Comparison of Modified Manual Acid-Phenol Chloroform Method and Commercial RNA Extraction Kits for Resource Limited Laboratories

Abstract

Background and Aim. RNA extraction is a commonly used technique in molecular biology. In recent years, commercially available RNA extraction kits have largely replaced conventional approaches. However, these commercial kits are expensive and are not readily available in many resource-constrained institutions and laboratories. Tis study therefore compared the performance of the conventional acid guanidinium thiocyanate-phenol-chloroform (AGPC) extraction method to QIAamp® Viral RNA Mini Kit (QIAGEN, Cat. No. 52906) and OxGEn RNA Kit (OxGEn Molecular Solutions, GE-009) to build an in-house RNA extraction technique from blood and oral swab samples. Method. In a comparative experimental cross-sectional study, RNA was extracted from oral swabs and blood samples from 25 healthy individuals at the Department of Molecular Medicine, KNUST. RNA was extracted by the manual AGPC extraction method and commercial RNA extraction kits. Te quantity (ng/μl) and purities (260/ 280 nm) of the extracted RNA were measured spectrophotometrically using the IMPLEN NanoPhotometer® N60. Te presence of RNA in the extracts was confrmed using 2% agarose gel electrophoresis. Statistical analyses were conducted using R language. Results. Te yield of RNA extracted from blood and oral swab samples using modifed AGPC was signifcantly higher compared to the commercial methods (p < 0.0001). However, the purity of RNA extracted by the manual AGPC method from blood was signifcantly lower than the commercial methods (p < 0.0001). Moreover, the purity from oral swabs using the manual AGPC method was signifcantly lower compared to QIAamp (p < 0.0001) and the OxGEn kits method (p < 0.001). Conclusion. Te modifed manual AGPC method has a very high yield of RNA extracts using blood samples, which could serve as an alternate costefective method for RNA extraction in resource-limited laboratories; however, its purity may not be suitable for downstream Hindawi International Journal of Clinical Practice Volume 2023, Article ID 9593796, 8 pages https://doi.org/10.1155/2023/9593796 processes. Moreover, the manual AGPC method may not be suitable for extracting RNA from oral swab samples. Future investigation is needed to improve the purity of the manual AGPC RNA extraction method and also confrmation of the obtained results by PCR amplifcation and RNA purity verifcation by sequencing