Aspergillus niger RNase belonging to RNase T2 family is purified to homogeneity using ammonium sulfate precipitation and anion-exchange chromatography from A. niger. The enzyme is glycosylated monomer with molecule mass of 28.5 kDa. Optimum activity of the enzyme is achieved at pH 3.5 and temperature 55 degrees C. The enzyme shows broad substrate specificity with poly (A), poly (C), poly (G), poly (U) and yeast RNA. The enzyme is highly stable against various metal ions and organic solvents, thus dictates its applicability in various industries. Two peptide sequences, PGGTLLQTQFWDYDP and TLDSYTALSDAG-ITPSEDATYK obtained by MS/MS analysis and confirmed by BLAST search, show substantial sequence homology with Aspergillus phoenicis, Aspergillus clavatus and P. merneffei. Multiple sequence analysis of the peptide sequences of purified enzyme shows 97%, 75% and 72% identity with A. phoenicis, A. clavatus and P. merneffei, respectively using Clustal W tool. Spectroscopic studies by absorbance, fluorescence, and circular dichroism reveal that the enzyme has alpha+beta type secondary structure with approximately 29% alpha-helix, 24% beta-sheet and 47% random coil by K2D software. (C) 2010 Elsevier Ltd. All rights reserved.