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Solid-state, dye-labeled DNA detects volatile compounds in the vapor phase.

White J, Truesdell K, Williams LB, Atkisson MS, Kauer JS - PLoS Biol. (2008)

Bottom Line: In designing biomimetic artificial noses, the challenge has been to generate a similarly large sensor repertoire that can be manufactured with exact chemical precision and reproducibility and that has the requisite combinatorial complexity to detect odors in the real world.These new solid-state DNA-based sensors are sensitive and show differential, sequence-dependent responses.Furthermore, we show that large DNA-based sensor libraries can be rapidly screened for odor response diversity using standard high-throughput microarray methods.

View Article: PubMed Central - PubMed

Affiliation: Department of Neuroscience, Tufts University School of Medicine, Boston, Massachusetts, United States of America. joel.white@cogniscentinc.com

ABSTRACT
This paper demonstrates a previously unreported property of deoxyribonucleic acid-the ability of dye-labeled, solid-state DNA dried onto a surface to detect odors delivered in the vapor phase by changes in fluorescence. This property is useful for engineering systems to detect volatiles and provides a way for artificial sensors to emulate the way cross-reactive olfactory receptors respond to and encode single odorous compounds and mixtures. Recent studies show that the vertebrate olfactory receptor repertoire arises from an unusually large gene family and that the receptor types that have been tested so far show variable breadths of response. In designing biomimetic artificial noses, the challenge has been to generate a similarly large sensor repertoire that can be manufactured with exact chemical precision and reproducibility and that has the requisite combinatorial complexity to detect odors in the real world. Here we describe an approach for generating and screening large, diverse libraries of defined sensors using single-stranded, fluorescent dye-labeled DNA that has been dried onto a substrate and pulsed with brief exposures to different odors. These new solid-state DNA-based sensors are sensitive and show differential, sequence-dependent responses. Furthermore, we show that large DNA-based sensor libraries can be rapidly screened for odor response diversity using standard high-throughput microarray methods. These observations describe new properties of DNA and provide a generalized approach for producing explicitly tailored sensor arrays that can be rationally chosen for the detection of target volatiles with different chemical structures that include biologically derived odors, toxic chemicals, and explosives.

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Changes in Fluorescence from ssDNA and OliGreen Dye Sensors during Short Odor Sniffs(A) Responses of a sensor made from OliGreen alone.(B) Responses of a sensor made from 20 μl of 10 μM oligomer SEQ01, stained with OliGreen.(C) Responses from SEQ01 to 10 repeated applications of 10−1 propionic acid (∼390 ppm), demonstrating return to baseline between sniffs. These 10 responses were used to calculate the mean shown in (B). See Figure 1 for details of odor presentation, odor dilutions, and description of data representation.
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pbio-0060009-g002: Changes in Fluorescence from ssDNA and OliGreen Dye Sensors during Short Odor Sniffs(A) Responses of a sensor made from OliGreen alone.(B) Responses of a sensor made from 20 μl of 10 μM oligomer SEQ01, stained with OliGreen.(C) Responses from SEQ01 to 10 repeated applications of 10−1 propionic acid (∼390 ppm), demonstrating return to baseline between sniffs. These 10 responses were used to calculate the mean shown in (B). See Figure 1 for details of odor presentation, odor dilutions, and description of data representation.

Mentions: In an initial test of this hypothesis, we constructed sensors of dsDNA using a standard 2.9-kb pBlueScriptSK plasmid mixed with the intercalating DNA dye YO-PRO (Molecular Probes), dried onto a polyethylene substrate material, and tested in our electronic nose device [13,14] (see Materials and Methods). YO-PRO alone showed no changes in fluorescence over the time course of brief (1.6 s) odor sniffs (Figure 1A) applied by negative pressure in our artificial nose device. In contrast, sensors made from plasmid mixed with YO-PRO and dried onto the substrate produced large and rapid decreases in fluorescence upon exposure to propionic acid, with smaller or no changes when exposed to water, methanol, and triethylamine (Figure 1B). These odor responses were relatively stable over repeated trials (see Figure 2C for ssDNA). Responses from sensors made from dsDNA differing significantly in primary sequence (unpublished data), however, were qualitatively similar to those from sensors made from the pBlueScriptSK DNA (Figure 1B). We also constructed hairpin 33mer sequences that were much smaller than the plasmids described above and of about the size of the ssDNA described below, also stained with YO-PRO. These constructs of complementary G-C or A-T pairs (see sequences DS001 and DS002 in Table S1), which were designed to hybridize over a distance of 15 base pairs, all responded similarly, giving sequence-independent responses to the same odor set tested on the plasmid (unpublished data). These tests showed that, at least for these dsDNA constructs, sequence did not govern odor response.


