Qualitative and Quantitative Optimization of FOXE1 Gene Polymerase Chain Reaction Product as a GC-Rich Gene

Abstract

Background: Approximately 3 of the human genome is rich in GCs. These regions are often found in the promoter of genes, especially housekeeping genes and tumor suppressor genes. Amplification of these GC-rich regions can be challenging. Because the stability of GC-rich DNA sequences is higher, secondary structures are easily formed in these regions. Type 4 non-medullary thyroid carcinoma has been linked to the FOXE1 gene as a risk factor. FOXE1 belongs to a large family of transcription factors principal for the development of the thyroid gland's morphology. Methods: With a high proportion of GC, a portion of the FOXE1 gene sequence cannot be amplified using the usual polymerase chain reaction. This work is an experimental study that deals with this issue. Findings: The results of the present study showed that the Touchdown polymerase chain reaction, in combination with CO-amplification materials such as betaine and Dimethyl Sulfoxide (DMSO), is effective in amplifying the sequence of this region of the FOXE1 gene by destruction of the secondary structures formed in the sequence and increasing the reaction product. Conclusion: Using this method, GC-rich regions in additional genes with a similar degree of GC as the FOXE1 gene can be amplified. © 2024 Isfahan University of Medical Sciences(IUMS). All rights reserved.