Antisense DNA oligomer targeting of histone deacetylase 1 (HDAC1) mRNA for potential knockdown effects

Author Info

Seung Chan Kim

Corresponding Author

Seung Chan Kim
Medical School & College of Medicine, Yonsei University, Seoul, Republic of Korea

A B S T R A C T

Histone Deacetylase(HDAC) is an enzyme that eliminates acetyl group from the histone octamer complex. The acetylation state of histone proteins is a major interest of epigenetic gene expression. HDAC1 inhibitors are used for anticancer therapeutics by controlling multiple signaling protein kinases like SAPK, ERK and TNF-alpha. Here, we used single strand DNA 18-oligomer to mimic RNA interference technology. We modeled the HDAC1 mRNA secondary structure and identified the possible four siRNA binding sites by higher possibility than miR-449 targeting site. Also, its possible configuration was modeled according to binding energies. Three places, where the possibility of siRNA binding is low, were randomly identified as positive controls. As a Result, the 18-omer single strand DNA was generated according to the identified sequences. This preliminary data can be further warranted to generate HDAC1 knockdown activity and its comparison to the current HDAC1 inhibitors. Furthermore, generation of single strand DNA as a antisense sequence to a specific mRNA can be utilized for therapeutics along with RNAi. With the thermodynamically stable structure of DNA compared to RNA, it can be applied for long term usage.

Article Info

Article Type

Short Communications

Publication history

Received: Wed 28, Mar 2018
Accepted: Fri 13, Apr 2018
Published: Mon 30, Apr 2018

Copyright

© 2023 Seung Chan Kim. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Hosting by Science Repository.
DOI: 10.31487/j.COR.2018.10.008