Sensitive Oligodeoxynucleotide Synthesis Using Dim and Dmoc as Protecting Groups

Shahsavari, Shahien; Eriyagama, Dhananjani; Chen, Jinsen; Halami, Bhaskar; Yin, Yipeng; Chillar, Komal; Fang, Shiyue

doi:10.1021/acs.joc.9b01527

Cited by 10 publications

(17 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…[17] Later, we tested the used of Dim for phosphate protection and Dmoc for amino protection. [20][21] The ODNs synthesized can be represented by 1c (Scheme 1). Deprotection and cleavage were achieved in two steps by oxidation with sodium periodate followed by excess aniline.…”

Section: Adim-admoc Protection For Odn Synthesis Allows Deprotection ...mentioning

confidence: 99%

aDim-aDmoc Protection for ODN Synthesis Allows Deprotection under Non-nucleophilic and Nearly Neutral Conditions

Chillar

Eriyagama

Yin

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

Over a hundred non-canonical nucleotides have been found in DNA and RNA. Many of these modified nucleotides are sensitive toward nucleophiles and bases. Because known solid phase DNA and RNA synthesis technologies require strongly nucleophilic and basic conditions for deprotection and cleavage, there is no technology for the synthesis of DNAs and RNAs containing these sensitive nucleotides. The Dim-Dmoc technology has been developed to overcome the challenge. With Dim-Dmoc protection, oligodeoxynucleotide (ODN) deprotection has be achieved with sodium periodate oxidation followed by β-elimination induced by the weak base aniline. Some sensitive groups have been shown to be stable under the deprotection conditions. Besides serving as a base, aniline also serves as a nucleophilic scavenger for the side products of Dim-Dmoc deprotection, which prevents the side products from reacting with the deprotected ODN. For this reason, excess aniline is needed. In this article, we report the use of alkyl Dim (aDim) and alkyl Dmoc (aDmoc) protecting groups for ODN synthesis. With aDim-aDmoc protection, deprotection is demonstrated to be achievable with sodium periodate oxidation followed by the non-nucleophilic base potassium carbonate at pH 8. No scavenger for the side products of deprotection is needed. Over 10 ODNs with length ranging from 10-mer to 23-mer were synthesized, and importantly, the ODNs could be easily purified with RP HPLC. It was further demonstrated that the highly sensitive N4-acetylcytidine nucleoside could survive the oxidative deprotection conditions, and ODNs containing this sensitive nucleotide could be readily synthesized and purified without the need of any special cautions. Work on extending the method for the synthesis of sensitive RNAs such as those containing the biologically important ac4C is in progress.

show abstract

Section: Adim-admoc Protection For Odn Synthesis Allows Deprotection ...mentioning

confidence: 99%

aDim-aDmoc Protection for ODN Synthesis Allows Deprotection under Non-nucleophilic and Nearly Neutral Conditions

Chillar

Eriyagama

Yin

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Under these nearly neutral and non-nucleophilic deprotection and cleavage conditions, a wide range of sensitive groups such as esters, thioesters, activated amides, N-aryl amides, alkyl halides, and α-chloroamides can survive, and therefore, the Dim-Dmoc ODN synthesis technology is well suited for the synthesis of sensitive ODNs. The technology has been demonstrated for the synthesis of ODNs that contain sensitive alkyl esters, phenyl esters, thioesters, alkyl chlorides, and 6-chloropurine (Halami et al, 2018;Lin et al, 2016;Shahsavari et al, 2019a;Shahsavari et al, 2019b). The sensitive ODNs were purified with trityl-on RP HPLC and were characterized with MALDI-TOF MS and enzymatic digestion assay.…”

Section: Of 31mentioning

confidence: 99%

“…The routes for the synthesis are shown in Figure 5. The synthesis has been reported previously (Lin et al, 2016;Shahsavari et al, 2019a).…”

Section: Synthesis Of Dim-dmoc Nucleoside Phosphoramiditesmentioning

confidence: 99%

“…The Dim-Dmoc technology described in this protocol uses Dmoc for the protection of the exo-amino groups of dA, dC, and dG; Dim for the protection of the hydroxyl group of the phosphoramidous acid of all the four nucleoside phosphoramidites; and Dmoc for linking the nascent ODN to solid support ( Fig. 1; Halami et al, 2018;Lin et al, 2016;Shahsavari et al, 2019a;Shahsavari et al, 2019b). Using the technology, the ODN synthesized has the structure represented by 3 (Fig.…”

