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Reverse transcriptase

Reverse transcriptase is an enzyme that catalyzes the synthesis of complementary DNA (cDNA) from an RNA template through a process known as reverse transcription.^[1] This RNA-dependent DNA polymerase is essential for the replication of retroviruses, such as HIV and Moloney murine leukemia virus (M-MuLV), where it converts the virus's single-stranded RNA genome into double-stranded DNA that integrates into the host cell's genome.^[1] The enzyme was independently discovered in 1970 by Howard Temin, working on Rous sarcoma virus, and David Baltimore, studying leukemia viruses, fundamentally challenging the central dogma of molecular biology that genetic information flows unidirectionally from DNA to RNA to protein.^[2] For this breakthrough, Temin, Baltimore, and Renato Dulbecco shared the 1975 Nobel Prize in Physiology or Medicine.^[3] Reverse transcriptase exhibits multiple activities, including DNA polymerase for synthesizing DNA strands and RNase H for degrading RNA in RNA-DNA hybrids, enabling efficient viral propagation.^[1] In addition to its viral roles, reverse transcriptase is encoded by endogenous retroelements in eukaryotic genomes, facilitating their transposition and contributing to genetic diversity, and it occurs naturally in some prokaryotes and eukaryotes.^[1] In molecular biology, engineered or purified forms of the enzyme, often derived from avian myeloblastosis virus (AMV) or M-MuLV, are widely used for applications such as reverse transcription polymerase chain reaction (RT-PCR) to detect and quantify RNA, cDNA library construction, RNA sequencing, and gene expression analysis.^[1] These techniques have revolutionized genomics and diagnostics, particularly for identifying RNA viruses and studying low-abundance transcripts.^[1]

Discovery and History

Initial Discovery

The discovery of reverse transcriptase emerged from independent investigations into the replication mechanisms of RNA tumor viruses in 1970. Howard Temin, along with Satoshi Mizutani, identified RNA-dependent DNA polymerase activity within virions of the avian Rous sarcoma virus, demonstrating an enzyme capable of synthesizing DNA using viral RNA as a template.^[4] Simultaneously, David Baltimore reported the same enzymatic activity in virions of multiple RNA tumor viruses, including the murine Rauscher leukemia virus and avian myeloblastosis virus.^[5] These findings directly challenged the prevailing central dogma of molecular biology, which posited that genetic information flows unidirectionally from DNA to RNA to protein, by revealing a reverse flow from RNA to DNA.^[6] Early experiments relied on biochemical assays to detect this novel polymerase activity. Researchers disrupted purified virions and incubated the extracts with synthetic RNA templates, such as polyriboadenylic acid, along with deoxynucleotide triphosphates, including radioactively labeled tritiated thymidine triphosphate (³H-TTP).^[4] The incorporation of ³H-TTP into acid-insoluble material—indicative of DNA polymer—occurred only in the presence of RNA templates and was abolished by RNase treatment, which degrades RNA, but not by DNase, confirming the RNA dependency.^[5] These assays required magnesium ions and all four deoxynucleotide triphosphates for optimal activity, establishing the enzyme's specificity for RNA-directed DNA synthesis in both avian and murine retroviruses.^[4] The groundbreaking nature of these discoveries was recognized with the 1975 Nobel Prize in Physiology or Medicine, awarded jointly to Temin, Baltimore, and Renato Dulbecco for their contributions to understanding tumor virus-host interactions and the reverse transcription process.^[7]

