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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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Odor Concentration-Response Curves Tested in the Artificial Nose for Two ssDNA Oligonucleotides Labeled with the Fluorescent Dye Cy3 during Synthesis(A) Responses from sequence SEQ02.(B) Responses from a different sequence SEQ03. Sensors were made from 20 μl of 10 μM oligomer. Each data point is the mean of 10 presentations; error bars indicate ± 1 SD.
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pbio-0060009-g004: Odor Concentration-Response Curves Tested in the Artificial Nose for Two ssDNA Oligonucleotides Labeled with the Fluorescent Dye Cy3 during Synthesis(A) Responses from sequence SEQ02.(B) Responses from a different sequence SEQ03. Sensors were made from 20 μl of 10 μM oligomer. Each data point is the mean of 10 presentations; error bars indicate ± 1 SD.

Mentions: In addition to response diversity, the sensitivities of a number of DNA-Cy3 sensors were also tested in our electronic nose device (similar to the tests shown in Figures 1 and 2) using an air-dilution olfactometer to deliver ranges of controlled odor concentrations. The dynamics of the responses of individual DNA-Cy3 sensors to sniffs of odorant were similar to those shown in Figure 2 for ssDNA stained with OliGreen. The concentration-response functions of different sequences for a small odorant test set summarize sensor concentration dependence as well as response diversity. For example, SEQ02 (Figure 4A) showed responses to propionic acid and triethylamine at lowest concentrations of 4 and 75 ppm, and to methanol, 2,4-dinitrotoluene (DNT; found in the vapor signature of TNT-containing landmines) [20–22], and dimethyl methylphosphonate (DMMP; precursor to Sarin nerve gas) at ∼33,900 ppm, ∼6 ppb, and ∼30 ppm, respectively. In contrast, SEQ03 (Figure 4B) responded to triethylamine at ∼75 ppm, to DMMP at ∼30 ppm, and showed no response to propionic acid, methanol, or DNT. The DNT response of SEQ02 (2 × 10−2 of DNT saturation is ∼6 ppb, or 2.3 × 10−10 M; see [23] for vapor pressure) indicates that these sensors are capable of detecting certain compounds with low vapor pressures at low concentrations. With the exception of polymers that are specifically synthesized for detecting nitroaromatic compounds [1,3], the DNA-based sensors described here are the only fluorescent polymeric sensor materials of which we are aware that show significant responses to DNT.


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)

Odor Concentration-Response Curves Tested in the Artificial Nose for Two ssDNA Oligonucleotides Labeled with the Fluorescent Dye Cy3 during Synthesis(A) Responses from sequence SEQ02.(B) Responses from a different sequence SEQ03. Sensors were made from 20 μl of 10 μM oligomer. Each data point is the mean of 10 presentations; error bars indicate ± 1 SD.
© Copyright Policy
Related In: Results  -  Collection

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

pbio-0060009-g004: Odor Concentration-Response Curves Tested in the Artificial Nose for Two ssDNA Oligonucleotides Labeled with the Fluorescent Dye Cy3 during Synthesis(A) Responses from sequence SEQ02.(B) Responses from a different sequence SEQ03. Sensors were made from 20 μl of 10 μM oligomer. Each data point is the mean of 10 presentations; error bars indicate ± 1 SD.
Mentions: In addition to response diversity, the sensitivities of a number of DNA-Cy3 sensors were also tested in our electronic nose device (similar to the tests shown in Figures 1 and 2) using an air-dilution olfactometer to deliver ranges of controlled odor concentrations. The dynamics of the responses of individual DNA-Cy3 sensors to sniffs of odorant were similar to those shown in Figure 2 for ssDNA stained with OliGreen. The concentration-response functions of different sequences for a small odorant test set summarize sensor concentration dependence as well as response diversity. For example, SEQ02 (Figure 4A) showed responses to propionic acid and triethylamine at lowest concentrations of 4 and 75 ppm, and to methanol, 2,4-dinitrotoluene (DNT; found in the vapor signature of TNT-containing landmines) [20–22], and dimethyl methylphosphonate (DMMP; precursor to Sarin nerve gas) at ∼33,900 ppm, ∼6 ppb, and ∼30 ppm, respectively. In contrast, SEQ03 (Figure 4B) responded to triethylamine at ∼75 ppm, to DMMP at ∼30 ppm, and showed no response to propionic acid, methanol, or DNT. The DNT response of SEQ02 (2 × 10−2 of DNT saturation is ∼6 ppb, or 2.3 × 10−10 M; see [23] for vapor pressure) indicates that these sensors are capable of detecting certain compounds with low vapor pressures at low concentrations. With the exception of polymers that are specifically synthesized for detecting nitroaromatic compounds [1,3], the DNA-based sensors described here are the only fluorescent polymeric sensor materials of which we are aware that show significant responses to DNT.

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