Trace-Level Determination of Acrylonitrile Generated in the Manufacturing Process of Oligonucleotides by Static Headspace Gas Chromatography with an Electron Impact(+) Mass Detector

Guo, Xianghai; Stolee, Jessica A.; Fillon, Yannick; Zou, Lanfang

doi:10.1021/acs.oprd.0c00527

Cited by 6 publications

(11 citation statements)

References 25 publications

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“… This redox-neutral platform, based on the native P(V)-oxidation state, challenges past assumptions of sluggish reactivity and enables access to five relevant P-linkages across a range of sugar backbones (DNA and LNA) and bases (A, T, G, mC) in one oligonucleotide construct. Aside from enabling straightforward access to a wide range of chimeric oligonucleotides, the implementation of this new protocol benefits from a reduced reliance on protecting group chemistry (which eliminates the labile cyanoethyl group and therefore acrylonitrile production upon deprotection), , bespoke additives, and redox manipulations. It is also of note that this new P(V) platform eliminates one full step in the standard SPOS protocol (namely, the phosphorus oxidation).…”

Section: Putting It All Together: Chimeric Oligonucleotides Using a P...mentioning

confidence: 99%

Nature Chose Phosphates and Chemists Should Too: How Emerging P(V) Methods Can Augment Existing Strategies

et al. 2021

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Phosphate linkages govern life as we know it. Their unique properties provide the foundation for many natural systems from cell biology and biosynthesis to the backbone of nucleic acids. Phosphates are ideal natural moieties; existing as ionized species in a stable P(V)-oxidation state, they are endowed with high stability but exhibit enzymatically unlockable potential. Despite intense interest in phosphorus catalysis and condensation chemistry, organic chemistry has not fully embraced the potential of P(V) reagents. To be sure, within the world of chemical oligonucleotide synthesis, modern approaches utilize P(III) reagent systems to create phosphate linkages and their analogs. In this Outlook, we present recent studies from our laboratories suggesting that numerous exciting opportunities for P(V) chemistry exist at the nexus of organic synthesis and biochemistry. Applications to the synthesis of stereopure antisense oligonucleotides, cyclic dinucleotides, methylphosphonates, and phosphines are reviewed as well as chemoselective modification to peptides, proteins, and nucleic acids. Finally, an outlook into what may be possible in the future with P(V) chemistry is previewed, suggesting these examples represent just the tip of the iceberg.

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Section: Putting It All Together: Chimeric Oligonucleotides Using a P...mentioning

confidence: 99%

Nature Chose Phosphates and Chemists Should Too: How Emerging P(V) Methods Can Augment Existing Strategies

et al. 2021

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show abstract

“…This redox-neutral platform, based on the native P(V)-oxidation state, challenges past assumptions of sluggish reactivity and enables access to five relevant P-linkages across a range of sugar backbones (DNA and LNA) and bases (A, T, G, mC) in one oligonucleotide construct. Aside from enabling straightforward access to a wide range of chimeric oligonucleotides, the implementation of this new protocol benefits from a reduced reliance on protecting group chemistry (which eliminates the labile cyanoethyl group and therefore acrylonitrile production upon deprotection), 27,28 bespoke additives, 29 and redox fluctuations. It is also of note that this new P(V) platform eliminates one full step in the standard SPOS protocol (namely the phosphorous oxidation).…”

Section: Introductionmentioning

confidence: 99%

“…37 With this milestone achieved, the incorporation of PO2 linkages into these constructs was pursued. These chimeric sequences (27)(28)(29)(30) could be accessed in high purity with no significant loss of sulfur during synthesis. Next, sequences bearing both PS and PS2 (31-34) linkages were prepared.…”

Section: Introductionmentioning

confidence: 99%

“…38,39 Given the differences in scale, chemical sequence, method of purification and quantification, a direct comparison between yields of this P(V)-platform and those of other stereopure methods is outside of the scope of this communication. In its present manifestation, these novel, homogeneous, chimeric oligonucleotides (21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38) were produced in 12-27% isolated yield using a sequence and linkage agnostic protocol. When compared directly to the stereorandom constructs (produced using state-of-the-art chemistry) that were produced in 30-60% yield, and the ability to prepare unique chimeric systems, this represents a relatively small gap to fill to bring homogeneous, stereopure oligonucleotides on par with their stereorandom counterparts.…”