Key Milestones and Researchers

Following the initial discovery of reverse transcriptase (RT) in retroviruses, Howard Temin and David Baltimore continued to advance understanding of its role in viral replication and oncogenesis. Temin's work in the mid-1970s further validated the provirus hypothesis by demonstrating that RT-mediated DNA synthesis integrates viral genetic material into the host genome, providing a mechanism for persistent infection and potential oncogenic transformation. Baltimore, meanwhile, characterized RT's biochemical properties, including its template specificity and primer requirements, which laid the groundwork for later enzymatic studies and applications in molecular biology. Their collaborative insights, culminating in the 1975 Nobel Prize, spurred research into RT's implications for cancer and viral diseases. In the 1980s, the identification of HIV as the causative agent of AIDS accelerated RT research, with key breakthroughs in cloning and sequencing the enzyme's gene. Flossie Wong-Staal and colleagues at the National Cancer Institute achieved the first cloning of the HIV genome in 1985, enabling the isolation and expression of the pol gene encoding RT, which confirmed its essential role in viral replication. Concurrently, Leroy Ratner and William Haseltine's team published the complete nucleotide sequence of the HIV-1 (HTLV-III) provirus that same year, revealing the RT coding region within the pol open reading frame and identifying conserved motifs critical for its polymerase and RNase H activities.^[8] These milestones facilitated the production of recombinant HIV RT for biochemical assays and early antiviral drug screening. The 1990s brought structural insights into RT through X-ray crystallography, transforming drug design efforts. In 1991, Jeffrey Davies and colleagues determined the crystal structure of the RNase H domain of HIV-1 RT at 2.9 Å resolution, highlighting its endonuclease fold and magnesium-binding sites essential for RNA degradation during reverse transcription.^[9] This was followed in 1992 by L. A. Kohlstaedt and colleagues' 3.5 Å structure of the full HIV-1 RT heterodimer (p66/p51) bound to the non-nucleoside inhibitor nevirapine, revealing the enzyme's asymmetric hand-like architecture with fingers, palm, thumb, connection, and RNase H subdomains that accommodate the nucleic acid template.^[10] These structures, refined in subsequent studies, provided atomic-level details of the active site and informed the rational design of RT inhibitors like nucleoside analogs. Post-2000 discoveries expanded RT's known roles beyond retroviruses, uncovering non-retroviral instances in bacteria and plants. In bacteria, retrons—genetic elements encoding RTs linked to non-coding RNAs—were identified as anti-phage defense systems in 2020 by Aude Millman and Rotem Sorek's team, who showed that retron RT produces abortive DNA products that trigger host cell death upon phage infection, protecting bacterial populations.^[11] Further studies in the early 2020s elucidated retron RT mechanisms, including msDNA synthesis for phage sensing. In 2025, additional bacterial RTs, such as DRT9, were found to defend against phages by synthesizing long poly(A)-rich cDNA in response to infection-induced elevations in intracellular dATP levels.^[12] In plants, genome sequencing revealed widespread endogenous pararetroviruses (EPRVs) with functional RT domains post-2000; for instance, a 2022 analysis by Cathaline Hickey and colleagues identified over 11,000 RT sequences from recently integrated EPRVs across 202 tracheophyte species, suggesting roles in gene regulation and stress responses via occasional transcriptional activation.^[13] These findings highlight RT's evolutionary diversification in innate immunity and genome evolution.

Biological Roles

Role in Retroviruses

Reverse transcriptase (RT) is indispensable in the replication cycle of retroviruses, where it catalyzes the conversion of the virus's single-stranded RNA genome into double-stranded proviral DNA, enabling subsequent integration into the host cell's genome.^[14] This process, known as reverse transcription, occurs shortly after the viral particle enters the host cell, allowing the retrovirus to hijack the host's cellular machinery for propagation.^[15] Without RT, retroviruses cannot generate the DNA intermediate required for establishing a latent infection, distinguishing them from other RNA viruses that replicate directly via RNA-dependent RNA polymerases.^[16] In lentiviruses such as HIV-1, a subtype of retrovirus, RT plays a pivotal role in producing a linear double-stranded DNA molecule flanked by long terminal repeats (LTRs) at both ends.^[17] These LTRs, generated through precise strand transfers during reverse transcription, contain regulatory sequences essential for viral gene expression and integration by the viral integrase enzyme.^[17] The enzyme's dual activities—polymerase for DNA synthesis and RNase H for RNA degradation—ensure the complete and accurate formation of this proviral DNA from the RNA template primed by a host tRNA.^[17] The absence of functional RT renders retroviruses, including HIV, incapable of completing their replication cycle, as they cannot produce the proviral DNA necessary for genomic integration and persistent infection.^[14] This dependency makes RT a primary target for antiretroviral therapies, which inhibit its activity to prevent viral propagation and chronic disease progression.^[18] In HIV infection, RT inhibition blocks the formation of integrated provirus, thereby halting the production of new virions and maintaining viral latency without progression to active replication.^[17]

