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Primer extension

Primer extension is a fundamental technique in molecular biology for mapping the 5′ ends of primarily RNA transcripts, enabling precise identification of transcription start sites (TSS) and processing events.^[1] The method relies on the hybridization of a short, labeled DNA primer complementary to a known sequence downstream from the expected 5′ end of the target nucleic acid, followed by enzymatic extension using reverse transcriptase to synthesize complementary DNA (cDNA) up to the 5′ terminus.^[2] This produces fragments whose lengths correspond to the distance from the primer annealing site to the 5′ end, which are then resolved by denaturing polyacrylamide gel electrophoresis alongside sequencing ladders for accurate positioning.^[3] Developed as an alternative to nuclease protection assays, primer extension offers high sensitivity and single-nucleotide resolution, making it particularly valuable for studying gene regulation in prokaryotes and eukaryotes.^[1] Key applications include quantifying RNA transcript levels under different conditions, detecting RNA modifications or cleavages (such as those induced by RNases or chemical treatments), and analyzing promoter architecture by locating elements like TATA boxes.^[2] Traditional implementations use radiolabeled primers for detection via autoradiography, though modern variants employ fluorescence-based labeling to enhance safety, speed, and compatibility with automated sequencers, reducing analysis time to a single day.^[3] While highly precise, the technique can be limited by RNA secondary structures that impede reverse transcription or by the need for high-quality RNA samples to avoid artifacts from degradation.^[1] It complements other methods like 5′ rapid amplification of cDNA ends (5′-RACE) by providing direct, in vivo mapping without cloning steps, and has been instrumental in studies of bacterial toxin-antitoxin systems and mRNA processing in organisms such as Escherichia coli and Staphylococcus aureus.^[3]

Definition and Principle

Overview

Primer extension is a molecular biology technique employed to map the 5' ends of RNA transcripts with high precision. The method entails hybridizing a radiolabeled or fluorescently labeled oligonucleotide primer to a complementary sequence on an RNA template, followed by enzymatic extension of the primer from its 3' end using reverse transcriptase, an RNA-dependent DNA polymerase. This process synthesizes a complementary DNA (cDNA) strand that terminates at the 5' terminus of the RNA template, yielding a product whose length reflects the distance from the primer-binding site to the RNA's 5' end.^[3] The core utility of primer extension lies in its ability to identify transcription start sites (TSS), quantify specific RNA molecules, and detect post-transcriptional modifications. For TSS mapping, the size of the extended cDNA is resolved via gel electrophoresis, providing nucleotide-level resolution of initiation points. In quantification applications, the signal intensity of the extension product correlates with RNA abundance, offering a sensitive assay for monitoring transcript levels without amplification artifacts. Additionally, RNA modifications like 2'-O-methylation impede reverse transcriptase progression, resulting in truncated products that pinpoint modification sites.^[4] In contrast to DNA primer extension techniques used in polymerase chain reaction (PCR) or Sanger sequencing, which rely on DNA polymerases and DNA templates, primer extension for RNA analysis is tailored to RNA substrates via reverse transcription, enabling direct interrogation of eukaryotic and prokaryotic transcripts in their native context. This specificity distinguishes it as a foundational tool in nucleic acid studies, particularly for unraveling gene regulation at the 5' end.^[3]

