Poster abstracts

Poster number 23 submitted by Yufeng Liang

Synthetic probes for labeling internal nucleic acid sites

Yufeng Liang (Chemistry), Shiqin Miao (Chemistry)

Abstract:
Internal labeling of nucleic acid is one of the efficient ways to assists the analysis on the molecular interaction interface. However, for the normal internal labeling strategy, it requires a synthetic approach of nucleic acids, which is limited by the length of the sequence, or the fluorescent molecule aptamer is incorporated into the sequence, which may perturb the original nucleic acid structure. To solve this problem, we design an internal labeling system called bPNAs, a series of synthetic molecules which contain melamines (M) for base tripling recognition and they specifically bind to T-T or U-U mismatches through hydrogen bonding, resulting a T-M-T or U-M-U triplex. The binding sites on nucleic acids are introduced by replacing a stem sequence with eight thymines/uridines, which have no influence on their original structure. Fluorescent dyes or chemically reactive molecules are conjugated to the bPNAs and the labeled bPNAs are applied to the modified DNA/RNA for specific binding. Therefore, the DNA/RNAs are internally labeled by fluorescent molecules or chemically reactive molecules through nonconvalent interactions. With this internal labeling design, we have verified the internal fluorescent labeling of DNA/RNA, RNA-RNA complex and RNA-protein complex by our fluorescent bPNAs and the complexes still maintain their original structure. Besides the internal fluorescent labeling, the sequence-specific nucleic acid cleavage is also investigated. Accumulation of Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) RNA causes cancer since it’s enzymatically stable. We design a chemically reactive bPNA where EDTA is coupled to bPNA as an iron chelator. When reducing agent appears, the EDTA-iron generates hydroxyl radicals, which may specifically cleave U-U mismatched strands in MALAT1 sequence. The cleaved MALAT1 may be easier for enzymatic degradation. In general, bPNAs show great prospect in internal labeling of nucleic acids.

Keywords: bPNA, internal labeling, sequence specific binding