Role in Other Organisms and Endogenous Activity

Endogenous retroviruses (ERVs), remnants of ancient retroviral infections integrated into host genomes, constitute approximately 8% of the human genome and play significant roles in gene regulation and evolutionary processes in mammals. These sequences, derived from reverse transcription and integration by retroviral reverse transcriptases, often retain long terminal repeats (LTRs) that function as enhancers or promoters, influencing the expression of nearby genes. For instance, in human neural progenitor cells, ERVs serve as docking platforms for transcription factors, with the protein TRIM28 binding to nearly 10,000 primate-specific ERVs to repress their activity via heterochromatin formation, thereby fine-tuning the expression of hundreds of protein-coding genes such as BMP3 and STK17B. In trophoblast cells, which are crucial for placental development, primate-specific ERVs like LTR10A act as tissue-specific enhancers, binding transcription factors such as JUN and GATA3 to regulate genes involved in placental function, including ENG and PSG5, with disruptions linked to conditions like preeclampsia. Evolutionarily, ERVs contribute to host adaptation by providing novel regulatory elements that drive species-specific gene expression patterns across vertebrates.^[19]^[20]^[21] Beyond ERVs, non-long terminal repeat (non-LTR) retrotransposons such as LINE-1 (L1) elements rely on their encoded reverse transcriptase for mobilization within eukaryotic genomes, contributing to insertional mutagenesis and genetic diversity. The LINE-1 reverse transcriptase, part of the ORF2 protein, catalyzes the conversion of an RNA intermediate into DNA via target-primed reverse transcription, enabling the element's integration into new genomic sites and often disrupting gene function through insertions in exons, introns, or regulatory regions. This process has been implicated in over 120 human diseases, including Duchenne muscular dystrophy, where LINE-1 insertions in the dystrophin gene cause exon skipping or frameshifts, and hemophilia A and B due to disruptions in the F8 and F9 genes, respectively. In cancers, deregulated LINE-1 retrotransposition, driven by this reverse transcriptase activity, generates somatic insertions that promote genomic instability, with hundreds of such events observed in esophageal cancers and dozens in colorectal tumors, occasionally acting as driver mutations by inactivating tumor suppressors like APC.^[22]^[23] In eukaryotes, the reverse transcriptase domain of telomerase reverse transcriptase (TERT) is essential for telomere maintenance, counteracting the progressive shortening of chromosome ends during replication. TERT, the catalytic subunit of the telomerase ribonucleoprotein complex, uses its reverse transcriptase motifs—shared with viral enzymes but including unique extensions like the T motif—to add telomeric repeats to the 3' end of chromosomes, employing an internal RNA template for synthesis. This activity is critical in progenitor and cancer cells to preserve genomic stability, with conserved aspartate residues in the active site enabling the polymerization of DNA from the RNA template. Dysregulation of TERT reverse transcriptase contributes to cellular immortalization in tumors by sustaining telomere length.^[24] Recent discoveries have elucidated the anti-phage defense function of reverse transcriptases in bacteria, particularly within retrons, which were first identified in the 1980s but recognized for their role in defense mechanisms analogous to CRISPR systems starting in 2020. Retrons consist of a reverse transcriptase paired with a non-coding RNA that serves as a template to produce single-stranded DNA, triggering abortive infection by killing phage-infected host cells and protecting bacterial populations. As of 2025, thousands of retron variants have been predicted bioinformatically across diverse bacterial species, with retrons classified into over 13 types based on effector function and operon structure, and ongoing research exploring their applications in genome editing.^[25]^[26]^[27]^[28]

Mechanism of Action

Reverse Transcription Process

Reverse transcription is a key enzymatic process catalyzed by reverse transcriptase (RT), an RNA-dependent DNA polymerase that synthesizes a complementary DNA (cDNA) strand from a single-stranded RNA template, ultimately producing double-stranded DNA (dsDNA) for integration into the host genome.^[29] In retroviruses, this process occurs within the viral core shortly after entry into the host cell cytoplasm and involves multiple steps, including primer binding, strand synthesis, template degradation, and strand transfers.^[29] The enzyme's dual activities—polymerase and ribonuclease H (RNase H)—enable the coordinated progression from RNA to dsDNA. The process initiates with the binding of a host-derived transfer RNA (tRNA) primer to the primer-binding site (PBS) near the 5' end of the viral RNA genome, typically an 18-nucleotide complementary sequence.^[29] For example, in HIV-1, tRNA^Lys3 serves as the primer, annealed via base pairing to the PBS. RT's RNA-dependent DNA polymerase activity then extends the 3' end of the tRNA primer, incorporating deoxynucleoside triphosphates (dNTPs) to synthesize the minus-strand strong-stop DNA (-sssDNA), a short segment of about 180 nucleotides that copies the U5 and R regions up to the RNA's 5' end.^[29]^[30] This polymerization reaction follows the equation:

