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Phosphoramidite

Phosphoramidites are phosphorus(III)-derived compounds, typically featuring a P-N bond, that serve as essential building blocks in organic synthesis, most notably for the automated production of oligonucleotides such as DNA and RNA analogs.^[1] These reagents enable the efficient construction of phosphodiester linkages through a solid-phase approach, allowing for the stepwise addition of nucleosides in the 3' to 5' direction with high yields and purity.^[2] The phosphoramidite method, pioneered by Serge L. Beaucage and Marvin H. Caruthers in 1981, revolutionized nucleic acid chemistry by replacing less stable phosphotriester intermediates with more robust phosphoramidite monomers, which are activated under mild acidic conditions for nucleophilic attack by a growing oligonucleotide chain.^[1] This approach involves a cyclic process: detritylation to remove the 5'-dimethoxytrityl (DMT) protecting group using an acid like dichloroacetic acid, coupling of the phosphoramidite monomer facilitated by an activator such as tetrazole, capping of unreacted hydroxyl groups with acetic anhydride to prevent chain truncation, and oxidation of the resulting phosphite triester to a stable phosphate triester using iodine in water.^[2] Each cycle achieves stepwise efficiencies of 98–99.5%, enabling the routine synthesis of oligonucleotides up to 100–200 nucleotides long, far surpassing earlier methods like phosphodiester or phosphotriester approaches in speed and scalability.^[3] Beyond oligonucleotide synthesis, phosphoramidites have found applications in creating modified backbones (e.g., phosphorothioates for therapeutic stability) and as chiral ligands in asymmetric catalysis, underscoring their versatility in both biochemical and synthetic chemistry contexts.^[4] The method's compatibility with automation has democratized access to custom nucleic acids, fueling advancements in genomics, therapeutics (such as antisense oligonucleotides approved for diseases like spinal muscular atrophy), and biotechnology.^[2] Ongoing innovations, including on-demand flow synthesis of phosphoramidites, continue to address scalability challenges for industrial production.^[5]

Chemical Structure and Properties

General Formula and Classification

Phosphoramidites are organophosphorus compounds characterized by the general formula (RO)_2PNR'_2, where R and R' represent alkyl or aryl groups. These molecules represent monoamides derived from phosphite diesters, in which one hydroxyl group of phosphorous acid is replaced by an amino substituent, resulting in a trivalent phosphorus center coordinated to two oxygen atoms and one nitrogen atom. This structural arrangement imparts distinct electronic properties to the phosphorus, making it highly electrophilic at the P center.^[6] As a class of trivalent phosphorus(III) compounds, phosphoramidites are fundamentally distinguished from pentavalent phosphorus(V) species such as phosphates, which feature a phosphoryl (P=O) bond and typically four coordinating substituents around the phosphorus atom. Unlike phosphates, the absence of the P=O bond in phosphoramidites renders the phosphorus more reactive toward nucleophilic attack. Additionally, phosphoramidites differ from related phosphonamidites, which incorporate a direct P-C bond in place of one P-O bond, altering their steric and electronic profiles for specialized applications in phosphorus chemistry.^[7]^[8] A representative example of a simple phosphoramidite is diisopropyl phosphoramidite chloride, often employed as an intermediate in synthetic routes due to its reactivity. In this compound, the diisopropyl groups on the nitrogen enhance solubility and stability while maintaining the core (RO)_2PNR'_2 motif. The P-N bond in phosphoramidites exhibits partial double bond character arising from resonance delocalization of the nitrogen lone pair into the empty p-orbital on phosphorus, which reduces the nucleophilicity of the nitrogen and increases the electrophilicity of the phosphorus center. This resonance stabilization influences the overall reactivity profile of phosphoramidites in chemical transformations.^[9]^[10]

Reactivity and Stability

Phosphoramidites are highly reactive electrophiles at the phosphorus atom due to the electron-withdrawing nature of the alkoxy substituents and the labile dialkylamino group, which facilitates nucleophilic substitution reactions. This reactivity is harnessed in coupling processes where the phosphorus center is activated by weak acids, such as 1H-tetrazole or 4,5-dicyanoimidazole (DCI), to protonate the nitrogen of the NR₂ moiety, rendering it a better leaving group and enhancing electrophilicity. Tetrazole, with a pKa of 4.9, has been the traditional activator, promoting rapid proton transfer to form a phosphonium-like intermediate that is susceptible to nucleophilic attack. In contrast, DCI (pKa 5.2) offers improved coupling efficiency, often achieving complete reaction in half the time of tetrazole while reducing side reactions, owing to its balanced acidity and nucleophilicity as the conjugate base.^[11]^[12]^[13] The mechanism of activation and coupling involves initial protonation of the phosphoramidite by the activator, followed by nucleophilic attack from the substrate (typically an alcohol, denoted as NuH) on the phosphorus, displacing the protonated amine. This proceeds via an SN2-like displacement at trivalent phosphorus, yielding a phosphite triester intermediate. A simplified representation of the overall process is:

(\ce{RO})_2\ce{PNR2} + \ce{NuH} \rightarrow (\ce{RO})_2\ce{POR'} + \ce{HNR2}

(where R' derives from Nu), though the actual pathway includes the transient protonated species (\ce{RO})_2\ce{P-NHR2+} to facilitate the leaving group departure. The pKa of the activator's conjugate acid influences the rate of protonation; stronger acids like tetrazole provide faster initial activation but can lead to over-acidification and branch formation, while milder ones like DCI optimize yields by minimizing such side products.^[11]^[12] Despite their reactivity, phosphoramidites exhibit moderate stability under controlled conditions but are highly sensitive to moisture and atmospheric oxygen, necessitating handling under inert atmospheres such as argon or nitrogen to prevent hydrolysis and oxidation. Hydrolysis proceeds via nucleophilic attack by water on phosphorus, leading to phosphoramidate or phosphate byproducts, while oxidation converts the P(III) center to P(V) species like phosphonates, which are inactive for coupling. In anhydrous acetonitrile solutions under inert gas, half-lives vary by nucleobase: thymidine phosphoramidites remain >95% pure after five weeks at room temperature, whereas guanosine derivatives degrade faster (purity dropping to ~80% in the same period) due to autocatalytic mechanisms involving trace impurities. These stability profiles underscore the importance of rigorous anhydrous protocols to maintain reagent integrity during use.^[14]^[15]