Mechanism of Extension

In primer extension, the core biochemical process involves the action of reverse transcriptase (RT), a specialized DNA polymerase capable of synthesizing complementary DNA (cDNA) strands using an RNA template. Commonly employed enzymes include those derived from Avian Myeloblastosis Virus (AMV RT) or Moloney Murine Leukemia Virus (MMLV RT), such as SuperScript variants, which initiate synthesis at the 3' end of an annealed DNA primer. These enzymes catalyze the template-directed polymerization of deoxynucleotide triphosphates (dNTPs), forming phosphodiester bonds to extend the primer in the 5' to 3' direction, thereby generating a cDNA product that mirrors the RNA sequence upstream of the primer binding site.^[5]^[6] The molecular steps begin with primer annealing, where the oligonucleotide primer, typically 20-25 nucleotides long and complementary to a specific RNA sequence, hybridizes to the target RNA via Watson-Crick base-pairing, often 50-150 nucleotides downstream from the RNA's 5' end. Upon addition of RT, dNTPs, and necessary cofactors (e.g., Mg²⁺ ions), the enzyme binds to the RNA-DNA hybrid at the primer's 3' terminus. Extension proceeds through sequential addition of dNTPs, with the RT's active site selecting the appropriate nucleotide based on base-pairing rules with the RNA template; each incorporation releases pyrophosphate and advances the primer by one nucleotide. The reaction terminates naturally upon reaching the RNA's 5' end, yielding a defined-length cDNA, or prematurely at sites of RNA modifications (e.g., bulky adducts like pseudouridine or methylation) that impede enzyme progression due to steric hindrance or altered base-pairing.^[5]^[3]^[7] Several factors influence the efficiency and accuracy of extension. The fidelity of RT, defined as its error rate during nucleotide incorporation, varies between enzymes—AMV RT exhibits lower fidelity (approximately 1 error per 10,000-20,000 nucleotides) compared to engineered MMLV variants like SuperScript III (1 per 20,000-30,000), impacting the sequence accuracy of the cDNA product. Processivity, the enzyme's ability to continuously extend without dissociating, is critical for complete synthesis; MMLV RT typically achieves 5-7 kb per binding event, sufficient for the short extensions in this assay, while AMV RT offers higher thermostability for GC-rich templates. Additionally, labeled dNTPs (e.g., radiolabeled α-³²P-dNTPs or fluorescent analogs) can be incorporated during extension to enable downstream detection via autoradiography or fluorescence, enhancing sensitivity without altering the core mechanism.^[6]^[8]^[5] Extension products in primer extension assays generally range from 50 to 500 nucleotides, determined by the primer's position relative to the transcription start site (TSS); shorter distances (e.g., 50-150 nt) are preferred for optimal resolution on denaturing gels, while longer extensions up to 500 nt accommodate variable TSS positions or modification mapping.^[5]^[3]

Experimental Procedure

Primer Design and Preparation

Primers for primer extension assays are synthetic DNA oligonucleotides designed to be complementary to a specific region of the target RNA, typically positioned 50-150 nucleotides downstream from the anticipated 5' end to produce extension products of resolvable length on denaturing polyacrylamide gels. These primers are generally 15-30 nucleotides long to balance specificity and annealing efficiency, with a GC content of 40-60% to promote stable hybridization without excessive bias toward G-C pairing.^[9] The melting temperature (Tm) is optimized to approximately 55-65°C, ensuring efficient annealing under standard reverse transcription conditions while minimizing non-specific binding. Primer design requires careful consideration to avoid artifacts such as secondary structures, primer-dimer formation, or off-target annealing, which can lead to inaccurate mapping of RNA ends. Software tools like Primer3 are widely employed for this purpose, allowing users to input target sequences and generate candidates that minimize self-complementarity (ΔG > -9 kcal/mol for 3' end) and ensure specificity through BLAST analysis against relevant genomes. The positioning of the primer is selected to yield products in the 50-200 nucleotide range, facilitating clear separation and sizing during downstream analysis without overloading the gel resolution limits. Labeling of primers is essential for detecting extension products and is typically performed at the 5' end to monitor the precise length from the primer to the RNA 5' terminus. Radioactive labeling with ^{32}P is achieved by incubating the primer with [\gamma-^{32}P]ATP and T4 polynucleotide kinase, providing high sensitivity for autoradiographic detection. Alternatively, non-radioactive fluorescent labeling, such as with dyes like HEX or IRDye at the 5' end during oligonucleotide synthesis, offers safer handling and compatibility with capillary electrophoresis or laser scanners.^[3] To ensure high-quality primers free from contaminants that could interfere with reverse transcription, purification is a critical step post-synthesis. High-performance liquid chromatography (HPLC) or denaturing polyacrylamide gel electrophoresis (PAGE) is used to isolate full-length primers, removing truncated failure sequences and salts that might cause non-specific stops or low yields.^[10] PAGE purification, in particular, provides superior resolution for primers longer than 20 nucleotides, yielding >95% full-length product essential for reproducible experiments.^[11]

