RNase H

The enzyme RNase H is a non-specific endonuclease and catalyzes the cleavage of RNA via a hydrolytic mechanism. Members of the RNase H family can be found in nearly all organisms, from archaea to bacteria and eukaryota.

RNase H’s ribonuclease activity cleaves the 3’-O-P bond of RNA in a DNA/RNA duplex to produce 3’-hydroxyl and 5‘-phosphate terminated products. In DNA replication, RNase H is responsible for removing the RNA primer, allowing completion of the newly synthesized DNA.

Structure
The 3-D structure of RNase H commonly consists of a 5-stranded β-sheet surrounded by a distribution of α-helices. In some RNase H, such as the one found in HIV-1, the enzyme is missing one of the helices known as the C-helix, a positively charged α-helix whose protrusive shape increases substrate binding capacity. The active site of the enzyme is centered around a conserved DEDD motif (composed of residues: D443, E478, D498, and D549) which performs the hydrolysis of the RNA substrate. A magnesium ion is commonly used as a cofactor during the hydrolysis step. It is also a potential but unconfirmed mechanism in which multiple ions are necessary for to perform the hydrolysis. The enzyme also contains a nucleic acid binding cleft about 60 Å in length that can encompass a region of 18 bound RNA/DNA base pairs.

Function
In a molecular biology laboratory, as RNase H specifically degrades the RNA in RNA:DNA hybrids and will not degrade DNA or unhybridized RNA, it is commonly used to destroy the RNA template after first-strand complementary DNA (cDNA) synthesis by reverse transcription, as well as procedures such as nuclease protection assays. RNase H can also be used to degrade specific RNA strands when the cDNA oligo is hybridized, such as the removal of the poly(A) tail from mRNA hybridized to oligo(dT), or the destruction of a chosen non-coding RNA inside or outside the living cell. To terminate the reaction, a chelator, such as EDTA, is often added to sequester the required metal ions in the reaction mixture.

Genes
The following human genes encode proteins with RNase H activity:


 * ERVK6
 * RNASEH1
 * RNASEH2A
 * RNASEH2B
 * RNASEH2C

Role in Disease
It is associated with Aicardi–Goutieres syndrome.

Retroviral RNase H, a part of the viral reverse transcriptase enzyme, is an important pharmaceutical target, as it is absolutely necessary for the proliferation of retroviruses, such as HIV and murine leukemia virus. Inhibitors of this enzyme could therefore provide new drugs against diseases like AIDS. While not an effective treatment option, incorporation of 6-deoxythioguanosine has been shown to inhibit RNase H cleavage of the DNA/RNA complex.

HIV-1
Within human immunodeficiency virus type 1 (HIV-1), RNase H exists as a domain in the heterodimeric HIV-1 reverse transcriptase enzyme. HIV-1 carries out reverse transcription, a process that produces new double-stranded DNA from the viral genome's single-stranded RNA. During DNA synthesis, a DNA/RNA hybrid is formed as a replication intermediate and must be cleaved by RNase H before the process can continue. RNase H performs three types of cleaving actions: non-specific degradation of the (+)-strand RNA genome, specific removal of the (-)-strand tRNA primer, and removal of the (+)-strand PPT primer. RNase H plays a role in the priming of the (+)-strand, but not in the conventional method of synthesizing a new primer sequence. Rather RNase H creates a "primer" from the purine-rich polypurine tract (PPT) that is resistant to RNase H cleavage. By removing all bases but the PPT, the PPT is used as a marker for the end of the U3-LTR.