Towards a Real-Time, Label-Free, Diamond-Based DNA Sensor
Most challenging in the development of DNA sensors is the ability to distinguish between fully complementary target ssDNA (single-strand DNA) and 1-mismatch ssDNA. To deal with this problem, we performed impedance spectroscopy on DNA-functionalized nanocrystalline diamond (NCD) layers during hybridi...
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Veröffentlicht in: | Langmuir 2007-12, Vol.23 (26), p.13193-13202 |
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creator | Vermeeren, V. Bijnens, N. Wenmackers, S. Daenen, M. Haenen, K. Williams, O. A. Ameloot, M. vandeVen, M. Wagner, P. Michiels, L. |
description | Most challenging in the development of DNA sensors is the ability to distinguish between fully complementary target ssDNA (single-strand DNA) and 1-mismatch ssDNA. To deal with this problem, we performed impedance spectroscopy on DNA-functionalized nanocrystalline diamond (NCD) layers during hybridization and denaturation. In both reactions, a difference in behavior was observed for 1-mismatch target DNA and complementary target DNA in real-time. During real-time hybridization, a decrease of the impedance was observed at lower frequencies when the complementary target DNA was added, while the addition of 1-mismatch target ssDNA caused no significant change. Fitting these results to an electrical circuit demonstrates that this is correlated with a decrease of the depletion zone in the space charge region of the diamond. During real-time denaturation, differentiation between 1-mismatch and complementary target DNA was possible at higher frequencies. Denaturation of complementary DNA showed the longest exponential decay time of the impedance, while the decay time during 1-mismatch denaturation was the shortest. The real-time hybridization and denaturation experiments were carried out on different NCD samples in various buffer solutions at temperatures between 20 and 80 °C. It was revealed that the best results were obtained using a Microhyb hybridization buffer at 80 °C and 10× PCR buffer at 30 °C for hybridization and 0.1 M NaOH at temperatures above 40 °C for denaturation. We demonstrate that the combination of real-time hybridization spectra and real-time denaturation spectra yield important information on the type of target. This approach may allow a reliable identification of the mismatch sequence, which is the most biologically relevant. |
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Fitting these results to an electrical circuit demonstrates that this is correlated with a decrease of the depletion zone in the space charge region of the diamond. During real-time denaturation, differentiation between 1-mismatch and complementary target DNA was possible at higher frequencies. Denaturation of complementary DNA showed the longest exponential decay time of the impedance, while the decay time during 1-mismatch denaturation was the shortest. The real-time hybridization and denaturation experiments were carried out on different NCD samples in various buffer solutions at temperatures between 20 and 80 °C. It was revealed that the best results were obtained using a Microhyb hybridization buffer at 80 °C and 10× PCR buffer at 30 °C for hybridization and 0.1 M NaOH at temperatures above 40 °C for denaturation. We demonstrate that the combination of real-time hybridization spectra and real-time denaturation spectra yield important information on the type of target. 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A.</creatorcontrib><creatorcontrib>Ameloot, M.</creatorcontrib><creatorcontrib>vandeVen, M.</creatorcontrib><creatorcontrib>Wagner, P.</creatorcontrib><creatorcontrib>Michiels, L.</creatorcontrib><title>Towards a Real-Time, Label-Free, Diamond-Based DNA Sensor</title><title>Langmuir</title><addtitle>Langmuir</addtitle><description>Most challenging in the development of DNA sensors is the ability to distinguish between fully complementary target ssDNA (single-strand DNA) and 1-mismatch ssDNA. To deal with this problem, we performed impedance spectroscopy on DNA-functionalized nanocrystalline diamond (NCD) layers during hybridization and denaturation. In both reactions, a difference in behavior was observed for 1-mismatch target DNA and complementary target DNA in real-time. During real-time hybridization, a decrease of the impedance was observed at lower frequencies when the complementary target DNA was added, while the addition of 1-mismatch target ssDNA caused no significant change. Fitting these results to an electrical circuit demonstrates that this is correlated with a decrease of the depletion zone in the space charge region of the diamond. During real-time denaturation, differentiation between 1-mismatch and complementary target DNA was possible at higher frequencies. Denaturation of complementary DNA showed the longest exponential decay time of the impedance, while the decay time during 1-mismatch denaturation was the shortest. The real-time hybridization and denaturation experiments were carried out on different NCD samples in various buffer solutions at temperatures between 20 and 80 °C. It was revealed that the best results were obtained using a Microhyb hybridization buffer at 80 °C and 10× PCR buffer at 30 °C for hybridization and 0.1 M NaOH at temperatures above 40 °C for denaturation. We demonstrate that the combination of real-time hybridization spectra and real-time denaturation spectra yield important information on the type of target. This approach may allow a reliable identification of the mismatch sequence, which is the most biologically relevant.