Performing the Extension Reaction

The primer extension reaction involves assembling the necessary reagents and executing a series of temperature-controlled incubations to enable reverse transcription from the annealed primer. Typical reagents include 1-10 μg of total RNA or poly(A)+ RNA as the template, 0.1-1 pmol of 5'-end-labeled oligonucleotide primer complementary to the RNA of interest, 10-50 units of reverse transcriptase (such as AMV or M-MLV), and 0.5 mM each of the four dNTPs (dATP, dCTP, dGTP, dTTP). The reaction buffer is commonly composed of 50 mM Tris-HCl (pH 8.3), 75 mM KCl, and 3 mM MgCl₂, often supplemented with 10 mM DTT to maintain enzyme activity. The total reaction volume is usually 10-50 μL to ensure efficient mixing and temperature equilibration.^[12]^[13]^[14] To initiate the reaction, the RNA sample and labeled primer are first denatured to disrupt secondary structures, typically by heating at 65°C for 5 minutes or 90°C for 2 minutes, followed by snap-cooling on ice to prevent re-annealing of the RNA alone. Primer annealing then occurs by incubating the mixture at 42-50°C (optimized near the primer's melting temperature) for 30-60 minutes, allowing specific hybridization to the target RNA site. The reverse transcriptase is added after annealing to minimize non-specific interactions, and extension proceeds at 42-50°C for 30-60 minutes, during which the enzyme synthesizes complementary DNA using the RNA as template and incorporating the dNTPs. Temperature control is critical throughout, as deviations can lead to primer dissociation, incomplete extension, or enzyme inactivation.^[12]^[13]^[14] The reaction is terminated by adding EDTA to chelate Mg²⁺ (final concentration 10-20 mM) or by heating at 90-95°C for 5 minutes to inactivate the enzyme. For enhanced reliability, an RNase inhibitor (20-40 units) should be included during annealing and extension to prevent RNA degradation by contaminating RNases. Control reactions, such as those omitting reverse transcriptase, are essential to verify the absence of non-specific primer extension or RNA self-priming artifacts. These steps ensure the production of defined cDNA products ready for downstream analysis.^[12]^[13]^[14]

Analysis of Products

Following the primer extension reaction, the products are typically separated by size to resolve the extended cDNA fragments from unincorporated primers and other reaction components. Denaturing polyacrylamide gel electrophoresis (PAGE) is the most common separation technique, using gels with 6-12% acrylamide concentration in the presence of 7 M urea to ensure single-stranded conformation and high resolution of fragments differing by as little as one nucleotide.^[12] For applications requiring even higher throughput and precision, capillary electrophoresis can be employed, offering automated separation in a polymer-filled capillary under denaturing conditions, which minimizes band distortion and enables analysis of multiple samples simultaneously.^[15] Detection of the separated products relies on the labeling strategy used for the primer, such as radioactive or fluorescent tags incorporated during primer preparation. For radioactively labeled primers (e.g., with ^{32}P or ^{33}S), autoradiography via exposure to X-ray film or phosphorimaging screens visualizes the bands, providing high sensitivity for low-abundance transcripts.^[12] Fluorescently labeled primers allow detection through laser-induced fluorescence imaging systems, which offer real-time quantification and reduced exposure times compared to radioactivity-based methods.^[3] Size calibration is achieved by running a DNA sequencing ladder (e.g., from a dideoxy sequencing reaction) alongside the samples, enabling precise determination of fragment lengths in nucleotides. Interpretation of the gel or electropherogram focuses on the position and intensity of the product bands relative to the size markers. The length of the extended product directly corresponds to the distance from the 3' end of the primer to the 5' end of the RNA, indicating the transcription start site (TSS) position; for instance, a 150-nucleotide product signifies a TSS 150 nucleotides upstream of the primer annealing site. Multiple discrete bands may reveal alternative TSS usage, RNA processing events like capping or cleavage, or heterogeneous primer annealing due to secondary structures.^[12] Quantification of specific RNA targets is performed by measuring band intensities using densitometry for film autoradiographs or digital analysis via phosphorimaging or fluorescence scanners, often normalized against internal controls or known standards to estimate transcript abundance.^[12] This approach achieves high sensitivity, detecting as little as 0.1-1 pg of specific RNA, making it suitable for analyzing rare transcripts in complex samples.