Solid-state, dye-labeled DNA detects volatile compounds in the vapor phase.

White J, Truesdell K, Williams LB, Atkisson MS, Kauer JS - PLoS Biol. (2008)

Changes in Fluorescence from ssDNA and OliGreen Dye Sensors during Short Odor Sniffs(A) Responses of a sensor made from OliGreen alone.(B) Responses of a sensor made from 20 μl of 10 μM oligomer SEQ01, stained with OliGreen.(C) Responses from SEQ01 to 10 repeated applications of 10−1 propionic acid (∼390 ppm), demonstrating return to baseline between sniffs. These 10 responses were used to calculate the mean shown in (B). See Figure 1 for details of odor presentation, odor dilutions, and description of data representation.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2211549&req=5

pbio-0060009-g002: Changes in Fluorescence from ssDNA and OliGreen Dye Sensors during Short Odor Sniffs(A) Responses of a sensor made from OliGreen alone.(B) Responses of a sensor made from 20 μl of 10 μM oligomer SEQ01, stained with OliGreen.(C) Responses from SEQ01 to 10 repeated applications of 10−1 propionic acid (∼390 ppm), demonstrating return to baseline between sniffs. These 10 responses were used to calculate the mean shown in (B). See Figure 1 for details of odor presentation, odor dilutions, and description of data representation.
Mentions: In an initial test of this hypothesis, we constructed sensors of dsDNA using a standard 2.9-kb pBlueScriptSK plasmid mixed with the intercalating DNA dye YO-PRO (Molecular Probes), dried onto a polyethylene substrate material, and tested in our electronic nose device [13,14] (see Materials and Methods). YO-PRO alone showed no changes in fluorescence over the time course of brief (1.6 s) odor sniffs (Figure 1A) applied by negative pressure in our artificial nose device. In contrast, sensors made from plasmid mixed with YO-PRO and dried onto the substrate produced large and rapid decreases in fluorescence upon exposure to propionic acid, with smaller or no changes when exposed to water, methanol, and triethylamine (Figure 1B). These odor responses were relatively stable over repeated trials (see Figure 2C for ssDNA). Responses from sensors made from dsDNA differing significantly in primary sequence (unpublished data), however, were qualitatively similar to those from sensors made from the pBlueScriptSK DNA (Figure 1B). We also constructed hairpin 33mer sequences that were much smaller than the plasmids described above and of about the size of the ssDNA described below, also stained with YO-PRO. These constructs of complementary G-C or A-T pairs (see sequences DS001 and DS002 in Table S1), which were designed to hybridize over a distance of 15 base pairs, all responded similarly, giving sequence-independent responses to the same odor set tested on the plasmid (unpublished data). These tests showed that, at least for these dsDNA constructs, sequence did not govern odor response.

Bottom Line: In designing biomimetic artificial noses, the challenge has been to generate a similarly large sensor repertoire that can be manufactured with exact chemical precision and reproducibility and that has the requisite combinatorial complexity to detect odors in the real world.These new solid-state DNA-based sensors are sensitive and show differential, sequence-dependent responses.Furthermore, we show that large DNA-based sensor libraries can be rapidly screened for odor response diversity using standard high-throughput microarray methods.

View Article: PubMed Central - PubMed

Affiliation: Department of Neuroscience, Tufts University School of Medicine, Boston, Massachusetts, United States of America. joel.white@cogniscentinc.com

ABSTRACT
This paper demonstrates a previously unreported property of deoxyribonucleic acid-the ability of dye-labeled, solid-state DNA dried onto a surface to detect odors delivered in the vapor phase by changes in fluorescence. This property is useful for engineering systems to detect volatiles and provides a way for artificial sensors to emulate the way cross-reactive olfactory receptors respond to and encode single odorous compounds and mixtures. Recent studies show that the vertebrate olfactory receptor repertoire arises from an unusually large gene family and that the receptor types that have been tested so far show variable breadths of response. In designing biomimetic artificial noses, the challenge has been to generate a similarly large sensor repertoire that can be manufactured with exact chemical precision and reproducibility and that has the requisite combinatorial complexity to detect odors in the real world. Here we describe an approach for generating and screening large, diverse libraries of defined sensors using single-stranded, fluorescent dye-labeled DNA that has been dried onto a substrate and pulsed with brief exposures to different odors. These new solid-state DNA-based sensors are sensitive and show differential, sequence-dependent responses. Furthermore, we show that large DNA-based sensor libraries can be rapidly screened for odor response diversity using standard high-throughput microarray methods. These observations describe new properties of DNA and provide a generalized approach for producing explicitly tailored sensor arrays that can be rationally chosen for the detection of target volatiles with different chemical structures that include biologically derived odors, toxic chemicals, and explosives.

Show MeSH
Related in: MedlinePlus