\text{(RNA-DNA)}_n + \text{dNTP} \rightarrow \text{(RNA-DNA)}_{n+1} + \text{PP}_\text{i}

where (RNA-DNA)_n represents the RNA-templated DNA-primer complex, dNTP is the incoming nucleotide, and PPi is pyrophosphate released. The reaction requires two Mg²⁺ ions as cofactors in the active site, coordinated by conserved aspartate residues (e.g., Asp110, Asp185, Asp186 in HIV-1 RT), which stabilize the transition state, align the dNTP's α-phosphate for nucleophilic attack by the primer's 3'-OH, and facilitate PPi release. Following -sssDNA synthesis, RT's RNase H domain degrades the RNA template in the RNA:DNA hybrid, except for RNase H-resistant regions like the polypurine tract (PPT).^[29] This degradation exposes the -sssDNA's terminal repeat (R) sequence, enabling the first strand transfer: the -sssDNA anneals to the complementary R region at the 3' end of the RNA template via intra- or intermolecular jumping, often facilitated by nucleocapsid protein.^[29] Minus-strand DNA synthesis then resumes, extending from the tRNA primer across the full template until RNase H removes the tRNA, leaving the minus-strand DNA with PBS complementarity at its 5' end. The central PPT, a purine-rich segment resistant to RNase H, primes plus-strand synthesis, generating plus-strand strong-stop DNA (+sssDNA) that includes the PBS.^[29] The second strand transfer occurs when the +sssDNA's PBS anneals to the complementary PBS on the minus-strand DNA, displacing any remaining RNA fragments.^[29] Concurrently, RT's DNA-dependent DNA polymerase activity completes both strands: minus-strand synthesis proceeds using the plus-strand as template (after RNase H removal of PPT RNA), and plus-strand synthesis uses the minus-strand, resulting in linear dsDNA flanked by long terminal repeats (LTRs). The dsDNA is then processed by host ligases to form the mature provirus ready for integration.^[29] While the core mechanism is conserved, differences arise in non-retroviral contexts, such as LTR retrotransposons. In these elements, like yeast Ty1, reverse transcription also uses tRNA or self-priming and involves similar strand transfers, but template switching—facilitated by two RNA copies—is more prominent during minus-strand synthesis to repair template discontinuities, without the intercellular transmission seen in retroviruses.^[16] The RT structure, with its p66/p51 heterodimer and catalytic domains, supports these activities through coordinated polymerase and RNase H functions.

Replication Fidelity and Error Mechanisms

Reverse transcriptase (RT) exhibits significantly lower replication fidelity than cellular DNA polymerases, primarily due to its error-prone polymerization process. Typical error rates for retroviral RTs range from 10^{-4} to 10^{-5} errors per nucleotide incorporated, which is orders of magnitude higher than the 10^{-7} to 10^{-9} rates achieved by proofreading-proficient DNA polymerases. In human immunodeficiency virus type 1 (HIV-1), this translates to approximately 0.3 to 1 mutation per genome per replication cycle, fostering substantial genetic diversity that enables immune evasion and drug resistance.^[31]^[32]^[33]^[34] The primary mechanisms underlying this low fidelity stem from the absence of a 3'→5' exonuclease proofreading domain in RT, which prevents the removal of misincorporated nucleotides during synthesis. Unlike DNA polymerases that utilize this activity to correct errors in real time, RT relies solely on its polymerase domain, leading to frequent base substitutions, insertions, and deletions. To mitigate certain replication challenges, such as damaged or discontinuous templates, RT employs template switching as an alternative error-correction strategy; this process allows the enzyme to dissociate from a flawed template and reanneal to a homologous one, often facilitating recombination or bypass of lesions.^[35]^[36] Template switching is particularly critical during minus-strand DNA synthesis, where RT performs obligatory intramolecular jumps to complete long terminal repeats (LTRs) in the proviral DNA. According to the strand transfer or "jumping" model, synthesis of the minus-strand strong-stop DNA initiates at the primer-binding site and proceeds to the 5' end of the RNA template, after which RT dissociates and transfers to the 3' end of the same or another RNA molecule using repeated sequences (R regions) for alignment. This mechanism not only ensures genome completion but also promotes high-frequency recombination in heterozygous virions, with most events occurring during minus-strand extension. Experimental reconstitution of these transfers has confirmed that homology and pausing at template ends enhance switching efficiency, underscoring its role in viral propagation.^[37]^[38]^[39] The elevated error rate of RT has profound evolutionary implications for retroviruses, driving the formation of quasispecies—dynamic populations of closely related variants within a host. This mutational cloud, generated primarily by RT infidelity during each replication cycle, allows rapid adaptation to selective pressures such as host immunity or antiviral therapies, as seen in HIV-1 where quasispecies diversity correlates with disease progression. While cellular factors like APOBEC3G can further increase mutations, RT errors remain the dominant contributor to this hypervariability.^[40]^[41]^[42]

