plasmonics as well as sensor optimization.
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Affiliation(s)
- Hsin-I Peng
- Department of Biomedical Engineering, University of Rochester, Rochester, New York 14627, USA
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13
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Song S, Liang Z, Zhang J, Wang L, Li G, Fan C. Gold-nanoparticle-based multicolor nanobeacons for sequence-specific DNA analysis. Angew Chem Int Ed Engl 2010; 48:8670-4. [PMID: 19731289 DOI: 10.1002/anie.200901887] [Citation(s) in RCA: 352] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shiping Song
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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14
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Song S, Liang Z, Zhang J, Wang L, Li G, Fan C. Gold-Nanoparticle-Based Multicolor Nanobeacons for Sequence-Specific DNA Analysis. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200901887] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Zubtsova ZI, Zubtsov DA, Savvateeva EN, Stomakhin AA, Chechetkin VR, Zasedatelev AS, Rubina AY. Hydrogel-based protein and oligonucleotide microchips on metal-coated surfaces: enhancement of fluorescence and optimization of immunoassay. J Biotechnol 2009; 144:151-9. [PMID: 19770011 DOI: 10.1016/j.jbiotec.2009.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 08/27/2009] [Accepted: 09/11/2009] [Indexed: 10/20/2022]
Abstract
Manufacturing of hydrogel-based microchips on metal-coated substrates significantly enhances fluorescent signals upon binding of labeled target molecules. This observation holds true for both oligonucleotide and protein microchips. When Cy5 is used as fluorophore, this enhancement is 8-10-fold in hemispherical gel elements and 4-5-fold in flattened gel pads, as compared with similar microchips manufactured on uncoated glass slides. The effect also depends on the hydrophobicity of metal-coated substrate and on the presence of a layer of liquid over the gel pads. The extent of enhancement is insensitive to the nature of formed complexes and immobilized probes and remains linear within a wide range of fluorescence intensities. Manufacturing of gel-based protein microarrays on metal-coated substrates improves their sensitivity using the same incubation time for immunoassay. Sandwich immunoassay using these microchips allows shortening the incubation time without loss of sensitivity. Unlike microchips with probes immobilized directly on a surface, for which the plasmon mechanism is considered responsible for metal-enhanced fluorescence, the enhancement effect observed using hydrogel-based microchips on metal-coated substrates might be explained within the framework of geometric optics.
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Affiliation(s)
- Zh I Zubtsova
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, Russia.
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16
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Zubtsova ZI, Filippova MA, Savvateeva EN, Zubtsov DA, Chechetkin VR, Grishin EV, Zasedatelev AS, Rubina AY. Fluorescence signal amplification on the gel biochips with a mirror surface and optimization of immunoassay procedure. DOKL BIOCHEM BIOPHYS 2009; 427:171-4. [DOI: 10.1134/s1607672909040012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Peng HI, Strohsahl CM, Leach KE, Krauss TD, Miller BL. Label-free DNA detection on nanostructured Ag surfaces. ACS NANO 2009; 3:2265-2273. [PMID: 19585997 DOI: 10.1021/nn900112e] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The dramatic local electric-field enhancement property of Ag nanoparticles was used as the basis to significantly increase the signal output of a novel label-free (or "self-labeled") fluorescence-based DNA detection system. In response to identical amounts of analyte, nanostructured Ag substrates provided a posthybridization fluorescent sensor response over 10-fold larger than the response from planar Au substrates. Detection performance strongly depended upon the Ag substrate roughness. Consistent with work by others on metal-enhanced fluorescence, fluorescence intensity also depended strongly on the distance between the fluorophore and the Ag substrate surface. Adjusting the surface roughness, amount of the Ag deposited on the surface, and the DNA probe length allowed for production of an optimized response. In addition to constituting a novel label-free DNA sensor, we anticipate that these structures will provide a unique platform for testing concepts in plasmonics.
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Affiliation(s)
- Hsin-I Peng
- Department of Biomedical Engineering, University of Rochester, Rochester, New York 14627, USA
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18
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Misra A, Shahid M. Immobilization of self-quenched DNA hairpin probe with a heterobifunctional reagent on a glass surface for sensitive detection of oligonucleotides. Bioorg Med Chem 2009; 17:5826-33. [PMID: 19632849 DOI: 10.1016/j.bmc.2009.07.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 07/03/2009] [Accepted: 07/07/2009] [Indexed: 01/05/2023]
Abstract
A new sensitive method for the detection of nucleic acids on a glass surface has been described. The self-quenched DNA hairpin probe is immobilized on a glass surface utilizing heterobifunctional reagent, N-(3-triethoxysilylpropyl)-4-(isothiocyanatomethyl)-cyclohexane-1-carboxamide (TPICC). In the closed state fluorescence intensity was quenched due to the presence of guanosine residues in close vicinity of fluorophore while on hybridization with perfectly matched complementary target strand fluorescence was restored. Efficiency and specificity of immobilization as well as thermal stability at variable temperature and pH conditions have been discussed in detail. The method employed has potential for the detection of single nucleotide variations and other diagnostic studies.
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Affiliation(s)
- Arvind Misra
- Department of Chemistry, Banaras Hindu University, Varanasi, India.
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19
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Kenward M, Dorfman KD. Brownian dynamics simulations of single-stranded DNA hairpins. J Chem Phys 2009; 130:095101. [PMID: 19275427 DOI: 10.1063/1.3078795] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a Brownian dynamics model which we use to study the kinetics and thermodynamics of single-stranded DNA hairpins, gaining insights into the role of stem mismatches and the kinetics rates underlying the melting transition. The model is a base-backbone type in which the DNA bases and sugar-phosphate backbone are represented as single units (beads) in the context of the Brownian dynamics simulations. We employ a minimal number of bead-bead interactions, leading to a simple computational scheme. To demonstrate the veracity of our model for DNA hairpins, we show that the model correctly captures the effects of base stacking, hydrogen bonding, and temperature on both the thermodynamics and the kinetics of hairpin formation and melting. When cast in dimensionless form, the thermodynamic results obtained from the present model compare favorably with default predictions of the m-fold server, although the present model is not sufficiently robust to provide dimensional results. The kinetic data at low temperatures indicate frequent but short-lived opening events, consistent with the measured chain end-to-end probability distribution. The model is also used to study the effect of base mismatches in the stem of the hairpin. With the parameters used here, the model overpredicts the relative shift in the melting temperature due to mismatches. The melting transition can be primarily attributed to a rapid increase in the hairpin opening rate rather than an equivalent decrease in the closing rate, in agreement with single-molecule experimental data.
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Affiliation(s)
- Martin Kenward
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, USA.
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20
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Russ Algar W, Massey M, Krull UJ. The application of quantum dots, gold nanoparticles and molecular switches to optical nucleic-acid diagnostics. Trends Analyt Chem 2009. [DOI: 10.1016/j.trac.2008.11.012] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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