Romanian Reports in Physics, Vol. 68, No. 3, P. 1178–1188, 2016 A COMPARATIVE ANALYSIS OF THREE METHODS USED FOR RNA QUANTITATION SORINA SCHIPOR 1 , SUZANA VLADOIU 1 , ANCUŢA ELENA BACIU 1,2 , ANA MARIA NICULESCU 3 , ANDRA CARAGHEORGHEOPOL 1 , IULIA IANCU 4 , ADRIANA PLESA 4 , A. I. POPESCU 2 , DANA MANDA 1 1 “C. I. Parhon” National Institute of Endocrinology, Bucharest, Romania 2 University of Bucharest, Faculty of Physics, P.O. Box MG-11, Magurele, Romania 3 Agilrom Scientific, Bucharest, Romania 4 “Stefan S. Nicolau” Institute of Virology, Bucharest, Romania Received July 27, 2014 Abstract. The high RNA sample quality is essential for downstream molecular biology applications. Two simultaneous conditions should be accomplished by the RNA samples: the structural integrity of the molecules and an adequate concentration. The objective of this study is to do a comparative analysis between three different methods of measuring RNA concentration. The three methods considered here are: UV spectrophotometry, spectrophotofluorimetry, and microfluidic capillary electrophoresis. Sixteen RNA samples were assayed by these three methods. The principles and the results of each method as well as advantages, disadvantages and perturbations factors are analyzed and discussed. Fluorescent labelling of RNA gives more accurate results even in the presence of the frequent contaminants like DNA and proteins. Knowing the strength and the limits of each method required for RNA quantitation, the scientist can choose the most cost-effective protocol. Key words: RNA quantitation, UV spectrophotometry, spectrophotofluorimetry, microfluidic capillary electrophoresis. 1. INTRODUCTION RNA quantification is an essential step for downstream molecular biology applications, RNA-based like gene expression analysis, RNA-sequencing (transcriptome profiling using deep-sequencing technologies), and RNA interference (an endogenous post-transcriptional gene regulatory mechanism mediated by non-coding RNA molecules known as microRNAs). There are several techniques used to determine RNA concentration, purity and integrity: ultraviolet spectroscopy, fluorescence, agarose and acrylamide gel electrophoresis, on-chip electrophoresis, reverse transcription coupled with real-time polymerase chain reaction (PCR) or inductively coupled plasma-optical emission spectroscopy (ICP-