Applications

Mapping Transcription Start Sites

Primer extension serves as a precise method for mapping transcription start sites (TSS) by adapting the standard extension reaction to target the 5' ends of RNA transcripts. A radiolabeled or fluorescently labeled oligonucleotide primer, complementary to a sequence approximately 100-200 nucleotides downstream of the predicted promoter region, is annealed to isolated total RNA or poly(A)+ RNA. Reverse transcriptase then extends the primer upstream to the 5' terminus of the transcript, generating a complementary DNA (cDNA) product whose length, visualized via denaturing polyacrylamide gel electrophoresis alongside a sequencing ladder, directly indicates the distance from the primer annealing site to the TSS. This allows nucleotide-resolution mapping when aligned with the known genomic sequence.^[16] The technique excels at resolving TSS heterogeneity, particularly in eukaryotic genes driven by TATA-less promoters, which often exhibit multiple initiation sites clustered within a narrow window of 10-50 nucleotides. In such cases, primer extension produces a series of discrete bands on the gel, each corresponding to a distinct TSS; these can be quantified for relative usage and precisely positioned by comparison to adjacent genomic promoter elements, such as initiator (Inr) motifs or downstream promoter elements (DPE). For instance, studies of human TATA-less promoters containing the XCPE2 core element have shown that mutations in this motif abolish specific TSS clusters, confirming its role in directing multiple start sites.^[17] In prokaryotic systems, primer extension has mapped TSS in operons like the lac operon of Escherichia coli, where the primary start site is located 7 nucleotides downstream of the -10 hexamer motif, facilitating integration with promoter architecture such as the -35 region and upstream elements. Similarly, in eukaryotic mRNAs, the method integrates with motifs like the TATA box, positioning the TSS typically 25-35 nucleotides downstream; this was exemplified in early applications to the human β-globin gene, where primer extension in the 1980s identified the predominant cap site at position +1 relative to the translation start, amid heterogeneous 5' ends.^[18]

Quantification of Specific RNAs

Primer extension serves as a quantitative method to measure the relative or absolute abundance of specific RNA transcripts by reverse transcribing RNA using a gene-specific primer and detecting the resulting cDNA products. This approach leverages the enzymatic extension by reverse transcriptase to produce labeled or amplified products proportional to the input RNA levels, enabling precise assessment without the need for full-length cDNA synthesis.^[19] For accurate quantification, protocols incorporate internal standards such as synthetic RNA spikes or normalization to stable housekeeping RNAs like 5.8S rRNA to account for variations in RNA input, reverse transcription efficiency, and detection sensitivity. The linear range of reverse transcriptase, typically spanning several orders of magnitude (e.g., from femtomolar to picomolar RNA concentrations), ensures that extension products reflect true transcript levels within this dynamic window, provided the reaction conditions maintain enzyme processivity. In miRNA-specific assays, DNA standards are often included to generate calibration curves via real-time PCR following extension, allowing absolute quantification in copies per unit of total RNA.^[20]^[21]^[22] The technique exhibits high sensitivity for low-abundance RNAs, detecting as few as tens to thousands of molecules per cell, which surpasses traditional Northern blotting in both limit of detection and RNA economy. Validation against Northern blots confirms its reliability, with primer extension requiring less total RNA (e.g., 1-20 µg) while yielding comparable or superior signal-to-noise ratios for rare transcripts. Protocols optimized in the late 1990s and early 2000s for microRNA quantification achieve low replicate variation, often below 10%, through enhancements like locked nucleic acid (LNA) primers that improve specificity and extension efficiency.^[22]^[20]^[21] Applications include monitoring dynamic changes in gene expression, such as upregulation of stress-response transcripts following environmental stimuli like heat shock or chemical exposure. Multiplexing is facilitated by using pools of primers targeting multiple RNAs, enabling simultaneous quantification of several transcripts in a single reaction, as demonstrated in targeted RNA-seq variants of the method. Product detection typically involves gel electrophoresis or sequencing for size-based readout, ensuring accurate measurement of extension lengths corresponding to RNA abundance.^[23]^[19]