Section: Background Informationmentioning

confidence: 99%

“…The new ODN synthesis technology described in this article aims to solve the problem (Halami et al, 2018;Lin et al, 2016;Shahsavari et al, 2019a;Shahsavari et al, 2019b). In this technology, the exo-amino groups of dA, dC, and dG are protected with 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) and the hydroxyl group of the phosphoramidous acid in dA, dC, dG, and dT phosphoramidites, which are later converted to the phosphate diester linkage of the ODN, is protected with 1,3-dithian-2-yl-methyl (Dim).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Dim and Dmoc Protecting Groups for Oligodeoxynucleotide Synthesis

Fang

Eriyagama

Yuan

et al. 2020

CP Nucleic Acid Chemistry

Self Cite

View full text Add to dashboard Cite

This protocol provides details for the preparation of nucleoside phosphoramidites with 1,3-dithian-2-yl-methyl (Dim) and 1,3-dithian-2-ylmethoxycarbonyl (Dmoc) as protecting groups, and a linker with Dmoc as the cleavable function, then using them for solid phase synthesis of sensitive oligodeoxynucleotides (ODNs). Using these Dim-Dmoc phosphoramidites and Dmoc linker, ODN synthesis can be achieved under typical conditions using phosphoramidite chemistry with slight modifications, and ODN deprotection and cleavage can be achieved under mild conditions involving oxidation with sodium periodate at pH 4 followed by aniline at pH 8. Under the mild deprotection and cleavage conditions, many sensitive functional groups including but not limited to esters, thioesters, alkyl halides, N-aryl amides, and α-chloroamides-which cannot survive the basic and nucleophilic deprotection and cleavage conditions such as concentrated ammonium hydroxide and dilute potassium methoxide used in typical ODN synthesis technologies-can survive. Thus, it is expected that the Dim-Dmoc ODN synthesis technology will find applications in the synthesis of ODNs that contain a wide range of sensitive functional groups.

show abstract

Effects of Epitranscriptomic RNA Modifications on the Catalytic Activity of the SARS‐CoV‐2 Replication Complex**

et al. 2023

Self Cite

View full text Add to dashboard Cite

SARS-CoV-2 causes individualized symptoms. Many reasons have been given. We propose that an individual's epitranscriptomic system could be responsible as well. The viral RNA genome can be subject to epitranscriptomic modifications, the modifications can be different for different individuals, and thus epitranscriptomics can affect many events including RNA replication differently. In this context, we studied the effects of modifications including pseudouridine (Ψ), 5methylcytosine (m 5 C), N 6 -methyladenosine (m 6 A), N 1 -methyladenosine (m 1 A) and N 3methylcytosine (m 3 C) on the activity of SARS-CoV-2 replication complex (SC2RC). We found that Ψ, m 5 C, m 6 A and m 3 C had little effects, while m 1 A inhibited the enzyme. Both m 1 A and m 3 C disrupt canonical base-pairing, but they had different effects. The fact that m 1 A inhibits SC2RC implies that the modification can be difficult to detect. The fact also implies that individuals with upregulated m 1 A including cancer, obesity and diabetes patients may have milder symptoms. However, this contradicts clinical observations. Relevant discussions are provided.

show abstract

Sensitive Oligodeoxynucleotide Synthesis Using Dim and Dmoc as Protecting Groups

Cited by 10 publications

References 29 publications

aDim-aDmoc Protection for ODN Synthesis Allows Deprotection under Non-nucleophilic and Nearly Neutral Conditions

aDim-aDmoc Protection for ODN Synthesis Allows Deprotection under Non-nucleophilic and Nearly Neutral Conditions

Dim and Dmoc Protecting Groups for Oligodeoxynucleotide Synthesis

Effects of Epitranscriptomic RNA Modifications on the Catalytic Activity of the SARS‐CoV‐2 Replication Complex**

Contact Info

Product

Resources

About