Synthesis

Classical Preparation Routes

The classical preparation of phosphoramidites for oligonucleotide synthesis relies on phosphorus halide chemistry, involving sequential nucleophilic substitutions starting from phosphorus trichloride (PCl₃) to ultimately form unsymmetric dialkoxy phosphoramidites of the general formula (RO)(R'O)PNR₂, where one alkoxy group (RO) is typically 2-cyanoethyl and the other (R'O) is a protected nucleoside. The process begins with the reaction of PCl₃ with one equivalent of an alcohol (ROH, e.g., 2-cyanoethanol), in the presence of a base such as triethylamine to neutralize the generated HCl, yielding the alkoxy phosphorodichloridite intermediate ROPCl₂. The reaction is conducted under anhydrous conditions at low temperatures (e.g., 0–25°C) in an inert solvent like dichloromethane or diethyl ether to prevent side reactions or hydrolysis.^[16]^[17] The key steps for the phosphitylating agent can be represented as follows:

\ce{PCl3 + ROH ->[base] ROPCl2 + HCl}

\ce{ROPCl2 + HNR2 ->[base] ROPCl NR2 + HCl}

This chlorophosphoramidite intermediate (ROPCl NR₂) then reacts with the 3'-OH group of a 5'-protected nucleoside (R'OH) in the presence of a base to form the final nucleoside phosphoramidite (RO)(R'O)PNR₂:

\ce{ROPCl NR2 + R'OH ->[base] (RO)(R'O)PNR2 + HCl}

This route was foundational in the development of phosphoramidite reagents for oligonucleotide synthesis, where the 2-cyanoethyl group is commonly employed for its compatibility with subsequent deprotection steps.^[1]^[18] In the second step, the phosphorodichloridite intermediate reacts with a secondary amine, such as diisopropylamine (HN(iPr)₂), which has historically been favored due to the steric bulk of the diisopropylamino group, enhancing the reactivity and stability of the resulting chlorophosphoramidite as a phosphitylating agent. The reaction proceeds rapidly at room temperature under anhydrous conditions, with the base (e.g., diisopropylethylamine) scavenging HCl to drive completion. Yields typically exceed 80–90% for these steps when using activated alcohols like 2-cyanoethanol. The final coupling with the nucleoside also achieves high yields under similar conditions.^[17]^[1] Variants employing phosphorus oxychloride (POCl₃) have been used for preparing protected forms of phosphoramidite precursors, particularly in routes leading to P(V)-containing analogs or stabilized intermediates for nucleotide phosphorylation, though these are less common for standard trivalent phosphoramidites.^[19] Purification of the final phosphoramidite is critical due to its sensitivity to moisture, which can lead to hydrolysis and formation of phosphonate byproducts. The crude product is typically isolated by filtration to remove amine hydrochloride salts, followed by distillation under high vacuum (e.g., 0.1–1 mmHg) to achieve purity greater than 95%, often monitored by ³¹P NMR. Storage under nitrogen at low temperatures ensures stability.^[18]^[17]

Modern Synthetic Variations

Modern synthetic variations of phosphoramidite preparation have focused on streamlining processes to enhance efficiency, reduce steps, and improve scalability, particularly for oligonucleotide synthesis applications. One prominent approach involves one-pot flow syntheses utilizing immobilized phosphitylating agents derived from 2-cyanoethyl N,N-diisopropylchlorophosphoramidite precursors. In this method, the precursor is loaded onto a nitrotriazole-functionalized resin packed in a flow reactor, followed by direct reaction with alcohols such as nucleosides in the presence of a base like 9-azajulolidine, yielding the corresponding phosphoramidites without intermediate purification. This enables >98% conversion for a range of substrates within 6 minutes and supports immediate use in automated synthesis, achieving average cycle yields of 98.0% for up to 51-mer oligonucleotides.^[5] Chiral phosphoramidites, essential for asymmetric catalysis, are commonly prepared from atropisomeric diols like BINOL through sequential phosphitylation and amination steps. A representative procedure begins with the reaction of (R)-BINOL with phosphorus trichloride (PCl₃) under reflux to form the chlorophosphite intermediate, followed by nucleophilic substitution with a chiral diamine such as (-)-bis[(S)-1-phenylethyl]amine in the presence of n-butyllithium. The overall process yields the axially chiral phosphoramidite ligand in 86% for the amination step, with the chlorophosphite obtained in quantitative yield after workup. This two-step sequence contrasts with classical PCl₃-based routes by incorporating stereogenic phosphorus control for enhanced enantioselectivity in downstream applications.^[20] To address industrial demands, scalable methods have incorporated microwave assistance and solvent-free conditions to boost reaction rates and yields while minimizing environmental impact. Microwave-assisted phosphitylation of nucleosides, for instance, completes in 10-15 minutes at elevated temperatures, delivering DNA and RNA phosphoramidites in yields of 50-79% for sterically hindered analogs, surpassing traditional heating methods that often require hours. Solvent-free variants, such as those using diisopropylamine and 3-hydroxypropionitrile with PCl₃, achieve >99% purity and excellent overall yields (80-95%) on multi-kilogram scales through controlled impurity management and vacuum distillation. The β-cyanoethyl protecting group is routinely incorporated in these syntheses to confer oxidative stability during storage, preventing premature P(III) to P(V) conversion and ensuring shelf-life extension for commercial reagents.^[21]^[22]^[23]^[24]