Molecular Structure

Overall Protein Architecture

Reverse transcriptase (RT) enzymes typically function as monomers in some organisms, such as in bacterial group II introns, but in retroviruses like HIV-1, they form heterodimers essential for stability and activity. The HIV-1 RT heterodimer consists of a p66 subunit (approximately 66 kDa, 560 amino acids) and a p51 subunit (approximately 51 kDa, 440 amino acids), where p51 is generated by proteolytic cleavage of p66, retaining the N-terminal polymerase domain but lacking the C-terminal RNase H domain.^[43] The p66 subunit exhibits a right-hand architecture characteristic of polymerases, comprising five distinct domains: fingers (residues 1–84 and 118–155), palm (residues 85–117 and 156–237), thumb (residues 238–318), connection (residues 319–426), and RNase H (residues 427–560).^[43] In contrast, the p51 subunit folds into a more compact structure with fingers, palm, and thumb domains but adopts a closed conformation that supports the p66 active site without catalytic function.^[43] The overall architecture of RT reveals a cleft formed by the fingers, palm, and thumb domains of p66, which binds the primer-template nucleic acid in a manner analogous to a hand gripping a substrate.^[44] This structural motif facilitates the positioning of the RNA-DNA hybrid for polymerization. The first high-resolution crystal structure of HIV-1 RT, determined in 1992 at 3.5 Å resolution in complex with the non-nucleoside inhibitor nevirapine, provided seminal insights into this domain organization and the asymmetric nature of the heterodimer.^[44] Evolutionarily, RTs trace their origins to an ancient polymerase superfamily shared with DNA-dependent DNA polymerases, particularly family A enzymes like Escherichia coli DNA polymerase I, as evidenced by conserved motifs in the palm domain responsible for nucleotide binding and catalysis.^[45] However, RTs exhibit unique adaptations, including a larger thumb subdomain and specialized residues for RNA template recognition, distinguishing them from standard DNA polymerases while enabling reverse transcription.^[45]

Catalytic Domains and Active Sites

Reverse transcriptase (RT) possesses distinct catalytic domains that enable its polymerase and RNase H activities, integral to the reverse transcription process. The polymerase domain, located primarily in the palm subdomain of the p66 subunit, houses the active site responsible for DNA synthesis from an RNA template. This site features three conserved aspartic acid residues—Asp110, Asp185, and Asp186—that coordinate two magnesium ions (Mg²⁺) essential for the nucleotidyl transfer reaction.^[46] These residues facilitate the two-metal-ion mechanism, where one Mg²⁺ ion polarizes the α-phosphate of the incoming dNTP, while the other stabilizes the transition state during phosphodiester bond formation.^[47] The RNase H domain, situated at the C-terminus of the p66 subunit, catalyzes the hydrolysis of the RNA strand in RNA-DNA hybrids. Its active site contains a conserved DEDD motif comprising Asp443, Glu478, Asp498, and Asp549, which similarly coordinate two Mg²⁺ ions to enable endonucleolytic cleavage.^[48] This motif positions the ions to activate a water molecule for nucleophilic attack on the RNA phosphodiester backbone, resulting in the reaction:

\text{RNA-DNA hybrid} \xrightarrow{\ce{H2O}} \text{cleaved RNA fragments} + \text{DNA}

The cleavage occurs preferentially 5' to the RNA-DNA junction, producing 5'-phosphate and 3'-hydroxyl termini on the RNA products.^[49] Beyond the primary active sites, RT exhibits allosteric regulation and dynamic conformational shifts that modulate catalysis. Allosteric sites, such as the non-nucleoside inhibitor binding pocket near the polymerase active site, influence enzyme flexibility without directly participating in substrate binding.^[50] During nucleotide incorporation, the polymerase domain undergoes an open-to-closed transition, wherein the fingers subdomain rotates approximately 20° toward the palm upon dNTP binding, closing around the incoming nucleotide to align it precisely for catalysis.^[51] This motion, driven by interactions between conserved residues like Tyr115 and the template-primer, enhances fidelity and efficiency by excluding water and stabilizing the active conformation.^[52]

