Monitoring Herbicide Residue with Aptamers

Herbicides, insecticides, and fungicides are used to maximize yields of many agriculturally important crops; including wheat, soybean, corn, cotton, peanut, onions, vegetables, and rice.

Unfortunately, inadvertent crop, pollinator, and pollinator habitat damage caused by these chemicals can be devastating.

Dicamba

Dicamba (3,6-dichloro-2-methoxybenzoic acid) is a widely used broad-spectrum herbicide that was first approved for use in pastures and non-crop areas in 1962. 9in 1967 was approved for removing weeds in croplands prior to planting [https://www.epa.gov/ingredients-used-pesticide-products/registration-dicamba-use-dicamba-tolerant-crops].  In 2016, it was approved for “over the top” use with certain genetically engineered, tolerant strains of soybeans and cotton. It is also widely used in non-agricultural areas for controlling broadleaf weeds. [ibid]

Dicamba, like 2,4D (2,4-dichlorophenoxyacetic acid), is derived from and related to powerful, naturally occurring hormones that control plant growth.  In the presence of even very small concentrations of these chemicals, non-tolerant weeds and sensitive crops grow rapidly, exhausting available soil nutrients, leaving crops with reduced energy to produce seeds or flower, resulting in reduced productivity and/or plant death.  As little as 1/1000th of the recommended working concentration of dicamba can cause non-tolerant soybeans and cotton to die.  As little as 1/10,000th has been shown to cause damage and reduce crop yields.  Contamination of pollinator habitat with such chemicals also causes damage, since wildflowers growing in such areas are not herbicide-resistant.  In 2018, 1.1M acres of soybeans were inadvertently damaged by dicamba in the U.S. alone.  Cotton and other crops have also been damaged by dicamba and other herbicides.

Modes of Inadvertent Crop Damage

Why does the high sensitivity of non-tolerant plants to such chemicals matter?  There are four common modes for herbicides and related chemicals to cause damage. 

  • Drift, or movement of air-borne droplets or other particles from the desired location to other fields or sites during application
  • Vaporization of chemicals after application to tolerant plants
  • Soil or ground water contamination of chemicals that are applied to fields
  • Spray equipment contamination

Early versions of many herbicide formulations formed very small droplets, resulting in a significant amount of airborne drift, causing extensive damage.  Recent formulations of dicamba in particular produce much larger droplets, reducing drift significantly.  Airborne droplet drift is also highly dependent on weather, including temperature and wind.

Early versions of many herbicides, including dicamba, were also very volatile, vaporizing after application and being carried to adjacent plants or even fields miles away. Volatilization can be affected by the nozzles used for application, boom height, temperature, humidity, and wind18. Though new formulations of dicamba and other herbicides have clearer instructions and training requirements regarding how and when to apply them have helped reduce drift, some risk persists17.

Dicamba and other herbicides and insecticides can also contaminate surface water, ground water, and soil, enabling spread to sensitive crops and pollinator habitat through root adsorption.

Spray equipment contamination is a controllable problem, yet because there is currently no way for a grower or custom applicator to know if their equipment is clean, growers and spray applications frequently cause inadvertent damage to their own crops or those of their clients, due to herbicide residue lodged in nozzles or spray boom end caps.  

Spray Equipment Contamination

Spray equipment contamination is one of the greatest challenges for agricultural crop producers.1, 6, 7, 8, 15 The same spraying equipment is used for resistant and non-resistant crops, requiring extensive cleaning between applications. Dicamba is so potent that 1/1000th of the recommended concentration can reduce yields of non-resistant soybeans by up to sixty percent.4 Unfortunately, sprayer cleaning is not a simple task. Experts have warned, “There are all kinds of nooks and crannies and hiding places, not only for the active ingredient but also for sediment and residue which the active ingredient can bind to”.5 Without a method to test for residual dicamba, farmers must hope that equipment cleaning is sufficient from one operator to another and one day to the next.

In addition, farmers and other applicators that mix or combine formulations of herbicides and/or insecticides can exacerbate the problem since such combinations frequently have reduced solubility.

An easy to use, rapid, field-based test for these chemicals could empower growers and applicators alike to ensure that such equipment is clean and free of residue.

Small Molecule Detection with Aptamers

Developing tests to accurately detect small molecules using traditional methods has been difficult. Using proprietary techniques Base Pair Biotechnologies has successfully developed a DNA aptamer that selectively binds dicamba and has initiated the development of aptamers that bind other agriculturally important chemicals.

Aptamers are small, single strands of DNA or RNA that can selectively bind almost any compound. (Learn more about aptamers and aptamer selection.) Aptamers are chemically synthesized and can be selected to bind small molecules, including the active ingredients in many herbicides.13 Aptamers can be selected to differentiate between very similar small molecules, enabling future detection of a number of different herbicides and pesticides.12

Proof-of-Concept Test for Dicamba

The lateral flow assay format is ideal for rapid, field-based testing. Sample is added to a cartridge (much like a pregnancy test) and results are observed (signal or no signal at the test line) within 5 to 10 minutes. 