History and Development

Early Discoveries

The initial synthesis of phosphoramidites, specifically trivalent phosphorus acid amides of the general form (RO)₂P-NR₂, emerged in the late 1950s as part of broader explorations in organophosphorus chemistry. These compounds were first prepared through the reaction of dialkyl phosphites or chlorophosphites with amines, marking a key advancement in forming stable P-N bonds. Independent discoveries occurred in three laboratories during this period, with one seminal report detailing the preparation and properties of simple dialkyl phosphoramidites in 1961. This work by Petrov and colleagues established the reactivity of these species, highlighting their potential as intermediates in phosphorus-nitrogen compound synthesis. In the pre-1980s era, phosphoramidites played a role in early research on organophosphorus applications, including investigations into pesticides and flame retardants. During the 1950s and 1960s, they were examined as precursors for bioactive phosphorus compounds amid the rapid development of organophosphate insecticides, contributing to the understanding of P-N bonded structures in potential agrochemicals. By the 1970s, studies extended to flame retardant formulations, where phosphorus amides, including phosphoramidite derivatives, were evaluated for enhancing fire resistance in textiles like cotton through phosphorylation mechanisms. A key 1973 study compared various phosphorus amides, demonstrating their efficacy in imparting durable flame retardancy via nitrogen-phosphorus synergy, though challenges in stability limited widespread adoption.^[25] Key publications in the 1970s advanced the mechanistic understanding of P-N bond formation in phosphoramidites, focusing on transamination and substitution reactions. Research employing NMR spectroscopy elucidated addition-elimination pathways involving hydrophosphorane intermediates, confirming catalytic effects from amine hydrochlorides first noted in 1965 but refined through kinetic studies. These efforts, building on earlier foundational work, shifted phosphoramidites from academic curiosities toward versatile synthetic intermediates by the late 1970s, enabling their use in targeted phosphorylations for diverse organophosphorus derivatives.

Key Milestones in Applications

In the 1980s, phosphoramidites were introduced as key reagents in solid-phase DNA synthesis, revolutionizing the automated production of oligonucleotides. Marvin H. Caruthers developed this approach, detailed in a 1983 patent that described the use of nucleoside phosphoramidite compounds for efficient coupling on solid supports, enabling the scalable synthesis of DNA sequences previously limited by labor-intensive methods.^[26] This innovation facilitated the rapid assembly of custom DNA probes and primers, laying the foundation for molecular biology tools and early genomic research. During the mid-1990s, phosphoramidites emerged as chiral ligands in asymmetric catalysis, particularly for copper-catalyzed conjugate additions. In 1996, Ben L. Feringa and colleagues reported the first highly enantioselective 1,4-additions of dialkylzinc reagents to cyclic and acyclic enones using chiral copper complexes of binaphthol-derived phosphoramidites, achieving enantiomeric excesses up to 97% with low catalyst loadings.^[27] This breakthrough expanded phosphoramidite applications beyond nucleic acid synthesis into stereoselective organic transformations, influencing the synthesis of enantiopure pharmaceuticals. The 2000s saw the extension of phosphoramidite chemistry to RNA synthesis and analogs like peptide nucleic acids (PNAs), enhancing therapeutic potential. Advances in protecting group strategies allowed efficient solid-phase assembly of RNA oligonucleotides, with yields improving for sequences up to 100 mers, as phosphoramidites adapted for 2'-O-protected ribonucleosides.^[28] For PNA analogs, phosphoramidite monomers enabled the incorporation of modified backbones, supporting hybrid designs with improved binding affinity.^[29] A 2010 review highlighted the versatility of phosphoramidites as ligands in diverse asymmetric reactions, including hydrogenations and allylic alkylations, underscoring their broad catalytic impact.^[30] By the 2010s, phosphoramidite-synthesized oligonucleotides achieved regulatory milestones in therapeutics, with several FDA approvals validating their clinical utility. For instance, mipomersen, an antisense oligonucleotide for familial hypercholesterolemia synthesized via automated phosphoramidite methods, received approval in 2013, demonstrating efficacy in reducing LDL cholesterol.^[31] This period marked the transition from research tools to approved drugs, including nusinersen in 2016 for spinal muscular atrophy, further establishing phosphoramidite chemistry's role in precision medicine.^[32] Subsequent approvals, such as inclisiran in 2019 for hypercholesterolemia and vutrisiran in 2022 for hereditary transthyretin-mediated amyloidosis (as of November 2025), continued to highlight their therapeutic impact.^[33]^[34]

Applications

In Oligonucleotide and Nucleic Acid Synthesis

Nucleoside phosphoramidites serve as the key building blocks in the solid-phase synthesis of oligonucleotides, enabling the automated assembly of DNA, RNA, and their analogs in the 3' to 5' direction. In this method, originally developed by Marvin Caruthers and colleagues, a 3'-O-phosphoramidite derivative of a protected nucleoside couples to the free 5'-hydroxyl group of a growing oligonucleotide chain attached to a solid support, forming a phosphite triester internucleotide linkage. This intermediate is then oxidized to a stable phosphate triester, which mimics the natural phosphodiester backbone. The process relies on orthogonal protecting groups to control reactivity, ensuring selective chain extension without unwanted side reactions.^[35]^[36] The synthesis cycle consists of four main steps repeated for each nucleotide addition: detritylation, coupling, capping, and oxidation. Detritylation removes the 5'-O-dimethoxytrityl (DMT) protecting group from the terminal nucleoside using a mild acid like dichloroacetic acid in dichloromethane, exposing the 5'-OH for the next coupling. In the coupling step, the incoming 3'-O-(N,N-diisopropylamino)(cyanoethoxy)phosphoramidite monomer is activated by tetrazole or a similar weak acid, facilitating nucleophilic attack by the chain's 5'-OH to form the phosphite triester. Capping with acetic anhydride acetylates any unreacted 5'-OH groups to prevent further extension of truncated chains, while oxidation with iodine in water converts the fragile phosphite to a stable phosphate. A representative coupling reaction can be depicted as:

\text{dA}^{\text{Bz}}-\text{phosphoramidite} + \text{chain-OH} \rightarrow \text{chain-O-P(OR)}_2\text{-O-dA}^{\text{Bz}}

where dA^{Bz} denotes N6-benzoyl-2'-deoxyadenosine, and OR groups are typically cyanoethyl protections. This cycle achieves stepwise elongation with minimal manual intervention on automated synthesizers.^[36] The monomers used are deoxyribo- or ribo-nucleoside phosphoramidites, each with specific protecting groups: the 5'-OH is shielded by a DMT group for acid-labile removal, while exocyclic amines on the bases are protected by benzoyl (for adenine and cytosine) or isobutyryl (for guanine) groups to prevent side reactions during synthesis; thymine and uracil typically require no base protection. These protections are removed post-synthesis via ammonolysis or other deprotection protocols. The method's advantages include exceptionally high coupling efficiencies exceeding 99% per step, allowing reliable synthesis of oligonucleotides up to 200 nucleotides in length, and its compatibility with automation for high-throughput production. However, limitations such as depurination—acid-induced loss of purine bases (particularly adenine) during detritylation—can reduce yields for longer sequences, though this is mitigated by optimized conditions and alternative protecting groups.^[36]^[37]

As Chiral Ligands in Catalysis

Chiral phosphoramidites serve as effective ligands in metal-catalyzed asymmetric reactions, particularly due to their modular structure that allows for tuning of steric and electronic properties to enhance stereoselectivity. These ligands are commonly derived from enantiopure diols such as (R)-BINOL, which imparts axial chirality, or TADDOL, which provides central chirality. A representative example is the (R)-BINOL-based phosphoramidite, where the phosphorus atom is bonded to the two phenolic oxygen atoms of (R)-BINOL and to the nitrogen of a chiral secondary amine, such as (S)-1-(1-naphthyl)ethylamine, forming the P(III) center with a lone pair available for coordination.^[38] This design enables the ligands to form stable complexes with transition metals like copper and palladium, facilitating enantioselective transformations of prochiral substrates.^[39] One of the most prominent applications is in copper(I)-catalyzed enantioselective conjugate additions of dialkylzinc reagents to α,β-unsaturated ketones (enones). In this reaction, the phosphoramidite ligand coordinates to Cu(I), promoting transmetalation from the dialkylzinc to form an alkylcopper intermediate that adds to the β-position of the enone, yielding chiral β-alkyl carbonyl compounds with enantiomeric excesses often exceeding 95%. For instance, the seminal work demonstrated up to 99% ee in additions to cyclic enones using BINOL-derived ligands.^[40] The general reaction scheme is depicted as:

\text{CuX} + (\text{RO})_2\text{PNR}_2 + \text{R}_2\text{Zn} + \ce{enone} \rightarrow \text{chiral } \beta\text{-alkyl enone product}

where RO represents the chiral diolate moiety and NRR' the amine substituent.^[38] Beyond conjugate additions, phosphoramidite ligands have been utilized in enantioselective hydrosilylation reactions since the early 2000s, notably in palladium-catalyzed additions of trichlorosilane to styrenes, achieving high enantioselectivities (up to 99% ee) for the formation of chiral silanes.^[41] Similarly, in palladium-catalyzed allylic alkylations, these ligands enable stereoselective substitution of allylic acetates with carbon or nitrogen nucleophiles, with enantiomeric excesses reaching 95% or higher for various substrates.^[42] The high stereoselectivity in these transformations stems from the bidentate coordination mode of the phosphoramidite ligands to the metal center via the phosphorus and nitrogen donors, creating a chiral environment that restricts substrate approach to one enantiotopic face. This coordination influences the facial selectivity during nucleophilic addition or insertion steps, as elucidated through computational studies on copper-phosphoramidite complexes. Chiral variants of these ligands can be synthesized via modern routes involving phosphitylation of the diol with a chlorophosphoramidite derived from the chiral amine, allowing for systematic variation to optimize performance in specific reactions.^[43]

