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What is a viral integrase and how does it insert DNA into a host genome? A viral integrase is a retrovirus-encoded enzyme that joins newly made viral DNA to a chromosome in an infected cell. Reverse transcriptase first copies the retrovirus’s RNA genome into linear double-stranded DNA. Integrase then cuts the viral DNA ends, assembles them into an intasome, and transfers those ends into host DNA. Cellular repair enzymes fill the resulting gaps, leaving an integrated provirus that can be transcribed and persist as part of the chromosome.
Integrase is therefore not the enzyme that converts RNA into DNA; that job belongs to reverse transcriptase. Integrase acts on the DNA product and performs the decisive insertion chemistry.
What viral integrase does
In the usual retroviral life cycle, integrase is the enzyme responsible for integration: the permanent joining of viral DNA to host chromosomal DNA. The integrated form is called a provirus. Once cellular repair has completed the junctions, host transcription machinery can read proviral genes and produce viral RNAs and proteins.
The enzyme acts on both ends of one linear viral DNA molecule. It does not insert the original viral RNA directly, and it does not make the DNA substrate itself. Those distinctions explain why reverse transcriptase and integrase are separate drug targets and separate steps in infection.
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The NIH ClinicalInfo HIV/AIDS Glossary summarizes the process plainly: “HIV uses integrase to insert (integrate) its viral DNA into the DNA of the host CD4 cell.” The statement refers specifically to HIV, but the underlying sequence—reverse transcription followed by integrase-catalyzed insertion—is characteristic of retroviral replication.
How a retrovirus makes DNA for integrase
1. Reverse transcriptase copies the RNA genome
A retrovirus enters a cell carrying an RNA genome. Reverse transcriptase converts that RNA information into a DNA copy and ultimately produces a linear double-stranded viral DNA molecule. The DNA ends contain long terminal repeat (LTR) sequences that provide the recognizable ends used by the integration machinery.
This order matters. Integrase’s substrate is DNA, not the incoming RNA. If reverse transcription has not produced the correct linear DNA ends, integrase has no normal substrate on which to perform strand transfer.
2. The DNA remains associated with viral and cellular factors
After reverse transcription, the viral DNA is handled in a nucleoprotein assembly often described as a pre-integration complex. Integrase binds the two viral DNA ends within this assembly. The complex helps protect the substrate, brings both ends together, and presents them to a host chromosome.
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How the intasome assembles
Integrase molecules do not normally act as two unrelated enzymes, one at each end. They assemble with the two ends of the same viral DNA molecule into an intasome, a multi-protein nucleoprotein machine. The intasome positions the viral ends in the geometry required for the two catalytic reactions and helps coordinate their attack on target DNA.
Terminology can vary by experimental system. A pre-integration complex refers to the larger viral DNA–protein assembly in the cell; an intasome emphasizes the integrase-centered catalytic core bound to the two viral DNA ends. Both concepts describe organization that is essential for accurate two-ended integration.
In mature HIV-1 particles, an estimate published by Maertens, Engelman and Cherepanov in 2022 placed the amount of integrase at about 120 copies per virion. That is an estimate for mature HIV-1 particles, not a universal copy number for every retrovirus or every particle.
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The two catalytic steps of integration
3′ processing exposes the reactive viral ends
Integrase first cleaves specific phosphodiester bonds near each end of the viral DNA. This reaction removes a short terminal segment and leaves a reactive 3′-hydroxyl (3′-OH) group on each viral DNA strand. The exposed hydroxyls are the nucleophiles that will make the next chemical attack.
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Because the cuts occur near the LTR termini, the processed ends are structurally prepared for insertion. This is called 3′ processing. It occurs before the viral DNA is joined to the chromosome, so it is distinct from the later cuts made in host DNA.
Strand transfer joins viral DNA to the chromosome
In the second reaction, called strand transfer, each viral 3′-OH attacks a phosphodiester bond in host chromosomal DNA. The reaction is a transesterification: target DNA is cut while the viral DNA end is joined to a host 5′ phosphate. Both viral ends are transferred into the chromosome, generally at nearby but offset positions.
The immediate product is not a perfectly sealed, fully repaired chromosome. The staggered target cuts leave short gaps and unprocessed viral or host DNA ends at the two junctions. Integrase has carried out the joining chemistry; the host cell must finish the structure.
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Cellular DNA-repair pathways fill the short single-stranded gaps, remove remaining mismatched or extra nucleotides, and seal the phosphodiester backbone. The exact repair proteins can vary with the cell and retrovirus, but the functional outcome is the same: viral DNA becomes covalently embedded in host chromosomal DNA.
