Final answer:
In agarose gel electrophoresis, you load a DNA ladder, amplicons, positive and negative control samples, and water into the wells at the top of the gel. These enable the sizing of DNA fragments, validation of the process, and control for contamination.
Step-by-step explanation:
In the context of agarose gel electrophoresis, the samples that you will put in the wells at the top of your gel include:
- A DNA ladder, which contains DNA fragments of known sizes and serves as a molecular weight marker to determine the sizes of other DNA samples in the gel.
- Amplicons, which are typically PCR products to be separated based on size.
- Positive and negative control samples, which are used to validate the gel electrophoresis results. Positive controls contain DNA of a known structure and behavior in the gel, while negative controls usually contain no DNA.
- Water, which can serve as a blank to ensure that there is no contamination affecting the results.
In practice, the DNA ladder is essential as it allows for the estimation of the size of the PCR fragments, while control samples are critical for verifying the efficacy and specificity of the experiment. The amplicons generated from PCR reactions provide the experimental data you are interested in observing. Including water in one of the wells can also serve as a blank to rule out contamination. Remember, DNA has a negative charge, so it will migrate towards the positive electrode during electrophoresis, with smaller molecules moving more quickly through the gel matrix.