Applications and Inhibitors

Antiretroviral Drugs and Inhibition

Reverse transcriptase (RT) inhibitors form a cornerstone of antiretroviral therapy for HIV-1 infection, targeting the viral enzyme essential for reverse transcription of RNA into DNA. These drugs are classified into two main categories: nucleoside reverse transcriptase inhibitors (NRTIs), which mimic natural nucleosides and act as substrate analogs, and non-nucleoside reverse transcriptase inhibitors (NNRTIs), which bind to a distinct allosteric site on the enzyme. Both classes disrupt viral replication but through different mechanisms, and their combined use in highly active antiretroviral therapy (HAART) regimens has dramatically improved patient outcomes by suppressing viral loads and preventing disease progression. Emerging classes include nucleoside reverse transcriptase translocation inhibitors (NRTTIs) like islatravir, which entered phase 3 trials by 2023 for long-acting formulations (as of 2025).^[53] NRTIs, such as zidovudine (AZT), were the first class approved for HIV treatment, with AZT receiving FDA approval in 1987 as a monotherapy option before the shift to combinations. These prodrugs are intracellularly phosphorylated to their triphosphate forms, which compete with endogenous deoxyribonucleoside triphosphates (dNTPs) for incorporation into the growing DNA chain by HIV-1 RT. Once incorporated, NRTIs like AZT-triphosphate lack a 3'-hydroxyl group, preventing formation of the next phosphodiester bond and causing chain termination of viral DNA synthesis. This competitive inhibition at the polymerase active site effectively halts reverse transcription, though NRTIs can also exhibit some non-competitive effects depending on the assay conditions. NNRTIs, exemplified by efavirenz, bind non-competitively to an allosteric pocket approximately 10 Å from the active site, inducing conformational changes that distort the enzyme's polymerase domain and inhibit DNA polymerization without directly competing with dNTP substrates. Efavirenz, approved in 1998, exemplifies this class by stabilizing RT in an inactive conformation, with typical IC₅₀ values around 2 nM against wild-type HIV-1 RT in enzymatic assays. Resistance to NNRTIs often arises rapidly due to their low genetic barrier; the K103N mutation in RT, for instance, alters the allosteric pocket to reduce efavirenz binding affinity by up to 20-fold, conferring cross-resistance to other first-generation NNRTIs. In terms of inhibition kinetics, NRTIs function primarily as competitive inhibitors with respect to the dNTP substrate, where their efficacy depends on the Km for natural nucleotides, leading to IC₅₀ values in the 0.1–1 μM range for AZT-triphosphate under saturating template-primer conditions. In contrast, NNRTIs exhibit non-competitive kinetics, showing IC₅₀ values largely independent of substrate concentration, typically 1–100 nM for efavirenz, reflecting their allosteric mode that locks RT in a catalytically impaired state. These kinetic profiles guide dosing and combination strategies to maximize potency while minimizing toxicity. Clinically, RT inhibitors are integral to HAART regimens, which combine at least three drugs from different classes to achieve undetectable plasma viral loads in over 90% of adherent patients with modern regimens, with early HAART trials from the late 1990s demonstrating suppression rates of 50-70% and dramatically reducing HIV-related mortality by more than 70%. However, monotherapy or suboptimal regimens often lead to resistance emergence via mutations like M184V for NRTIs or K103N for NNRTIs, necessitating multi-drug approaches with boosted protease inhibitors or integrase strand transfer inhibitors to suppress replication and preserve future options. Ongoing monitoring of viral load and genotypic resistance testing underpins these strategies, ensuring sustained virologic suppression and immune reconstitution.