Emerging Uses in Therapeutics

Phosphoramidite chemistry plays a pivotal role in the synthesis of therapeutic oligonucleotides, such as small interfering RNAs (siRNAs) and antisense oligonucleotides (ASOs), where modified phosphoramidite building blocks enable the incorporation of phosphorothioate (PS) linkages through sulfurization steps to enhance nuclease resistance and pharmacokinetic properties.^[44] In this process, standard phosphite triester intermediates formed during solid-phase synthesis are converted to PS bonds using sulfurizing agents like phenylacetyl disulfide or 3H-1,2-benzodithiol-3-one, which replace the oxidation step to introduce sulfur atoms, thereby improving the stability of these molecules in biological environments without compromising their hybridization capabilities.^[45] This modification is essential for therapeutic applications, as unmodified oligonucleotides degrade rapidly in vivo, and PS linkages have become a cornerstone in approved drugs targeting RNA interference or splice modulation.^[46] A prominent example of phosphoramidite-derived therapeutics is givosiran, approved by the FDA in 2019 for the treatment of acute hepatic porphyria, which utilizes GalNAc-conjugated siRNA synthesized via automated phosphoramidite methods to achieve liver-targeted delivery.^[47] The triantennary GalNAc ligand is incorporated as a phosphoramidite conjugate during solid-phase synthesis, binding to the asialoglycoprotein receptor on hepatocytes to facilitate endocytosis and enable subcutaneous administration with potent gene silencing of ALAS1 mRNA.^[48] Similarly, inclisiran, approved in 2020 for hypercholesterolemia, employs the same GalNAc-siRNA platform to inhibit PCSK9 expression, demonstrating how phosphoramidite versatility supports precise conjugation for tissue-specific efficacy.^[49] Backbone modifications using specialized phosphoramidites further optimize therapeutic performance; for instance, 2'-fluoro (2'-F) phosphoramidites introduce fluorine at the 2' position of the ribose, conferring high RNA binding affinity and substantial resistance to nuclease degradation while maintaining a north conformation similar to RNA.^[50] Locked nucleic acid (LNA) phosphoramidites, featuring a methylene bridge between the 2'-O and 4'-C atoms, lock the sugar in a rigid C3'-endo conformation, resulting in unprecedented duplex thermal stability—up to 10°C increase per substitution—and enhanced specificity for mismatch discrimination in ASOs targeting disease-related transcripts.^[51] These modifications, often combined in chimeric designs, have been integral to clinical successes, such as in exon-skipping therapies for Duchenne muscular dystrophy.^[52] Despite these advances, challenges persist in phosphoramidite-based oligonucleotide therapeutics, including immunogenicity from PS linkages that can trigger immune responses via Toll-like receptor activation, and off-target effects arising from unintended hybridization to partially complementary RNAs, potentially leading to toxicity.^[53] Strategies to mitigate these include sequence optimization and additional chemical shielding, though they require rigorous preclinical assessment.^[54] By 2020, the cumulative impact of these technologies had transformed gene therapy landscapes, with oligonucleotide therapeutics achieving a market value of approximately $0.88 billion amid several FDA approvals, underscoring their role in expanding precision medicine for rare and chronic diseases.^[55] Since then, the field has continued to expand, with additional approvals including tofersen (Qalsody) in 2023 for amyotrophic lateral sclerosis (ALS) in patients with SOD1 mutations, imetelstat (Rytelo) in 2024 for myelodysplastic syndromes, and donidalorsen (Dawnzera) in August 2025 for prophylactic treatment of hereditary angioedema in patients aged 12 and older.^[56]^[57]^[58] As of April 2025, the FDA has approved 22 oligonucleotide therapeutics. The market has grown substantially, reaching approximately $6.2 billion in 2025.^[59]

Recent Advances

Sustainable and Green Chemistry Approaches

Efforts to reduce the use of hazardous solvents in phosphoramidite-based oligonucleotide synthesis have focused on replacing acetonitrile, the primary solvent in solid-phase synthesis, with greener alternatives such as acetone, tetrahydrofuran (THF), 2-methyltetrahydrofuran (2-MeTHF), and gamma-valerolactone (GVL). These water-miscible or bio-based options, adapted from advancements in solid-phase peptide synthesis, aim to minimize environmental toxicity and volatility while maintaining coupling efficiency. For instance, studies have demonstrated the feasibility of PEG-based liquid-phase systems, which enable solvent-efficient precipitation and isolation of growing oligonucleotide chains, potentially reducing overall solvent consumption by up to 30-50% compared to traditional solid-phase methods.^[60]^[61] Recycling of phosphoramidite reagents has emerged as a key strategy to address phosphorus waste, with methods involving the recovery of unreacted amidites and phosphorus-containing byproducts for reuse in phosphitylation steps. Techniques such as solvent extraction and chromatographic recovery of the 4,4'-dimethoxytriphenylmethyl (DMT) protecting group allow for up to 90% recovery rates, significantly cutting waste generation. In optimized processes, this approach has achieved approximately 50% reduction in overall reagent waste for oligonucleotide production, promoting a more circular economy in phosphorus utilization.^[62]^[63] Fluorinated and hydrophobic phosphoramidite variants enhance purification efficiency by improving separation from hydrophilic impurities during reverse-phase chromatography, reducing the need for extensive solvent washes. The FluoPHOS project, launched in 2023, develops such variants through ionic and radical synthesis routes, incorporating fluorinated groups at the 2'-position of nucleosides to boost oligonucleotide hydrophobicity and stability without compromising yield. These modifications facilitate easier downstream processing and lower solvent usage in purification, contributing to greener manufacturing workflows.^[64] Life-cycle assessments of phosphoramidite synthesis highlight substantial environmental benefits from green modifications, with bio-based starting materials and process optimizations reducing the carbon footprint by 20-30% relative to conventional routes. For example, analyses of solid-phase protocols show that switching to renewable feedstocks for nucleoside cores and minimizing protecting group overhead lowers greenhouse gas emissions primarily from solvent production and energy-intensive steps. Process mass intensity (PMI) metrics further quantify improvements, dropping from an average of 4300 kg waste per kg oligonucleotide to lower values through integrated recycling and solvent recovery.^[62]^[63]

