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

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.

Figure 1. Changes in Fluorescence from Double-Stranded pBlueScriptSK DNA and YO-PRO Dye Sensors during Short Odor Sniffs

The odor pulse began at 0 s and lasted for 1.6 s, indicated by horizontal black bar. (A) Responses of a sensor made from YO-PRO alone, then rinsed in 70% ethanol for 5 min. (B) Responses of a sensor made from YO-PRO and 5 ng total pBlueScriptSK DNA. Odor dilutions, expressed as fractions of saturated vapor, were: water, 10⁻¹; methanol (MeOH), 10⁻¹ (∼16,700 ppm); triethylamine, 10⁻² (∼750 ppm); and propionic acid, 10⁻¹ (∼390 ppm). Each trace represents the mean of 10 presentations; error bars indicate ± 1 SD.

Figure 2. 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.

Figure 3. 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.

Figure 4. 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.