Principle of the Dicamba Test:

Due to their small size, small molecules are typically detected in a competitive-binding assay in which the presence of the target molecule in a sample interferes with signal development at a test line.  To demonstrate feasibility, Base Pair Biotechnologies developed a prototype competitive-binding, lateral flow assay as diagrammed below. The conjugate pad contains our dicamba aptamer conjugated to gold nanoparticles and a control gold nanoparticle conjugate of IgG. A dicamba-bovine serum albumin (BSA) conjugate is immobilized on the test line. The control line contains immobilized anti-IgG. When sample is added to the sample pad, it flows by capillary action through the conjugate pad, test line and control line, to the wick.

Dicamba LFA schematic

If dicamba is not present in the sample, the aptamer-gold nanoparticle conjugate is free to bind to the dicamba-BSA conjugate immobilized on the test line. Strong signals are visible at both test and control lines. The signal at the control line confirms that the sample has flowed past both test and control lines.

If dicamba is present in the sample, the aptamer is not available to bind at the test line. The aptamer binds more tightly to free-solution dicamba than to its bovine serum albumin conjugate. Only a faint signal is visible at the test line when a sample containing dicamba is used.

Completing Base Pair’s Field-Based Test for Dicamba

As described above, there is a powerful need for a cost-effective field test that can detect residual dicamba at the lowest level that could damage non-tolerant crops or pollinator habitat. Additional development, manufacturing, and testing are required for launch of a commercial test for detection of residual dicamba. Base Pair is currently pursuing funding for completion of development and commercialization of the test. We envision the rapid launch of the dicamba test with additional tests for glyphosate, glufosinate and 2,4D to follow.  We are committed to developing products that will best meet the needs of growers and applicators.  To that end, if you are interested in learning more about our agricultural test development plans or in participating in the design and development of these products, please let us know.  We are currently seeking partners in several areas:

  • Beta Test / Field-Test Sites
  • Growers and Applicators willing to participate in an in-depth Interview to help finalize product specifications
  • Distribution Partners

Submit a Request to be a beta test site for the Dicamba LFA

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Register for an in-depth interview and tell us which tests are most important and which test formats would work best for you.

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Submit a Request to become a distributor of Base Pair agricultural tests.

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REFERENCES:

  1. 2,4-D, Cotton, and Sprayer Contamination : Extension : Clemson University : South Carolina, (n.d.) http://www.clemson.edu/extension/pest_ed/safety_ed_prog/containers/24dresdu.html.
  2. Alie Arp. Dicamba impact straight from farmers. Iowa Soybean Association. 11/9/2017. https://www.iasoybeans.com/news/articles/dicamba-impact-straight-from-farmers/.
  3. Alsager, O. M., et al. Lateral flow adsorption and desorption interactions on gold nanoparticles. Analytical Chemistry. 2017. 89(14):7416-7427.
  4. Bauerle, M.J. Evaluation of Volatility and Physical Drift of 2,4-D, Dicamba, and Triclopyr Formulations, Master’s Thesis, Louisiana State University, School of Plant, Environmental, and Soil Sciences, 2014. Page 33.
  5. Don’t Skimp on Tank Cleanout with New Dicamba Herbicides, DTN Progressive Farmer. (n.d.). https://www.dtnpf.com/agriculture/web/ag/news/crops/article/2017/02/17/skimptank-cleanout-new-dicamba-3.
  6. Drifting and Sprayer Contamination on Potatoes (06/20/13) — Crop & Pest Report, (n.d.). https://www.ag.ndsu.edu/cpr/weeds/drifting-and-sprayer-contamination-on-potatoes-06-20-13.
  7. G4852 Cleaning Field Sprayers to Avoid Crop Injury | University of Missouri Extension, (n.d.). http://extension.missouri.edu/p/G4852.
  8. Glyphosate and Dicamba Drift Problems in Potatoes, (n.d.). https://www.ag.ndsu.edu/potatoextension/glyphsoate-and-dicamba-drift-problmes-inpotatoes/image/image_view_fullscreen.
  9. IBIS World. Soybean Farming – U.S. Market Research Report. September 2017.
  10. Missouri Legislature Passes Regulations for Herbicide Use | Missouri News | US News, (n.d.). https://www.usnews.com/news/best-states/missouri/articles/2017-03-16/missourilegislature-passes-regulations-for-herbicide-use.
  11. Monsanto explains actions as dicamba drift fallout continues | Soybeans content from Delta Farm Press, (n.d.). http://deltafarmpress.com/soybeans/monsanto-explains-actions-dicambadrift-fallout-continues.
  12. Pfeiffer, F. et al. Selection and biosensor application of aptamers for small molecules. Frontiers in Chemistry. 2016. 4:25.
  13. Ruscito, A., et al. Small-molecule binding aptamers. Frontiers in Chemistry. 2016. 4:14
  14. Soybeans and Oil Crops: Background. USDA. https://www.ers.usda.gov/topics/crops/soybeans-oil-crops/background/. (accessed March 20, 2018).
  15. Sprayer tank contamination matters more in new herbicide era, (n.d.). http://farmprogress.com/story-sprayer-tank-contamination-matters-more-new-herbicideera-9-133311. \
  16. Dicamba. Wikipedia. https://en.wikipedia.org/wiki/Dicamba. Accessed April 11, 2018.
  17. https://www.epa.gov/ingredients-used-pesticide-products/registration-dicamba-use-genetically-engineered-crops
  18. https://www.realclearscience.com/articles/2017/12/12/the_real_story_behind_the_dicamba_controversy.html