Yafen Wang

A highly efficient fluorescence-based switch-on detection method of 5-formyluracil in DNA

The identification of hydroxylmethyl- and formylpyrimidines in genomic DNA was a landmark event in epigenetics. Numerous laboratories in related fields are investigating the biology of these and other nucleic acid modifications. However, limitations in the ability to detect and synthesize appropriate modifications are an impediment. Herein, we explored a remarkable development in the selective detection of 5-formyluracil in both single-stranded and double-stranded DNA under mild conditions. The “switch-on” specificity towards 5-formyluracil enabled a high signal-to-noise ratio in qualitatively and quantitatively detecting materials containing 5-formyluracil, which is not affected by the presence of abasic sites and 5-formylcytosine, the modified cytosine counterpart of 5-formyluracil. In summary, the innoxiousness, convenience, and cost-efficiency of the 5-formyluracil phosphoramidite synthetic routine would promote the understanding of the epigenetic role of this natural thymidine modification.

Highly Selective Detection of 5-Methylcytosine in Genomic DNA Based on Asymmetric PCR and Specific DNA Damaging Reagents

DNA methylation is a significant epigenetic modification of the genome that is involved in regulating many cellular processes. An increasing number of human diseases have been discovered to be associated with aberrant DNA methylation, and aberrant DNA methylation has been deemed to be a potential biomarker for diseases such as cancers. A safe, nontoxic, and sensitive method for accurate detection of 5-methylcytosine in genomic DNA is extremely useful for early diagnosis and therapy of cancers. In this paper, we established a novel system to detect 5-methylcytosine, which is based on bisulfite treatment, asymmetric PCR, and specific DNA damaging reagents. Our method could be used for identifying the loci of 5mC in genomic DNA and detecting the DNA methylation levels in tissues as well.

5‐Formyluracil as a Multifunctional Building Block in Biosensor Designs

In organisms 5-formyluracil (5fU), which is known as a vital natural nucleobase, is widely present. Despite the recent development of sensor designs for organic fluorescent molecules for selective targeting applications, biocompatible and easily operated probe designs that are based on natural nucleobase modifications have rarely been reported. Here, we introduce the idea of 5fU as a multifunctional building block to facilitate the design and synthetic development of biosensors. The azide group was derived from the sugar of a nucleoside, which can be further used in the selective binding of cells or organelles through click chemistry with alkynyl-modified targeting groups. The aldehyde group of 5fU can react with different chemicals to generate environmentally sensitive nucleobases that have obvious characteristics, which precious reactants cannot achieve for selective fluorogenic switch-on detection of a specific target. We first synthesized 5fU analogues that had aggregation-induced emission properties, and then we used triphenylphosphonium as a mitochondria-targeting group to selectively image mitochondria in cancer cells and mouse embryonic stem cells. Additionally, the reagents exhibit a high selectivity for reaction with 5fU, which means that the method can also be used for the detection of 5fU. Combining the two characteristics, the idea of 5fU as a multifunctional building block in biosensor designs may potentially be applicable in 5fU site-specific microenvironment detection in future research.

Luminescence Sensing for Qualitative and Quantitative Detection of 5-Methylcytosine

5-Methylcytosine (5mC) is revealed as a heritable epigenetic modification in genomic DNA. It has been reported that cytosine/guanine dinucleotides (CpG) hypermethylation in the promoter regions of tumor suppressor genes is related with inappropriate gene silencing, so the determination of 5mC in the CpG islands of mammals has attracted much attention. In this paper, a luminescence sensing strategy based on bisulfite treatment, asymmetric polymerase chain reaction (PCR), and adenosine triphosphate (ATP)-releasing nucleotide is proposed. With little background, this method can provide accurate quantitative information about methylation changes at CpG sites, even at a specific site. The proposed method can be successfully employed to determine the methylation status of three hepatocellular carcinomas (HCC) related genes in clinical tissues.

Application of Ammonium Persulfate for Selective Oxidation of Guanines for Nucleic Acid Sequencing

Nucleic acids can be sequenced by a chemical procedure that partially damages the nucleotide positions at their base repetition. Many methods have been reported for the selective recognition of guanine. The accurate identification of guanine in both single and double regions of DNA and RNA remains a challenging task. Herein, we present a new, non-toxic and simple method for the selective recognition of guanine in both DNA and RNA sequences via ammonium persulfate modification. This strategy can be further successfully applied to the detection of 5-methylcytosine by using PCR.