Detection of RNA Modifications

Primer extension serves as a sensitive method for detecting post-transcriptional RNA modifications by exploiting the reduced processivity of reverse transcriptase enzymes at modified sites, resulting in premature termination of cDNA synthesis and the production of truncated products. Certain modifications, such as pseudouridine (Ψ), N1-methyladenosine (m¹A), and 2'-O-methylation (Nm), impede the enzyme's progression, leading to stops or pauses that can be visualized as distinct bands on denaturing gels. For instance, Ψ detection typically involves prior chemical treatment with reagents like 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMC), which forms an adduct that blocks reverse transcription one nucleotide upstream of the modified site. In contrast, 2'-O-methylation causes direct pausing due to steric hindrance at low dNTP concentrations, while m¹A similarly halts extension by altering base-pairing. This approach is particularly effective for modifications that are RT-sensitive, though it is less suitable for "RT-silent" marks like N⁶-methyladenosine (m⁶A), which do not inherently cause stops without additional enzymatic engineering.^[7]^[4] The protocol for modification detection via primer extension requires targeted RNA annealing with a radiolabeled or fluorescently tagged DNA primer complementary to a sequence downstream of the suspected modification site, followed by reverse transcription under controlled conditions to enhance sensitivity to stops. Modification-sensitive enzymes, such as avian myeloblastosis virus (AMV) reverse transcriptase for 2'-O-methylation or SuperScript II for general RT pausing at sites like m¹A, are employed; reactions are performed at low dNTP concentrations (e.g., 0.04 mM) to amplify pausing effects, with parallel high-dNTP (e.g., 4 mM) controls to confirm modification-specific truncation rather than sequence-induced stops. Products are separated on urea-denaturing polyacrylamide gels and compared to dideoxy sequencing ladders for precise mapping, often using total RNA without prior purification to maintain endogenous context. Validation against unmodified synthetic RNA or in vitro transcribed controls ensures specificity, and the technique can detect single modifications with high resolution.^[4]^[7]^[24] In applications, primer extension has been widely used to map modification sites in structured RNAs like ribosomal RNA (rRNA), transfer RNA (tRNA), and select mRNAs, contributing to epitranscriptomics by revealing functional roles in stability, translation, and stress responses. For example, it has mapped Ψ and Nm sites in yeast rRNA and tRNA, elucidating their contributions to ribosome biogenesis and decoding accuracy. The method's single-nucleotide sensitivity has facilitated studies of yeast tRNA modifications since the early 2000s, often combined with dimethyl sulfate (DMS) probing for structural validation and to distinguish modification effects from base-pairing influences. These insights have advanced understanding of epitranscriptomic regulation in model organisms and beyond.^[7]^[24]^[25]

Advantages and Limitations

Advantages

Primer extension provides high precision in mapping the 5' ends of RNA transcripts to single-nucleotide resolution, enabling accurate determination of transcription start sites without the ambiguity often seen in lower-resolution techniques. This level of detail is achieved through the use of labeled primers and gel electrophoresis, which directly visualizes the extended products.^[3] The method exhibits strong sensitivity, capable of detecting low-abundance or rare transcripts directly from total RNA samples without requiring amplification steps that could introduce bias, such as those in PCR-based approaches like 5'-RACE. This direct extension minimizes artifacts and ensures faithful representation of transcript endpoints, even in complex mixtures. In terms of practicality, primer extension is straightforward and cost-effective, relying on standard molecular biology reagents and equipment—including reverse transcriptase, oligonucleotide primers, and polyacrylamide gel systems—without the need for cloning, specialized sequencing instruments, or extensive optimization in initial setups. It offers quicker results compared to amplification-dependent methods for TSS mapping, often completing in a single day with minimal hands-on time.^[3]^[26] The technique's versatility extends to diverse RNA species, including those from prokaryotic and eukaryotic sources, as well as small non-coding RNAs and long mRNAs, due to its reliance on specific primer annealing rather than global enzymatic processing. This allows reliable application across organismal kingdoms without adjustments for RNA capping or polyadenylation differences.^[3] Compared to S1 nuclease protection assays, primer extension excels in handling heterogeneous 5' ends, resolving multiple transcription start sites as discrete bands on gels rather than producing a diffuse smear that complicates interpretation.^[27]

