Herbicides are increasingly used to protect crops from fast-growing, fast-spreading weeds. While herbicides have increased crop yields, the misapplication of herbicide can have devastating effects. Proper management and application of herbicides is an ongoing challenge. Field-based tests for residual herbicide would go a long way in enabling farmers to detect the presence of residual herbicide and better contain/control herbicide application.


Dicamba (3,6-dichloro-2-methoxybenzoic acid) is a popular broad-spectrum herbicide that was first approved for use in pastures and non-crop areas in 1962. The herbicide acts like an auxin hormone. It dramatically increases plant growth, causing plants to exhaust available nutrients and die. With a growing number of weeds developing glyphosate resistance, dicamba use has increased over the years. In recent years, the introduction of dicamba-resistant soybean and cotton plants led to the approved use of dicamba on resistant crops. When accidentally sprayed on or near non-resistant crops, however, dicamba caused significant crop damage.

Spread of Herbicide

Early versions of dicamba were 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, the boom height above the crop, temperature, humidity, and wind18. Though new formulations of dicamba and clearer instructions and training regarding how and when to apply dicamba have helped limit drift, some risk of drift persists17. Dicamba can also contaminate surface water, ground water, and soil, enabling spread to sensitive crops through root adsorption.

Spray Tank Contamination

Spray tank 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.

Small Molecule Detection with Aptamers

While many tests utilize antibodies as selective detection reagents, developing antibodies for small molecules is difficult. Small molecules are not highly immunogenic. Attaching small molecules to larger carrier proteins can help, but such attachment often results in chemical modification of the small molecule, yielding antibodies with relatively poor affinity and/or selectivity.

Aptamers are small strands of single-stranded DNA or RNA that can selectively bind almost any compound. (Learn more about aptamers and aptamer selection.) Unlike antibodies, aptamers are chemically synthesized and can be selected in vitro to bind non-immunogenic small molecules and compounds that are toxic to antibody-producing cells or animals.13 Aptamers can even be selected to differentiate between very similar small molecules.12 Chemical synthesis reduces lot-to-lot variability and potential contaminants. Aptamers also offer enhanced temperature stability, avoiding refrigeration for storage or shipping of field tests.13 Base Pair Biotechnologies has developed aptamers that are selective for a wide range of small molecules, including amino acids, drugs of abuse and their metabolites, pharmaceutical drug compounds, neurotoxins, environmental contaminants and herbicides. Using proprietary techniques (under contract with Simply Green) Base Pair Biotechnologies has successfully developed a DNA aptamer that selectively binds dicamba. The equilibrium binding constant (KD) of the dicamba aptamer for its target was determined to be 228nm, suitable for a field-based test.

Proof-of-Concept Lateral Flow Assay for Dicamba

Due to their small size, small molecules are typically detected in a competitive-binding assay. While plate-based assays are commonly used in laboratory settings, the lateral flow assay (LFA) is a simple, fast, cost-effective method that is ideal for non-laboratory environments.3 To demonstrate feasibility, Base Pair Biotechnologies developed a competitive-binding LFA. The prototype conjugate pad contains the dicamba aptamer conjugated to signal-generating gold nanoparticles and a control IgG-gold nanoparticle conjugate. A dicamba-bovine serum albumin (BSA) conjugate is immobilized on the test line. The control line contains immobilized anti-IgG. In the prototype, a sample is added to the sample pad, then 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.

Launching a Field-Based Lateral Flow Assay (LFA) for Dicamba

There is a real need for a cost-effective field test with the ability to detect residual dicamba at the lowest level that could damage non-engineered crops. Additional aptamer development, lateral flow assay development, and prototype manufacturing are the next steps in progressing to field testing of the dicamba LFA. Completion of field testing, stability testing, and final manufacturing / QC testing will be required for launch of the commercial field test. Base Pair is currently pursuing grant funding for commercialization of the dicamba LFA.

Request Information on the dicamba LFA project or selection of aptamers to herbicides, pesticides, or other targets.


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  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/.
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  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.
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