Biocatalytic and Enzymatic Innovations

Recent innovations in oligonucleotide synthesis have shifted toward biocatalytic methods that leverage enzymes like terminal deoxynucleotidyl transferase (TdT) for de novo production, offering alternatives to traditional phosphoramidite-based approaches. TdT, a template-independent polymerase, facilitates the addition of modified nucleotides to the 3' end of DNA strands without requiring a template, enabling controlled chain elongation under mild conditions. Since 2021, researchers have engineered TdT variants to incorporate phosphoramidite-like substrates, such as 3'-O-NH₂-modified nucleotides, achieving stepwise yields up to 98.7% for sequences exceeding 100 nucleotides.^[65] For instance, a 2025 study evolved TdT-33 to handle 3'-phosphate terminators with 99.5% efficiency, supporting the synthesis of kilobase-length DNA.^[65] These advancements build on template-independent addition mechanisms, reducing reliance on harsh chemical reagents.^[66] Chemoenzymatic hybrids have further expanded these capabilities by engineering polymerases to incorporate 2'-modified nucleotides, such as 2'-O-methyl or 2'-azido variants, into oligonucleotides with high fidelity. Optimized enzymes, including modified DNA and RNA polymerases, enable precise positioning of modifications during synthesis, surpassing limitations in traditional in vitro transcription. A 2025 review highlights how these engineered polymerases achieve incorporation efficiencies exceeding 95% for mixed XNA (xeno-nucleic acid) polymers containing 2'-modifications, with overall sequence fidelity above 90%.^[67] For example, variants of T7 RNA polymerase have been evolved to transcribe multiple 2'-modified units sequentially, facilitating the production of therapeutic RNA analogs.^[67] This hybrid approach combines enzymatic catalysis with chemical blocking groups, like 3'-O-azidomethyl, to control addition and deblocking cycles.^[66] These biocatalytic methods provide key advantages over conventional phosphoramidite chemistry, including room-temperature reactions that eliminate the need for solid-phase supports and anhydrous solvents. Enzymatic synthesis occurs in aqueous buffers, promoting sustainability and compatibility with sensitive modifications, as demonstrated in the 2023 production of a 1005-nucleotide DNA strand with 99.9% stepwise yield.^[65] A representative example is the 2024 biocatalytic synthesis of 2'-modified ribonucleoside analogs using nucleoside transglycosylase-2 (LlNDT-2), which achieved up to 96% conversion in one step for arabino-configured nucleosides, bypassing multi-step chemical phosphoramidation.^[68] Such processes also exhibit superior stereoselectivity, yielding enantiomerically pure products without chiral resolution.^[68] Despite these benefits, enzymatic innovations face limitations, particularly in scale-up and yield consistency compared to chemical methods. While optimized TdT systems reach 97-99.5% coupling efficiencies for short to medium oligonucleotides, broader applications often yield 70-95% due to enzyme instability and substrate intolerance for complex modifications.^[66] In contrast, phosphoramidite synthesis routinely achieves 99% per step, enabling longer error-free sequences on solid supports.^[65] Scale-up challenges persist, with current enzymatic platforms limited to milligram quantities, hindering industrial adoption for therapeutic production.^[65] Ongoing engineering efforts aim to address secondary structure formation and polymerase robustness to close this gap.^[66]