Limitations and Alternatives

One major limitation of primer extension is its requirement for prior knowledge of the target RNA sequence to design a specific oligonucleotide primer that anneals downstream of the region of interest, limiting its applicability to genes with known sequences.^[28] Additionally, the reverse transcriptase enzyme used in the reaction can prematurely terminate at RNA secondary structures or post-transcriptional modifications, potentially leading to artifactual stops that misrepresent the true 5' end or modification sites.^[29]^[30] Without multiplexing strategies, the method is inherently low-throughput, suitable primarily for analyzing individual transcripts rather than genome-wide profiling.^[23] The technique is also highly sensitive to RNA degradation, as even partial breakdown of the sample can result in incomplete extension products and inaccurate mapping of transcript ends.^[31] For quantification, primer extension offers lower accuracy when detecting very low-abundance RNAs compared to amplification-based methods like quantitative PCR (qPCR), which provide greater sensitivity through exponential amplification. Alternatives to primer extension include 5' rapid amplification of cDNA ends (5' RACE), which enables mapping of unknown transcription start sites (TSSs) using a gene-specific primer (requiring some prior sequence knowledge) and a universal anchor, though it can introduce biases from nontemplated nucleotide additions by reverse transcriptase or incomplete cDNA synthesis.^[32]^[33] Cap analysis of gene expression (CAGE) serves as another option, particularly for identifying TSSs in capped mRNAs through selective capture of the 5' cap structure followed by sequencing, offering higher specificity for promoter-proximal regions but requiring intact caps.^[34] High-throughput RNA sequencing (RNA-seq) provides a genome-wide alternative for TSS mapping, capturing a broader range of transcripts without sequence-specific primers, yet it is more costly and may lack the single-nucleotide precision of primer extension for targeted loci due to alignment ambiguities.^[35] In the 2010s, primer extension was largely supplanted by next-generation sequencing (NGS)-based TSS sequencing methods like CAGE-seq and differential RNA-seq for large-scale studies, owing to their scalability and ability to profile thousands of TSSs simultaneously; however, primer extension remains favored for targeted validation of specific transcripts where high precision and simplicity are prioritized.^[35]

History and Development

Early Developments

The early developments of primer extension trace back to foundational experiments in DNA sequencing during the 1960s. Ray Wu and colleagues utilized Escherichia coli DNA polymerase I to perform controlled extension of short oligonucleotides annealed to single-stranded DNA templates, enabling the determination of nucleotide sequences at specific genomic locations. In a pivotal 1968 study, Wu and Kaiser applied this approach to fill in the 5' overhanging cohesive ends of bacteriophage λ DNA, successfully sequencing the 12-nucleotide single-stranded regions and establishing the core principle of location-specific primer extension.^[36] Building on this, Wu refined the method in 1972 by introducing synthetic oligonucleotides as primers to initiate enzymatic extension from defined positions along the template, allowing rapid sequencing of up to 50 nucleotides in a single reaction. This "primed synthesis" technique, demonstrated on bacteriophage φX174 DNA ends, marked a significant advancement in controlled DNA synthesis and directly inspired later adaptations for nucleic acid analysis.^[37] The adaptation of primer extension to RNA occurred in the 1970s, facilitated by the discovery of reverse transcriptase—an RNA-dependent DNA polymerase—in retroviral particles by David Baltimore and Howard Temin in 1970. This enzyme enabled the synthesis of complementary DNA (cDNA) from RNA templates, bridging the gap for RNA-specific applications. By the late 1970s, researchers adapted the DNA primer extension protocol for RNA mapping using reverse transcriptase to extend DNA primers annealed to RNA transcripts, precisely identifying 5' ends and internal sequences. A key methodological paper in 1978 by Ghosh et al. detailed this primer-directed cDNA synthesis for sequencing RNA, applied initially to map heterogeneous 5' termini of polyoma virus early region transcripts.^[38] In the 1980s, primer extension protocols matured for mapping transcription start sites (TSS) in eukaryotic genes, often integrated with restriction enzyme mapping to localize initiation points relative to genomic landmarks. For instance, in studies of the human β-globin gene introduced into mouse erythroleukemia cells, Charnay et al. (1984) employed primer extension alongside S1 nuclease protection to confirm accurate TSS usage and mRNA processing, revealing position-independent expression patterns that advanced understanding of globin gene regulation.