</description><subject>Base Sequence</subject><subject>Biosensing Techniques</subject><subject>Chemistry</subject><subject>Colloidal state and disperse state</subject><subject>Diamond - chemistry</subject><subject>DNA - analysis</subject><subject>DNA Probes</subject><subject>Exact sciences and technology</subject><subject>General and physical chemistry</subject><subject>Microscopy, Electron, Scanning</subject><subject>Nucleic Acid Denaturation</subject><subject>Nucleic Acid Hybridization</subject><subject>Surface physical chemistry</subject><issn>0743-7463</issn><issn>1520-5827</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp90E1rFEEQBuBGFLNGD_4BmYuKYJv-mv44JtlEA0sMZvTa1HRXw8T5SLp30fx7J-ySvUhOVVAPL8VLyFvOvnAm-FEPZh5KxmdkwWvBaG2FeU4WzChJjdLygLwq5YYx5qRyL8kBt4wp68SCuGb6AzmWCqofCD1tugE_VytosafnGed92cEwjZGeQMFYLS-Pq2scy5RfkxcJ-oJvdvOQ_Dw_a06_0dX3rxenxysKiss15TbqYIUQmKROqJRJWttWh5gCqAimTQyBiWQTVwlbpyFaWQdnhLACkjwkH7e5t3m622BZ-6ErAfseRpw2xZta1UorY2f54UmpHatroeQMP21hyFMpGZO_zd0A-d5z5h8a9Y-NzvbdLnTTDhj3clfhDN7vAJQAfcowhq7snXNCafbwHd26rqzx7-Md8m-vjTS1b66u5215-etk2fhmnwuh-Jtpk8e55f88-A9nJZYE</recordid><startdate>20071218</startdate><enddate>20071218</enddate><creator>Vermeeren, V.</creator><creator>Bijnens, N.</creator><creator>Wenmackers, S.</creator><creator>Daenen, M.</creator><creator>Haenen, K.</creator><creator>Williams, O. A.</creator><creator>Ameloot, M.</creator><creator>vandeVen, M.</creator><creator>Wagner, P.</creator><creator>Michiels, L.</creator><general>American Chemical Society</general><scope>BSCLL</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7TM</scope></search><sort><creationdate>20071218</creationdate><title>Towards a Real-Time, Label-Free, Diamond-Based DNA Sensor</title><author>Vermeeren, V. ; Bijnens, N. ; Wenmackers, S. ; Daenen, M. ; Haenen, K. ; Williams, O. 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A.</au><au>Ameloot, M.</au><au>vandeVen, M.</au><au>Wagner, P.</au><au>Michiels, L.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Towards a Real-Time, Label-Free, Diamond-Based DNA Sensor</atitle><jtitle>Langmuir</jtitle><addtitle>Langmuir</addtitle><date>2007-12-18</date><risdate>2007</risdate><volume>23</volume><issue>26</issue><spage>13193</spage><epage>13202</epage><pages>13193-13202</pages><issn>0743-7463</issn><eissn>1520-5827</eissn><coden>LANGD5</coden><abstract>Most challenging in the development of DNA sensors is the ability to distinguish between fully complementary target ssDNA (single-strand DNA) and 1-mismatch ssDNA. To deal with this problem, we performed impedance spectroscopy on DNA-functionalized nanocrystalline diamond (NCD) layers during hybridization and denaturation. In both reactions, a difference in behavior was observed for 1-mismatch target DNA and complementary target DNA in real-time. During real-time hybridization, a decrease of the impedance was observed at lower frequencies when the complementary target DNA was added, while the addition of 1-mismatch target ssDNA caused no significant change. Fitting these results to an electrical circuit demonstrates that this is correlated with a decrease of the depletion zone in the space charge region of the diamond. During real-time denaturation, differentiation between 1-mismatch and complementary target DNA was possible at higher frequencies. Denaturation of complementary DNA showed the longest exponential decay time of the impedance, while the decay time during 1-mismatch denaturation was the shortest. The real-time hybridization and denaturation experiments were carried out on different NCD samples in various buffer solutions at temperatures between 20 and 80 °C. It was revealed that the best results were obtained using a Microhyb hybridization buffer at 80 °C and 10× PCR buffer at 30 °C for hybridization and 0.1 M NaOH at temperatures above 40 °C for denaturation. We demonstrate that the combination of real-time hybridization spectra and real-time denaturation spectra yield important information on the type of target. This approach may allow a reliable identification of the mismatch sequence, which is the most biologically relevant.</abstract><cop>Washington, DC</cop><pub>American Chemical Society</pub><pmid>18004892</pmid><doi>10.1021/la702143d</doi><tpages>10</tpages></addata></record> |
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subjects | Base Sequence Biosensing Techniques Chemistry Colloidal state and disperse state Diamond - chemistry DNA - analysis DNA Probes Exact sciences and technology General and physical chemistry Microscopy, Electron, Scanning Nucleic Acid Denaturation Nucleic Acid Hybridization Surface physical chemistry |
title | Towards a Real-Time, Label-Free, Diamond-Based DNA Sensor |
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