Uses in Molecular Biology and Biotechnology

Reverse transcriptase plays a pivotal role in molecular biology by enabling the synthesis of complementary DNA (cDNA) from RNA templates, facilitating the study of gene expression and RNA-based processes. In reverse transcription polymerase chain reaction (RT-PCR), reverse transcriptase first converts RNA into cDNA, which is then amplified via PCR to detect and quantify specific transcripts. This technique is essential for analyzing gene expression levels, identifying transcript variants, and generating cDNA libraries for cloning and sequencing, particularly in challenging samples with low RNA abundance or secondary structures. One-step RT-PCR protocols integrate reverse transcription and amplification in a single reaction tube, minimizing contamination risks and streamlining workflows for rapid RNA detection, such as in loop-mediated isothermal amplification (RT-LAMP) assays completed in under 15 minutes at 60–65°C.^[54]^[55] Commercial reverse transcriptases, derived from viral sources, have been optimized for enhanced performance in quantitative RT-PCR (qRT-PCR). Moloney murine leukemia virus (M-MLV) reverse transcriptase, a single-subunit enzyme of 71 kDa, operates optimally at 37°C but engineered variants with reduced RNase H activity exhibit increased thermostability up to 55°C, allowing efficient cDNA synthesis from long RNAs (>5 kb) and structured templates. Avian myeloblastosis virus (AMV) reverse transcriptase, a 170 kDa heterodimer active across 25–58°C (optimal at 42–48°C), excels in transcribing shorter RNAs (<5 kb) with strong secondary structures due to its higher processivity and tolerance for divalent cations like Mn²⁺. Variants such as SuperScript IV RT, an M-MLV mutant, provide up to 100-fold higher cDNA yields, reduced cycle threshold values by up to 8 cycles in qRT-PCR, and resistance to inhibitors, making it ideal for high-throughput gene expression profiling in microarrays and RNA sequencing (RNA-Seq). These enzymes support unbiased representation of RNA populations and are widely used in two-step or one-step qRT-PCR formats for precise quantification normalized to housekeeping genes like GAPDH. In 2025, Promega licensed a novel engineered reverse transcriptase from Watchmaker Genomics to enhance accuracy and sensitivity in RNA analysis.^[56]^[57]^[58]^[59] Recombinant telomerase reverse transcriptase (TERT), the catalytic subunit of telomerase, is employed in biotechnology to investigate telomere maintenance and cellular senescence. In telomere studies, recombinant human TERT (hTERT) restores telomere length in somatic cells, overcoming replicative senescence and enabling indefinite proliferation for cell-based therapies, such as engineering telomerase-immortalized smooth muscle cells for vascular grafts. Overexpression of TERT in mouse models delays aging phenotypes by improving epithelial barrier fitness in skin and intestines, extending median lifespan by up to 26% in cancer-resistant strains through reduced DNA damage and enhanced stem cell function. These applications extend to anti-aging research, where TERT activation counters age-related telomere attrition without oncogenic cooperation, supporting tissue engineering and autotransplantation strategies.^[60]^[61] In the 2020s, engineered reverse transcriptases from bacterial retrons have advanced synthetic biology and genome editing by producing multicopy single-stranded DNA (ssDNA) in vivo for precise insertions. Retrons, which encode reverse transcriptase fused to noncoding RNA templates, generate ssDNA via self-primed reverse transcription, enabling efficient recombineering in prokaryotes and eukaryotes. Recent discoveries of retrons like Asa1 and Squ1 from environmental bacteria have been optimized into "recombitrons" for phage genome editing and multiplexed modifications, achieving up to 30% efficiency in 10 bp deletions in E. coli. These systems, triggered by phage elements for natural defense, now support donor template production for CRISPR-independent editing in mammalian cells and vertebrates, expanding tools for synthetic biology applications such as pathway engineering and therapeutic DNA delivery.^[27]