Modern Advancements

In the late 1990s and early 2000s, quantitative variants of primer extension emerged, particularly for microRNA (miRNA) analysis, through the development of real-time reverse transcription polymerase chain reaction (RT-PCR) methods that leverage stem-loop primers to enable specific and sensitive quantification of mature miRNAs.^[39] These approaches improved upon traditional primer extension by incorporating TaqMan probes for real-time monitoring, allowing precise measurement of miRNA expression levels with high dynamic range and minimal preprocessing.^[39] Concurrently, the adoption of thermostable reverse transcriptases, such as engineered variants from Moloney murine leukemia virus, enhanced the fidelity and processivity of primer extension reactions, reducing error rates during cDNA synthesis and enabling more accurate quantification in complex samples.^[40] High-throughput adaptations in the 2010s integrated primer extension with next-generation sequencing (NGS), exemplified by multiplexed primer extension sequencing (MPE-seq), which employs pools of gene-specific reverse transcription primers to enrich and sequence targeted RNA regions, including transcription start sites (TSS), at high resolution.^[23] This method supports parallel analysis of thousands of transcripts by generating barcoded cDNA libraries, facilitating genome-wide TSS mapping and isoform quantification without the need for full transcriptome sequencing, thus improving efficiency and cost-effectiveness for large-scale studies.^[23] Barcoded primers further enable combinatorial indexing, allowing simultaneous processing of multiple samples or targets in a single NGS run while maintaining traceability and reducing off-target noise.^[41] Specialized variants addressed detection of RNA modifications, such as N6-methyladenosine (m6A), through modification-sensitive reverse transcription strategies developed in the 2000s and refined later; these exploit altered reverse transcriptase processivity at m6A sites, often using engineered polymerases that induce stops or misincorporations for site-specific mapping via primer extension followed by sequencing. Additionally, non-radioactive fluorescent labeling replaced traditional radiolabeling, with methods like fluorescence-based primer extension (FPE) using dye-conjugated primers or dideoxynucleotides to visualize extension products via capillary electrophoresis, thereby reducing hazards and enabling high-sensitivity detection of TSS and processing sites.^[3] A landmark 2018 study utilized time-resolved X-ray crystallography to visualize nonenzymatic primer extension on RNA templates, capturing atomic-level intermediates of activated nucleotide incorporation and revealing mechanistic insights that inform synthetic biology efforts toward enzyme-independent RNA replication.^[42]

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[37]
Real-time quantification of microRNAs by stem–loop RT–PCR
A novel microRNA (miRNA) quantification method has been developed using stem–loop RT followed by TaqMan PCR analysis.
[38]
Increased Thermostability and Fidelity of DNA Synthesis of Wild ...
In this study, we report on the thermal stability and fidelity of DNA synthesis of O_WT RT. Thermal stabilities of O_WT, BH10_WT and MLV RTs have been compared ...
[39]
BART-Seq: cost-effective massively parallelized targeted ...
Aug 6, 2019 · The barcode-primer assembly method produces differentially barcoded forward and reverse primer sets for combinatorial indexing and ...
[40]
Crystallographic observation of nonenzymatic RNA primer extension
May 31, 2018 · Here we report the direct observation of nonenzymatic RNA primer extension through time-resolved crystallography.