title: Intrinsic secondary structure of human TNFR-I mRNA influences the determination of gene expression by RT-PCR.
abstract: The secondary structure of human tumor necrosis factor receptor I (TNFR-I) mRNA based on its lowest folding energy was predicted. Three combinations of primers selected from open-regions and four combinations of primers from closed-regions of TNFR-I mRNA structure were employed for single-tube reverse transcription-polymerase chain reaction (RT-PCR) for the determination of TNFR-I gene expression in U937 cell. All the primers were designed with the same criteria. However, the different primers generated distinct quantities of RT-PCR products from the same concentration of TNFR-I mRNA, implying that the determination of gene expression by RT-PCR was affected by the mRNA secondary structure. In addition, the sensitivity of the open-region RT-PCR was approximately one hundred-fold higher than that in the closed-regions of TNFR-I mRNA. The low efficiency of the closed-region RT-PCR was not correlated with the G/C content of the TNFR-I mRNA structure. These results suggest that consideration of the influence of intrinsic mRNA structure of a gene is essential prior to the determination of gene expression by quantitative RT-PCR, and this open-region strategy of primer design may yield an efficient primer for in vitro amplification of cDNA by RT-PCR.
authors.affiliation: Department of Biochemistry, Kaohsiung Medical College, Taiwan.
authors.forename: K W
authors.initials: KW
authors.lastname: Kuo
authors.forename: M F
authors.initials: MF
authors.lastname: Leung
authors.forename: W C
authors.initials: WC
authors.lastname: Leung
mesh_terms: D015703:Antigens, CD / Q000235:genetics*; D005786:Gene Expression Regulation; D006801:Humans; D016403:Lymphoma, Large B-Cell, Diffuse; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction; D012313:RNA / Q000302:isolation & purification; D012333:RNA, Messenger / Q000737:chemistry* / Q000502:physiology; D018124:Receptors, Tumor Necrosis Factor / Q000235:genetics*; D047888:Receptors, Tumor Necrosis Factor, Type I; D013696:Temperature; D014407:Tumor Cells, Cultured
chemical_list: D015703:Antigens, CD; D012333:RNA, Messenger; D018124:Receptors, Tumor Necrosis Factor; D047888:Receptors, Tumor Necrosis Factor, Type I; D012313:RNA