References

[1]
Deoxynucleoside phosphoramidites—A new class of key ...
The development of a new class of nucleoside phosphites is described. These compounds are stable to normal laboratory conditions, are activated by mild acid ...
[2]
Oligonucleotides: evolution and innovation | Medicinal Chemistry ...
Nov 21, 2024 · This review examines several oligonucleotide synthesis techniques, including phosphodiester, phosphotriester, and phosphoramidite approaches.
[3]
Expansion of Phosphoramidite Chemistry in Solid-Phase ...
Feb 22, 2023 · Our strategy using this new phosphoramidite chemistry is promising for the tandem solid-phase synthesis of diverse oligonucleotides.Missing: review | Show results with:review
[4]
On-demand synthesis of phosphoramidites | Nature Communications
May 12, 2021 · The highly optimised automised chemical oligonucleotide synthesis relies upon phosphoramidites as the phosphate precursors and one of the ...
[5]
[PDF] Asymmetric catalysis with chiral monodentate phosphoramidite ...
compound with (RO)2PNR2 as a general structure) is their role as activated monomers (7.1) for the solid phase oligonucleotide synthesis (7.2) (Scheme 7.1).1.
[6]
Combined Approaches to Site-Specific Modification of RNA
A typical nucleotide phosphoramidite has a 3′ pentavalent phosphorous group (phosphate) on the nucleotide replaced with a trivalent phosphorous group. Post ...
[7]
Mechanisms of the substitution reactions of phosphoramidites and ...
Nov 17, 2003 · Mechanistic research on the nucleophilic substitution of trivalent phosphorus compounds is reviewed with emphasis on the reactions of ...
[8]
CN113248556A - Assembly of nucleic acid grafted azobenzene ...
... diisopropyl phosphoramidite chloride under the protection of the inert gas, and stirring and reacting for one hour at room temperature;. (3) and after the ...
[9]
[PDF] Synthesis, Structural Characterization and Catalytic Activity ... - CORE
Mar 3, 2016 · suggesting a substantial P=N double bond character in the phosphoramidite ligand.[13a,14a]. The elongated P-N bond lengths in the P(pyr)3 ...
[10]
Studies on the role of tetrazole in the activation of phosphoramidites
The mechanism of the tetrazole-activated coupling step in the synthesis of oligonucleotides via phosphoramidites is studied with the help of model reactions.
[11]
Efficient activation of nucleoside phosphoramidites with 4,5 ... - NIH
The observed time to complete coupling is twice as fast with 4, 5-dicyanoimidazole (DCI) as the activator, compared with 1 H -tetrazole.
[12]
US6642373B2 - Activators for oligonucleotide synthesis
Activators with a higher pKa (i.e., less acidic) than 1H-tetrazole (pKa 4.9) such as 4,5-dicyanoimidazole (pKa 5.2) have been used in the phosphitylation of 5′- ...
[13]
Solution stability and degradation pathway of deoxyribonucleoside ...
The solution stability of the phosphoramidites decreases in the order T, dC>dA>dG. After five weeks storage under inert gas atmosphere the amidite purity ...
[14]
Solution Stability and Degradation Pathway of Deoxyribonucleoside ...
Aug 7, 2025 · The reaction of 2'-deoxynucleoside phosphoramidites with water is an important degradation reaction that limits the lifetimes of reagents used ...
[15]
2-CYANOETHYL PHOSPHORODICHLORIDITE synthesis
For example, the reaction of phosphorous trichloride (PCl3) with either 2-cyanoethanol or trimethylsilyloxypropionitrile (TMSOP) gives CDP in good yield. If ...
[16]
Nucleic Acids Book - Chapter 5: Solid-phase oligonucleotide synthesis
Phosphoramidite oligo synthesis proceeds in the 3'- to 5'-direction (opposite to the 5'- to 3'-direction of DNA biosynthesis in DNA replication). One nucleotide ...Solid supports · The Phosphoramidite method · Oligonucleotide deprotection
[17]
2‐Cyanoethyl Diisopropylchlorophosphoramidite - Beaucage
Oct 15, 2002 · The reagent is prepared from the reaction of N,N-diisopropylamine or its N-trimethylsilyl derivative with (2-cyanoethoxy)dichlorophosphine in anhydrous diethyl ...
[18]
Use of phosphorus oxychloride in synthesizing nucleotides ... - NIH
Procedures are described for phosphorylating protected nucleotides, oligonucleotides and phosphoramidate oligonucleotide derivatives at the 3′-hydroxyl group.Missing: phosphoramidite | Show results with:phosphoramidite
[19]
phosphoramidite (feringa) ligands - Organic Syntheses Procedure
In general, two procedures starting with phosphorus(III) chlorides have been employed for the synthesis of phosphoramidites. Feringa used a phosphoryl ...Missing: dialkyl | Show results with:dialkyl
[20]
Microwave‐Assisted Phosphitylation of DNA and RNA Nucleosides ...
Feb 15, 2018 · ... yields of DNA and RNA phosphoramidites were obtained within 10 to 15 min. These results demonstrate that microwave-assisted phosphitylation ...
[21]
Microwave-assisted preparation of nucleoside-phosphoramidites
### Summary of Microwave-Assisted Synthesis of DNA and RNA Phosphoramidites
[22]
Large-scale synthesis of high purity “Phos reagent” useful for ...
Phosphoramidites 3 and solid-support 4 are the two critical raw materials that contribute >80% of the total raw material cost required for oligonucleotide ...
[23]
Chemical synthesis of biologically active oligoribonucleotides using ...
The preparation of fully protected diisopropylamino-β-cyanoethyl ribonucleoside phosphoramidites with regioisomeric purity > 99.95% is described. It is ...
[24]
A Comparison of Some Phosphorus Amides as Flame Retardants for Cotton1 - Cletus E. Morris, Leon H. Chance, 1973
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[25]
US4415732A - Phosphoramidite compounds and processes
The present new phosphoramidites are stable under normal laboratory conditions to hydrolysis and air oxidation, and are stored as dry, stable powders. Therefore ...
[26]
Enantioselective Conjugate Addition of Dialkylzinc Reagents to ...
Nov 1, 1996 · Enantioselective Conjugate Addition of Dialkylzinc Reagents to Cyclic and Acyclic Enones Catalyzed by Chiral Copper Complexes of New Phosphorus ...
[27]
New nucleoside phosphoramidites and coupling protocols for solid ...
New nucleoside phosphoramidites and coupling protocols for solid-phase RNA synthesis ... expansion of the genetic code. Nature 1992, 356 (6369) , 537-539 ...
[28]
synthesis of a monocharged peptide nucleic acid (pna) analog and ...
Nov 18, 1998 · ABSTRACT: The preparation of a novel phosphoramidite monomer based on thyminyl acetic acid coupled to the secondary nitrogen of ...
[29]
Phosphoramidites: Privileged Ligands in Asymmetric Catalysis
Mar 23, 2010 · Phosphoramidites have developed into one of the most effective ligands in enantioselective transition-metal catalysis.
[30]
Oligonucleotide Therapies: The Past and the Present - PMC - NIH
In this review we address the development of oligonucleotide (ON) medicines from a historical perspective by listing the landmark discoveries in this field.
[31]
Chemistry, structure and function of approved oligonucleotide ...
VITRAVENE (fomivirsen) was the first antisense therapeutic approved by the FDA, and the only antiviral oligonucleotide-based drug brought to market to date (9, ...