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The repaired structure is the provirus. Its genes can then be transcribed by host machinery, generating viral RNAs that serve as messenger RNAs or as genomes for new particles. Integration also gives the viral DNA the potential to persist in the infected cell’s chromosome rather than remaining only as a transient, unintegrated DNA molecule.
Reverse transcriptase and integrase are different enzymes
Confusing these enzymes leads to an incorrect picture of the life cycle. Reverse transcriptase creates the DNA molecule; integrase inserts that molecule. Their substrates, reactions and outcomes differ:
| Feature | Reverse transcriptase | Viral integrase |
|---|---|---|
| Primary substrate | Retroviral RNA genome plus a growing DNA strand | Linear double-stranded viral DNA with LTR ends |
| Main job | Copies RNA information into DNA and completes the viral DNA form | Processes viral DNA ends and joins them to host chromosomal DNA |
| Key chemistry | Nucleic-acid polymerization, with RNA-template processing in the reverse-transcription process | 3′ processing followed by strand-transfer transesterification |
| Product | Linear viral DNA substrate | Integrated provirus after host repair |
| Where the decisive substrate comes from | Viral RNA | DNA made by reverse transcriptase |
Stopping reverse transcription prevents formation of the normal integration substrate. Blocking integrase, by contrast, can leave viral DNA present but prevents its productive insertion into the chromosome.
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Integration sites are distributed across the host genome, but the process is not simply a uniform random insertion. Viral and cellular factors influence which chromatin environments are favored. Integrase can associate with host tethering or targeting factors that guide the intasome toward particular genomic regions, while the accessibility and state of host chromatin also affect where integration is more likely.
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These preferences are important for interpreting integration maps. A list of proviral sites reflects both the chemistry of strand transfer and the biology of the host chromosome. Different retroviruses can show different targeting tendencies because they use different integrase assemblies, cellular partners or chromatin contexts.
Targeting preference does not mean that every integration site is predictable for an individual infection. It means that, across many integration events, measurable biases can appear instead of an exactly even distribution over all DNA.
Integration, expression and persistence
After repair, the provirus is part of a host chromosome and is subject to host controls such as chromatin structure and transcriptional regulation. When proviral promoters and regulatory sequences are active, host RNA polymerase and other cellular factors produce viral transcripts. Those transcripts can encode viral proteins or serve as genomes for progeny particles.
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An integrated provirus can also remain transcriptionally quiet. Silence does not remove the DNA; it reflects the regulatory state of the surrounding chromosome and the proviral control elements. This distinction helps explain why integration is central to persistent retroviral infection: the viral genetic material can remain in cellular DNA even when production of viral RNA is limited.
Why integrase is a major HIV drug target
Because strand transfer is essential for productive HIV replication, integrase is a validated target for antiretroviral therapy. Integrase strand-transfer inhibitors block the step in which processed viral 3′ ends are joined to host DNA. They act on integration chemistry rather than on the earlier copying of RNA into DNA.
Clinical treatment choices, approved products and recommended combinations change over time and differ by patient circumstances and jurisdiction. Current HIV treatment guidance should therefore be consulted for medication decisions. The mechanistic point is stable: inhibiting strand transfer prevents formation of the normal integrated provirus, even though other parts of the viral life cycle may already have occurred.
Quick Recap
A step-by-step view of the complete insertion event
- Entry and uncoating: the retrovirus delivers its RNA genome and associated proteins into a susceptible cell.
- Reverse transcription: reverse transcriptase converts the RNA genome into linear double-stranded DNA with LTR-containing ends.
- End recognition: integrase binds both viral DNA ends and organizes them in an intasome or related pre-integration assembly.
- 3′ processing: integrase cleaves near each viral terminus, exposing reactive 3′-OH groups.
- Chromosome engagement: the intasome is positioned on host DNA, with chromatin and cellular tethering factors influencing site selection.
- Strand transfer: the viral 3′-OH groups attack host phosphodiester bonds, joining viral DNA to host 5′ phosphates.
- Gap repair: host enzymes fill short gaps, remove residual mismatches or ends, and seal both DNA backbones.
- Provirus activity: the repaired integrated DNA can be transcribed by the host and can persist in the chromosome.
What to remember
- Integrase is a viral enzyme encoded by a retrovirus.
- Reverse transcriptase makes the DNA; integrase inserts it.
- The integration substrate is linear double-stranded viral DNA, not viral RNA.
- The catalytic sequence is 3′ processing followed by strand transfer.
- An intasome holds both viral DNA ends in the configuration needed for insertion.
- Host repair completes the junctions and produces an integrated provirus.
- Chromatin and host tethering factors influence integration-site preferences.
- Integrase strand-transfer inhibitors target the insertion step in HIV replication.
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