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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 Responses of DNA-Cy3 Sensor Spots Read with Microarray Scanner(A) Thirty SEQ02 control sensors (rows) tested with eight odors (columns). Pairwise Pearson correlation coefficients ranged from 0.91 to 1.00 (mean = 0.98, SD = 0.016).(B) Twenty nine different DNA-Cy3 sensors and Cy3 alone (rows) tested with the same odor test set as (A) (columns). Pairwise correlation coefficients ranged from −0.54 to 0.98 (mean = 0.66, SD = 0.32). Dashed line denotes correlation coefficient of 0.90. Data matrices show log2 transforms of fluorescence change between clean air and odor with graded red colors indicating the degree of fluorescence increase above baseline and blue indicating the degree of decrease. Dendrograms drawn to the same scale. Abbreviations: DMMP, dimethyl methylphosphonate; DNT, dinitrotoluene.
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pbio-0060009-g003: Odor Responses of DNA-Cy3 Sensor Spots Read with Microarray Scanner(A) Thirty SEQ02 control sensors (rows) tested with eight odors (columns). Pairwise Pearson correlation coefficients ranged from 0.91 to 1.00 (mean = 0.98, SD = 0.016).(B) Twenty nine different DNA-Cy3 sensors and Cy3 alone (rows) tested with the same odor test set as (A) (columns). Pairwise correlation coefficients ranged from −0.54 to 0.98 (mean = 0.66, SD = 0.32). Dashed line denotes correlation coefficient of 0.90. Data matrices show log2 transforms of fluorescence change between clean air and odor with graded red colors indicating the degree of fluorescence increase above baseline and blue indicating the degree of decrease. Dendrograms drawn to the same scale. Abbreviations: DMMP, dimethyl methylphosphonate; DNT, dinitrotoluene.

Mentions: To measure odor responses using this method, we first tested control arrays in which the same DNA-Cy3 construct (SEQ02) was spotted at all locations. The responses of 30 replicates of the same SEQ02 construct (rows) to saturated vapors of eight odors (columns) are shown in Figure 3A (increases in fluorescence over baseline indicated by graded red colors and decreases indicated by graded blue colors). The responses of the replicated spots in this control array were highly correlated and therefore considered to be essentially identical. Pearson correlation coefficients calculated between pairs of sensors were all ≥0.90 (see Figure 3A, legend). This high degree of correlation is also represented by the compact cluster analysis dendrogram shown to the left of the data matrix in Figure 3B (see [19] for description of Pearson correlation coefficients and cluster analysis that are the standard methods applied to microarray data).


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 Responses of DNA-Cy3 Sensor Spots Read with Microarray Scanner(A) Thirty SEQ02 control sensors (rows) tested with eight odors (columns). Pairwise Pearson correlation coefficients ranged from 0.91 to 1.00 (mean = 0.98, SD = 0.016).(B) Twenty nine different DNA-Cy3 sensors and Cy3 alone (rows) tested with the same odor test set as (A) (columns). Pairwise correlation coefficients ranged from −0.54 to 0.98 (mean = 0.66, SD = 0.32). Dashed line denotes correlation coefficient of 0.90. Data matrices show log2 transforms of fluorescence change between clean air and odor with graded red colors indicating the degree of fluorescence increase above baseline and blue indicating the degree of decrease. Dendrograms drawn to the same scale. Abbreviations: DMMP, dimethyl methylphosphonate; DNT, dinitrotoluene.
© Copyright Policy
Related In: Results  -  Collection

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

pbio-0060009-g003: Odor Responses of DNA-Cy3 Sensor Spots Read with Microarray Scanner(A) Thirty SEQ02 control sensors (rows) tested with eight odors (columns). Pairwise Pearson correlation coefficients ranged from 0.91 to 1.00 (mean = 0.98, SD = 0.016).(B) Twenty nine different DNA-Cy3 sensors and Cy3 alone (rows) tested with the same odor test set as (A) (columns). Pairwise correlation coefficients ranged from −0.54 to 0.98 (mean = 0.66, SD = 0.32). Dashed line denotes correlation coefficient of 0.90. Data matrices show log2 transforms of fluorescence change between clean air and odor with graded red colors indicating the degree of fluorescence increase above baseline and blue indicating the degree of decrease. Dendrograms drawn to the same scale. Abbreviations: DMMP, dimethyl methylphosphonate; DNT, dinitrotoluene.
Mentions: To measure odor responses using this method, we first tested control arrays in which the same DNA-Cy3 construct (SEQ02) was spotted at all locations. The responses of 30 replicates of the same SEQ02 construct (rows) to saturated vapors of eight odors (columns) are shown in Figure 3A (increases in fluorescence over baseline indicated by graded red colors and decreases indicated by graded blue colors). The responses of the replicated spots in this control array were highly correlated and therefore considered to be essentially identical. Pearson correlation coefficients calculated between pairs of sensors were all ≥0.90 (see Figure 3A, legend). This high degree of correlation is also represented by the compact cluster analysis dendrogram shown to the left of the data matrix in Figure 3B (see [19] for description of Pearson correlation coefficients and cluster analysis that are the standard methods applied to microarray data).

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