Possibilities and challenges of small molecule organic compounds for the treatment of repeat diseases

The instability of repeat sequences in the human genome results in the onset of many neurological diseases if the repeats expand above a certain threshold. The transcripts containing long repeats sequester RNA binding proteins. The mechanism of repeat instability involves metastable slip-out hairpin DNA structures. Synthetic organic chemists have focused on the development of small organic molecules targeting repeat DNA and RNA sequences to treat neurological diseases with repeat-binding molecules. Our laboratory has studied a series of small molecules binding to mismatched base pairs and found molecules capable of binding CAG repeat DNA, which causes Huntington's disease upon expansion, CUG repeat RNA, a typical toxic RNA causing myotonic dystrophy type 1, and UGGAA repeat RNA causing spinocerebellar ataxia type 31. These molecules exhibited significant beneficial effects on disease models in vivo, suggesting the possibilities for small molecules as drugs for treating these neurological diseases.

High allele discrimination in the typing of single nucleotide polymorphisms of miRNA

MicroRNAs (miRNAs) belonging to the same family have similar sequences and are difficult to identify. Herein, we report the reverse transcription-hairpin-probe-polymerase chain reaction (RT-Hpro-PCR) technique, which utilises a reverse transcription (RT) primer containing a 5'-end deoxyribonucleic acid (DNA) tag, to detect miRNAs with similar sequences. This strategy follows a two-step RT-PCR method using 6-7-mer RT-primers with a ~ 10-mer tag sequence at the 5'-end and a probe with a hairpin structure (Hpro), including two C-bulges, attached. The findings demonstrate that the specificity of RT could be increased by shortening the complementary part of the RT primer containing a different base, wherein the PCR could successfully progress with the use of 5'-end DNA tag because of an increase in the length of the hybridised tagged primer. This study shows the potential of RT-Hpro-PCR to precisely detect miRNAs with similar sequences, which could help explore the roles of miRNAs in several biological processes.

Application of the Dimeric G-Quadruplex and toehold-mediated strand displacement reaction for fluorescence biosensing of ochratoxin A

Ochratoxin A (OTA) is one of the most toxic mycotoxins that exists in various agro-products and foods. Here, a non-label and enzyme-free fluorescence biosensor for highly specific detection of OTA has been developed by the combination of toehold-mediated strand displacement reaction (TMSD) and G-quadruplex dimer/ThT (G-dimer/ThT). The DNA duplex (aptamer-IP) is composed of the anti-OTA aptamer and a single stranded initiation probe (IP). In the presence of OTA, the attachment of target to aptamer leads to the liberation of the IP, which activates the cycle TMSD amplifications of two hairpin probes (H1 and H2) accompanied by the production of numerous H1-H2 assemblies. This double-stranded H1-H2 structure results in the proximity between the 5'-end overhang tail of H1 and the 3'-end stem of H2 to liberate the pre-blocked G-dimer sequence for lighting up ThT. In addition, the method displayed a stable fluorescence emission in the high-salt media. It was successfully applied to analyze OTA in real food samples. Hence, the constructed fluorescence biosensing platform might provide a new way for OTA and other toxin analysis detection.

RT-Hpro-PCR: A MicroRNA Detection System Using a Primer with a DNA Tag

MicroRNAs (miRNAs) are short RNAs that regulate the expression of complementary messenger RNAs and are involved in numerous human diseases. However, current detection techniques lack the sensitivity to detect miRNAs of low abundance. Moreover, at a length of 20-25 bases, miRNAs are too short for the reverse transcription (RT) polymerase chain reaction (PCR). Here we have developed a new, rapid, and simple miRNA detection system utilizing an RT primer containing a DNA tag at the 5'-end to increase the length of the cDNA. This strategy increases the length of the hybridized tagged primer and the complementary template DNA, as well as the melting temperature of the primer⋅template DNA duplex. PCR efficiency is thus increased, thereby enhancing miRNA detection sensitivity.