Exonuclease T (Exo T) (NEB #M0265) also known as RNase T, is a single-stranded RNA (1,2) or DNA (3,4) specific nuclease that requires a free 3´ terminus and removes nucleotides in the 3´→ 5´ direction. Exonuclease T can be used to generate blunt ends from RNA (5) or DNA molecules that have 3´ extensions (2).
RNase H (Ribonuclease H)(NEB #M0297) is an endoribonuclease that specifically hydrolyzes the phosphodiester bonds of RNA which is hybridized to DNA. This enzyme does not digest single or double-stranded DNA. It can be used to remove poly(A) tails of mRNA hybridized to poly(dT), or to remove mRNA during second strand cDNA synthesis.
Ribonuclease HII (RNase HII) (NEB #M0288) is an endoribonuclease that preferentially nicks 5´ to a ribonucleotide within the context of a DNA duplex. The enzyme leaves 5´ phosphate and 3´ hydroxyl ends (5). RNase HII will also nick at multiple sites along the RNA portion of an Okazaki fragment.
ShortCut® RNase III (NEB #M0245) used with its manganese-containing reaction buffer, converts long double-stranded RNA into a heterogeneous mix of short (18–25 bp) interfering RNAs (siRNA) suitable for RNA interference in mammalian cells (6–8). 1.5 units (1 µl) of ShortCut RNase III is sufficient to convert 1 µg of dsRNA into siRNA suitable for RNA interference in mammalian cells.
XRN-1 (NEB #M0338) is a highly processive 5´→3´ exoribonuclease, requiring 5´ monophosphate and can be used in removal of RNA containing 5´ monophosphate from a RNA mixture.
RNase If (NEB #M0243)
(1) Deutscher, M.P., Marlor, C.W. and Zaniewski, R. (1984) Proc. Natl. Acad. Sci. USA, 81, 4290-4293. PMID: 6379642
(2) Deutscher, M.P. and Marlor, C.W. (1985) J. Biol. Chem, 260, 7067-7071. PMID: 3888994
(3) Viswanathan, M., Dower, K. D. and Lovett, S. T. (1998) J. Biol. Chem, 273, 35126-35131. PMID: 9857048
(4) Zuo, Y. and Deutscher, M. P. (1999) Nucleic Acid Res, 27, 4077-4082. PMID: 10497273
(5) Rydberg, B. and Game, J. (2002) Proc. Natl. Acad. Sci., 99, 19954-16659. PMID: 12475934
(6) Morlighem, J.E. et al. (2007) Biotechniques, 42, 599-606. PMID: 17515198
(7) Yang, D. et al. (2002) Proc. Natl. Acad. Sci. USA, 99, 9942-9947. PMID: 12096193
(8) Calegari, F. et al. (2002) Proc. Natl. Acad. Sci. USA, 99, 14236-14240. PMID: 12391321