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.
Evaluation of RNase contamination is necessary for reagents to be used in experiments with RNA. The RNase Contamination Assay Kit detects general RNase activities, including non-enzyme based RNA degradation due to heavy metal contamination in samples and high pH.
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