5-Hydroxymethylcytosine and 5-formylcytosine containing deoxyoligonucleotides: Facile syntheses and melting temperature studies

Xuan, Shuguang; Wu, Qiong; Liang, Cui; Zhang, Dawei; Shao, Fangwei

doi:10.1016/j.bmcl.2015.01.070

Cited by 14 publications

(16 citation statements)

References 22 publications

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“…Nm and Nhm, were synthesized using standard phosphoramidite chemistry, where N (= 1, 2 etc.) and m/hm indicate the position and the type of modified bases, mC and hmC, respectively 36 (Table 1). In Fig.…”

Section: Resultsmentioning

confidence: 99%

Regulation of telomeric i-motif stability by 5-methylcytosine and 5-hydroxymethylcytosine modification

Devi

Shao

2015

Org. Biomol. Chem.

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The two important epigenetic markers in the human genome, 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC), are involved in gene regulation processes. As a major epigenetic target, cytosines in a C-rich DNA sequence were substituted with mC and hmC to investigate the thermal stability and pH sensitivity of the corresponding i-motifs. Circular Dichroism (CD) studies indicate the formation of i-motifs at acidic pH (<6.5) for mC- and hmC-modified DNA sequences. Thermal denaturation results suggest that DNA i-motifs are stabilized when modified with one or two mCs. However, hypermethylation with mC and single modification with hmC cause destabilization of the structure. A biomimetic crowding agent does not alter the stability effect trends resulting from mC and hmC modifications, though the corresponding i-motifs show elevated melting temperatures without significant changes in pKa values.

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Section: Resultsmentioning

confidence: 99%

Regulation of telomeric i-motif stability by 5-methylcytosine and 5-hydroxymethylcytosine modification

Devi

Shao

2015

Org. Biomol. Chem.

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“…Originally, we found that 5hmdU (6) could be efficiently obtained by hydrolyzing 5BrmdU (8) with TFA/H2O (10:1, v/v) in 71% yield. However, the following synthesis of cyanoethyl ether in the presence of TFA at 100 °C according to the previous reports [26,27] yielded the desired 9 in only 51% yield. Therefore, we abandoned the synthesis of 5hmdU and subsequent condensation with cyanoethanol under harsh conditions.…”

Section: Synthesis Of Cyanoethyl-protected 5hmdc Phosphoramidite (1)mentioning

confidence: 99%

“…Finally, phosphitylation with 2-cyanoethyl N,N-diisopropylchlorophosphoramidite in the present of triethylamine afforded the desired cyanoethyl-protected 5hmdC (1) in 83% yield. Compared to Schofield's and In 2011 and 2015, Schofield [26] and Shao [27] reported two improved methods for the synthesis of cyanoethyl-protected 5hmdC phosphoramidite (1) starting from 2'deoxyuridine (dU) and thymidine (dT), respectively (Figure 1B). Other than the classic benzoyl (Bz) protection and phosphitylation steps, most of key steps including the initial conversion to 5-hydroxymethyl-2'-deoxyuridine (5hmdU), cyanoethyl protection, DMT protection, and C 4 -amination steps still suffer from either low-yielding or slow reaction rate.…”

Section: Synthesis Of Cyanoethyl-protected 5hmdc Phosphoramidite (1)mentioning

confidence: 99%

An Improved Approach for Practical Synthesis of 5-Hydroxymethyl-2′-deoxycytidine (5hmdC) Phosphoramidite and Triphosphate

et al. 2022

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5-Hydroxymethyl-2′-deoxycytidine (5hmdC) phosphoramidite and triphosphate are important building blocks in 5hmdC-containing DNA synthesis for epigenetic studies. However, efficient and practical methods for the synthesis of these compounds are still limited. The current research provides an intensively improved synthetic method that enables the preparation of commercially available cyanoethyl-protected 5hmdC phosphoramidite with an overall yield of 39% on 5 g scale. On the basis of facile and efficient accesses to cyanoethyl protected-5hmdU and 5hmdC intermediates, two efficient synthetic routes for 5hmdC triphosphate were also developed.

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“…These and other insights were derived using synthetic site-specifically modified DNA prepared by solid-phase synthesis. Various protecting group strategies have been reported for the incorporation of 5fC in DNA and RNA [63,64], and the most successful approach appears to be masking the formyl moiety as an acetal group [65,66]. The availability of high-quality synthetic oligonucleotides is not only a prerequisite for biophysical investigations but also enabled the study of 5fC formation and repair and the identification of specific reader proteins by quantitative proteomics using SILAC-based DNA pulldown [24,67].…”

Section: Structural and Biophysical Properties Of 5fc And Recognitionmentioning

confidence: 99%

Chemoselective labeling and site‐specific mapping of 5‐formylcytosine as a cellular nucleic acid modification

2018

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DNA methylation has a profound impact on the regulation of gene expression in normal cell development, and aberrant methylation has been recognized as a key factor in the pathogenesis of human diseases such as cancer. The discovery of modified nucleobases arising from 5-methylcytosine (5mC) through consecutive oxidation to give 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) has stimulated intense research efforts regarding the biological functions of these epigenetic marks. This Review focuses on the sensitive detection and quantitation of 5fC in DNA and RNA by chemoselective labeling, which aims at discriminating between 5fC and its thymine counterpart 5-formyluracil (5fU), and summarizes single-base resolution sequencing methods for locus-specific mapping of 5mC and its oxidized derivatives.

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5-Hydroxymethylcytosine and 5-formylcytosine containing deoxyoligonucleotides: Facile syntheses and melting temperature studies

Cited by 14 publications

References 22 publications

Regulation of telomeric i-motif stability by 5-methylcytosine and 5-hydroxymethylcytosine modification

Regulation of telomeric i-motif stability by 5-methylcytosine and 5-hydroxymethylcytosine modification

An Improved Approach for Practical Synthesis of 5-Hydroxymethyl-2′-deoxycytidine (5hmdC) Phosphoramidite and Triphosphate

Chemoselective labeling and site‐specific mapping of 5‐formylcytosine as a cellular nucleic acid modification

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