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Thus recombination could occur during reverse transcription, by RNA template switching, or after reverse transcription, by breakage and reunion of DNA. It ...Missing: bypass | Show results with:bypass
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Determination of the site of first strand transfer during Moloney ...
Models for reverse transcription propose that reverse transcriptase must perform two specialized template switches, known as 'strand transfers' or 'jumps ...Introduction · Results · Discussion<|control11|><|separator|>
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Most Retroviral Recombinations Occur during Minus-Strand DNA ...
During reverse transcription, the first strand of DNA synthesized is minus in polarity since it is synthesized from the positive-sense RNA molecule, which is ...
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“Might as Well Jump!” Template Switching by Retroviral Reverse ...
One consequence of the template switching nature of reverse transcriptases is a high rate of intramolecular template switching, which leads to defective genome ...Missing: bypass | Show results with:bypass
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Mutation Rates and Intrinsic Fidelity of Retroviral Reverse ...
Although cellular polymerases and host factors contribute to retroviral mutagenesis, the RT errors play a major role in retroviral mutation.
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[PDF] 117 RETROVIRAL MUTATION RATES AND REVERSE ... - IMR Press
Retroviruses, like all RNA viruses, exhibit a high mutation rate. Polymerization errors during DNA synthesis by reverse transcriptase, which lacks a ...
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Molecular Biology and Diversification of Human Retroviruses
The extremely high error rates associated with HIV-1 and other retroviral polymerases are due in part to a lack of intrinsic proofreading ability, which ...
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Structure and function of HIV-1 reverse transcriptase - PubMed Central
The two enzymatic functions of RT, polymerase and RNase H, cooperate to convert the RNA into a double-stranded linear DNA. This conversion takes place in the ...
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Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase ...
A 3.5 angstrom resolution electron density map of the HIV-1 reverse transcriptase heterodimer complexed with nevirapine, a drug with potential for treatment of ...Missing: Arnold | Show results with:Arnold
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Natural History of DNA-Dependent DNA Polymerases - NIH
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HIV-1 Reverse Transcriptase/Integrase Dual Inhibitors
The palm subdomain contains three catalytic carboxylates (Asp110, Asp185, and Asp186), which bind two Mg2+ divalent ions needed for catalytic processing (60).
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Avoiding Drug Resistance in HIV Reverse Transcriptase
Jan 28, 2021 · Here we provide an in-depth review of HIV reverse transcriptase, current RT inhibitors, novel RT inhibitors, and mechanisms of drug resistance.
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HIV-1 Ribonuclease H: Structure, Catalytic Mechanism and Inhibitors
The residues of the conserved DEDD motif are shown and red and marked with arrows. B Crystal structures of the RNase H domain of HIV-1 RT (PDB code:1RTD) [5] ...
[40]
Inhibitors of HIV-1 Reverse Transcriptase—Associated ... - MDPI
The HIV RT RNase H active site contains four highly conserved catalytic acidic residues (D443, E478, D498 and D549) located in a cavity that also includes the ...
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Conformational Changes in HIV-1 Reverse Transcriptase Induced ...
In this article, we review the structural, computational and experimental evidence of the NNRTI-induced conformational changes in HIV-1 RT.
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An open and closed case for all polymerases - ScienceDirect
Feb 15, 1999 · Open (shown in thick lines) and closed (thin lines) conformations in (a) HIV-1 RT and (b) Taq DNA polymerase. The tip of the fingers subdomain ...
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Structure of HIV-1 reverse transcriptase cleaving RNA in an ... - PNAS
Jan 2, 2018 · Crystal Structure of the HIV ... K Das, SG Sarafianos, E Arnold, Structural requirements for RNA degradation by HIV-1 reverse transcriptase.
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Reverse Transcription Applications | Thermo Fisher Scientific - US
Common applications of RT-PCR include detection of expressed genes, examination of transcript variants, and generation of cDNA templates for cloning and ...
[45]
Application of Reverse Transcription-PCR and Real-Time PCR in ...
Reverse transcription involves the synthesis of DNA from RNA by using an RNA-dependent DNA polymerase. PCR can amplify a single or a few copies of a piece of ...
[46]
M-MuLV reverse transcriptase: Selected properties and improved ...
Nov 22, 2021 · The reverse transcriptase of Moloney MuLV is a typical RT, being a single subunit enzyme with a molecular mass of 71 kDa, length 671 a.a., ...
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How to Choose the Right Reverse Transcriptase
Prior to PCR, AMV must be inactivated because AMV RT, like M-MLV RT, can inhibit Taq DNA polymerase (9). The enzyme can be inactivated by heating at 70–100°C, ...
[48]
SuperScript IV Reverse Transcriptase | Thermo Fisher Scientific - US
SuperScript IV Reverse Transcriptase (RT) is a proprietary MMLV (Moloney Murine Leukemia Virus) RT mutant designed for reduced RNase H activity, ...
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Telomerase and the aging process - PMC - NIH
The absence of telomerase activity in most human somatic cells results in telomere shortening during aging. Telomerase activity can be restored to human cells ...
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https://pmc.ncbi.nlm.nih.gov/articles/PMC1298242/
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New retron systems from environmental bacteria identify triggers of ...
Retrons are bacterial immune systems that protect a bacterial population against phages by killing infected hosts. Retrons typically comprise a reverse ...Missing: 2020s | Show results with:2020s