[32]
Deoxyoligonucleotide synthesis via the phosphoramidite method
Deoxyoligonucleotide synthesis via the phosphoramidite method. Gene Amplif Anal. 1983:3:1-26. Authors. M H Caruthers , S L Beaucage, C Becker, J W Efcavitch ...Missing: paper | Show results with:paper
[33]
Synthesis of DNA/RNA and Their Analogs via Phosphoramidite and ...
Nov 18, 2013 · The chemical synthesis of DNA and RNA is universally carried out using nucleoside phosphoramidites or H-phosphonates as synthons.
[34]
Glen Report 22.19 - Technical Brief - Depurination
Depurination is more likely to occur in the base protected monomers used for oligonucleotide synthesis than in the nucleosides themselves.
[35]
Phosphoramidites: Marvellous Ligands in Catalytic Asymmetric ...
This Account presents the breakthrough realized in this field using chiral phosphoramidite ligands for copper-catalyzed dialkylzinc additions.
[36]
New biphenol-based, fine-tunable monodentate phosphoramidite ...
These ligands have found a wide range of applications in metal-catalyzed asymmetric transformations such as hydrogenation (5, 8–10), 1,4-additions of ...Missing: 1996 Angewandte
[37]
Highly Enantioselective Catalytic Conjugate Addition and Tandem ...
Dec 15, 1997 · Complete stereocontrol with the added advantage of functional-group tolerance in copper-catalyzed 1,4-additions of organozinc reagents to enones ...
[38]
Synthesis and application of bulky phosphoramidites - RSC Publishing
Asymmetric hydrosilylation of styrenes with trichlorosilane in the presence of palladium complexes of these bulky ligands gave chiral silanes in high yields ...
[39]
Chiral P-monodentate phosphoramidite and phosphite ligands for ...
In summary, a series of phosphoramidites and phosphites were tested in the palladium-catalyzed asymmetric allylic alkylation of different substrates with ...
[40]
Phosphoramidite Ligands Based on Simple 1,2‐Diols: Synthesis ...
Jul 12, 2016 · Phosphoramidite ligands are widely used in catalysis and normally constructed from large C2-symmetrical diols such as BINOL or TADDOL.
[41]
Modern approaches to therapeutic oligonucleotide manufacturing
Apr 12, 2024 · Synthetic methods typically use solid-phase phosphoramidite chemistry that involves iterative coupling, capping, oxidation, and deprotection ...
[42]
Sulfurizing Reagent II and its use in Synthesizing Oligonucleotide ...
The replacement of one non-bridging oxygen atom in the phosphodiester linkage of DNA or RNA by sulfur creates a phosphorothioate (PS) linkage. This is one of ...Missing: therapeutic | Show results with:therapeutic
[43]
Why and How to Control P-Chirality in Phosphorothioated ...
Dec 6, 2024 · The most common approach for synthesis of therapeutic oligonucleotides is the phosphoramidite ... Stereoselective Synthesis of Phosphorothioate- ...
[44]
Pharmacokinetics and Pharmacodynamics of GalNAc‐Conjugated ...
Aug 17, 2023 · In 2018, patisiran, a lipid nanoparticle (LNP)-formulated siRNA, was approved by the US Food and Drug Administration (FDA) for the treatment of ...
[45]
GalNAc-siRNA Conjugates: Leading the Way for Delivery of RNAi ...
GalNAc-siRNA conjugates use tris-GalNAc to bind to the ASGPR on liver cells, enabling rapid endocytosis and delivery of siRNAs into the cytoplasm.
[46]
General Platform for Efficient and Modular Assembly of GalNAc ...
Feb 24, 2025 · a) FDA-approved siRNA–tGalNAc therapeutics and the workflow of solid-phase synthesis of siRNA–tGalNAc conjugates. b) This work. PANAC ...Introduction · Experimental Section · Results and Discussion · Conclusion
[47]
Systematic evaluation of 2′-Fluoro modified chimeric antisense ...
Apr 15, 2019 · 2′-Fluoro (2′-F) is a potent RNA analogue that possesses high RNA binding affinity and resistance to nuclease degradation with good safety ...
[48]
Glen Report 16.24 - Locked Nucleic Acid (LNA™) Phosphoramidites
Oligonucleotides containing LNA exhibit unprecedented thermal stabilities towards complementary DNA and RNA2, which allows excellent mismatch discrimination. In ...
[49]
Locked nucleic acid (LNA): High affinity targeting of RNA for ...
A key feature of oligonucleotides containing LNA nucleotides is the very high thermal stability of duplexes towards complementary RNA [1, 2, 3, 5, 7, 8].
[50]
Off-target effects of oligonucleotides and approaches of preclinical ...
Off-target effects may arise via hybridization with unintended RNA targets exhibiting partial sequence homology (RNA off-target) or from non-nucleic acid ...
[51]
Nucleic acid drugs: recent progress and future perspectives - Nature
Nov 29, 2024 · Since then, siRNA drugs have had issues with stability, immunogenicity, off-target effects, safety, and the delivery system. However, after ...
[52]
Global Oligonucleotide Therapy Market Report 2020-2030
Mar 23, 2021 · The global oligonucleotide therapy market is expected to decline from $0.9 billion in 2019 to $0.88 billion in 2020 at a compound annual growth ...
[53]
From green innovations in oligopeptide to oligonucleotide ...
Jan 2, 2023 · Moreover, because SPOS chemistry is based on phosphoramidites, their stability is of primary importance in order to avoid the unwanted waste of ...
[54]
From liquid-phase synthesis to chemical ligation - PubMed Central
Nov 4, 2025 · ... phosphate protecting groups are usually used with phosphoramidite chemistry and phosphotriester chemistry, respectively. Cyanoethyl groups ...
[55]
Sustainability Challenges and Opportunities in Oligonucleotide ...
Nov 30, 2020 · In this Perspective, we summarize the present challenges in oligonucleotide synthesis, purification, and isolation; highlight potential solutions; and ...Missing: immunogenicity | Show results with:immunogenicity
[56]
Sustainable Approaches in Solid-phase Oligonucleotide Synthesis
Oct 18, 2024 · The use of bio-based raw materials allows a reduction of greenhouse gas emissions, making these protocols more sustainable to support the ...
[57]
Fluorinated phosphoramidite synthesis for the development of ... - ANR
Fluorinated phosphoramidite synthesis for the development of new oligonucleotides with improved stability and hydrophobicity – FluoPHOS ... project: December 2023 ...Missing: variants | Show results with:variants
[58]
Enzymatic Strategies for Next-Generation DNA Synthesis
Sep 3, 2025 · Computational Design of a Thermostable and Highly Active Terminal Deoxynucleotidyl Transferase for Synthesis of Long De Novo DNA Molecules.
[59]
Controlled enzymatic synthesis of oligonucleotides - Nature
Jun 18, 2024 · This Perspective article summarizes recent progress made in controlled enzymatic synthesis, where temporary blocked nucleotides are incorporated into ...
[60]
Recent Advances in Biocatalytic and Chemoenzymatic Synthesis of ...
Jan 24, 2025 · We review recent biocatalytic and chemoenzymatic methods to construct oligonucleotides, highlighting innovations in enzyme engineering, and substrate ...
[61]
Biocatalytic synthesis of ribonucleoside analogues using nucleoside ...
Dec 11, 2024 · In this study, we demonstrate enzymatic transglycosylation catalysed by LlNDT-2 using a 2′-modified nucleoside sugar donor either in the arabino ...