Section: Introductionmentioning

confidence: 99%

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A P(V)-Platform for Oligonucleotide Synthesis

Baran¹,

Knouse²,

Huang³

et al. 2021

Preprint

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<div><div><div><p>The early promise of gene-based therapies is currently being realized at an accelerated pace with over 155 active clinical trials for antisense compounds and multiple FDA-approved oligonucleotide therapeutics. Fundamental advances in this area are vital and present an unprecedented opportunity to both address disease states that have been resistant to other common modalities and improve the significant sustainability challenges associated with production of these complex molecules on a commercial scale. The advent of phosphoramidite coupling chemistry and solid-phase synthesis 40 years ago democratized oligonucleotide synthesis to the scientific community, paving the way for many of these stunning developments. The reliability and generality of this approach for the preparation of native phosphate-diesters is attributed to the high reactivity of phosphorus when in the P(III)-oxidation state versus the desired P(V), as it enables rapid P-heteroatom bond formation. However, the growing demand for more diverse phosphorus-based linkages has challenged the limits of this technology. For example, the phosphorothioate (PS) linkage, which stabilizes oligonucleotides towards nuclease cleavage, is universally employed in current oligonucleotide therapeutics but is generally incorporated in racemic form. Stereodefined PS oligonucleotides may have desirable biological and physical properties but are accessed with difficulty using phosphoramidite chemistry. Here we report a flexible and efficient [P(V)]-based platform that can install a wide variety of phosphate linkages at will into oligonucleotides. This approach uses readily accessible reagents and can efficiently install not only stereodefined or racemic thiophosphates, but can install any combination of (S, R or rac)-PS with native phosphodiester (PO2) and phosphorodithioate (PS2) linkages into DNA and other modified nucleotides. Importantly this platform easily accesses this diversity under a standardized coupling protocol with sustainably prepared, stable, P(V) reagents.</p></div></div></div>

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“…This redox-neutral platform, which is based on the native P(V) oxidation state, challenges past assumptions of sluggish reactivity and enables access to five relevant P linkages across a range of sugar backbones (DNA and LNA) and bases (A, T, G, and mC) in one oligonucleotide construct. Aside from enabling straightforward access to a wide range of chimeric oligonucleotides, the implementation of this new protocol benefits from a reduced reliance on protecting group chemistry (which eliminates the labile cyanoethyl group and therefore acrylonitrile production upon deprotection) ( 28 , 29 ), bespoke additives ( 30 ), and redox fluctuations. This new P(V) platform also eliminates one full step in the standard solid-phase oligonucleotide synthesis (SPOS) protocol (namely the phosphorus oxidation).…”

mentioning

confidence: 99%

A P(V) platform for oligonucleotide synthesis

Huang

Knouse

Qiu

et al. 2021

Science

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Platform for the synthesis of diverse oligos DNA is primarily viewed as a carrier of information encoded in the sequence of bases, but the chemistry of the phosphodiester backbone is crucial to oligonucleotide stability and structure. Building on previous work in synthetic P(V) phosphorothioate coupling chemistry, Huang et al . developed two new reagents for making phosphorodithioate- and phosphate-based linkages (see the Perspective by Virta). The authors incorporated all of these reagents into a unified P(V)-based synthesis platform capable of running at high efficiency on a commercial automated solid-phase synthesizer. They demonstrate the flexibility of this system by producing oligonucleotides with all three linkage types in specific positions. Access to such precisely constructed molecules opens new approaches to therapeutic oligonucleotide design. —MAF

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Trace-Level Determination of Acrylonitrile Generated in the Manufacturing Process of Oligonucleotides by Static Headspace Gas Chromatography with an Electron Impact(+) Mass Detector

Cited by 6 publications

References 25 publications

Nature Chose Phosphates and Chemists Should Too: How Emerging P(V) Methods Can Augment Existing Strategies

Nature Chose Phosphates and Chemists Should Too: How Emerging P(V) Methods Can Augment Existing Strategies

A P(V)-Platform for Oligonucleotide Synthesis

A P(V) platform for oligonucleotide synthesis

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