Which of the following is a method scientists use to overcome the limitations of DNA microarray technology when studying gene interactions?

• A. Reducing the hybridization time to minimize background noise
• B. Increasing the number of fluorescent dyes used in microarrays
• C. Relying solely on single-gene knockout experiments
• D. Utilizing RNA sequencing (RNA-seq) for higher sensitivity and broader dynamic range

Answer: (D)

Verified step by step guidance

1. Understand the limitation of DNA microarray technology: it has a limited dynamic range and sensitivity, which can affect the detection of low-abundance transcripts and subtle gene expression changes.
2. Recognize that DNA microarrays rely on hybridization of fluorescently labeled cDNA to probes on a chip, which can introduce background noise and limit the number of genes analyzed simultaneously.
3. Consider alternative methods that provide higher sensitivity and a broader dynamic range, such as RNA sequencing (RNA-seq), which sequences cDNA fragments directly and quantifies gene expression more accurately.
4. Evaluate why other options are less effective: reducing hybridization time may reduce background noise but does not address sensitivity; increasing fluorescent dyes is limited by spectral overlap; single-gene knockouts do not capture complex gene interactions.
5. Conclude that utilizing RNA-seq is a method scientists use to overcome microarray limitations because it allows for more comprehensive and precise analysis of gene expression and interactions.