Antisense Approaches — Mechanisms and Targets

An important area of our basic research is to understand the molecular mechanisms of antisense drugs. There are at least 12 known antisense mechanisms that can be exploited once an antisense drug binds to its target RNA. We have created proprietary chemical modifications to trigger many of these mechanisms for drug discovery.

An antisense mechanism is defined as the process in which an antisense drug works after it binds (hybridizes) to a target RNA forming a duplex. The formation of this duplex, or two-stranded molecule, prevents the RNA from functioning normally and from producing a protein. The majority of our late-stage antisense drugs in development bind to their target RNA and activate a cellular enzyme called RNase H. Progress in our research program is illustrated by our accomplishments in understanding RNase H.

The majority of the antisense drugs in our pipeline bind to mRNAs and inhibit the production of disease-causing proteins through the RNase H mechanism described below. Recently the scientific community has discovered many new types of RNAs, including non-coding RNAs, such as microRNAs and long non-coding RNAs. MicroRNAs are involved in the regulation of protein production within the cell. Our antisense technology is uniquely suited to exploit these exciting new RNA targets, as we have done with microRNAs through Regulus Therapeutics.

RNase H

The antisense mechanism that has been the main focus of our research involves a cellular enzyme, RNase H. This cellular enzyme is activated when antisense drugs bind to their target RNA and activate RNase H. Upon activation, RNase H seeks out and destroys the target mRNA, inhibiting a cell’s production of a specific protein.

We have cloned and characterized human RNase H and have effectively used that information to optimize the design of many of our antisense drugs. We will continue to advance our understanding of antisense mechanisms, including RNase H, in order to improve the pharmaceutical properties of our drugs.

In addition to our RNase H expertise, we are the leaders in understanding and exploiting all antisense mechanisms, including the RNAi mechanism.


RNAi is an antisense mechanism that involves using small interfering RNA, or siRNA, to target a mRNA sequence. With siRNA, the cell utilizes a protein complex called RISC to destroy the mRNA, thereby preventing the production of a disease-causing protein. Ionis’ research led to one of the first scientific publications and key issued patents that address this mechanism.

We have a strong and growing intellectual property position in RNAi methodology and chemistries used to develop siRNA therapeutics. Our intellectual property led us to establish a strategic collaboration with Alnylam Pharmaceuticals in the development of double-stranded RNAi drugs.

We have identified the critical drug design elements required to achieve RNAi activity with a single-stranded RNAi drug. We have also begun to chemically optimize these design elements to ensure that they survive long enough under physiological conditions to produce the desired activity in animals. As a result, we have created single-stranded RNAi compounds that, when administered systemically, distribute in a manner similar to our second-generation RNase H antisense drugs, without requiring the complex formulation or delivery vehicle typically necessary for double-stranded RNAi oligonucleotides. These new single-stranded RNAi drug designs are an exciting advance in RNAi technology.

Alternative Splicing

To understand alternative splicing, it’s important to understand how DNA creates mRNA.

mRNA is created when the entire DNA strand is copied. This includes the sequences that encode for proteins and regions that are unnecessary for making proteins. Before mRNA can function, the regions that are unnecessary for making proteins are deleted from the RNA strand. The natural process that removes these regions and re-forms the finished mRNA is called “splicing.” Through the splicing process, the cell can create many diverse proteins from a single gene and splicing accounts for most of the diversity in proteins in the cell. In fact, of the approximately 25,000 genes in the human genome, approximately 90% have alternative splice forms. Alternative splicing of proteins can result in the production of proteins that are involved in disease. In some cases, using antisense technology, we can direct alternate splicing to produce a protein critical for normal cellular function to correct for a genetic defect. Examples of applications of antisense modulation of splicing to treat genetic diseases include spinal muscular atrophy (SMA), thalessemia, cystic fibrosis and Duchenne’s muscular dystrophy.

We design antisense drugs to control splicing to make one protein versus another. In 2010, we identified an antisense drug, SPINRAZATM, to treat SMA. SMA is a splicing disease and the leading genetic cause of infant mortality. The discovery of SPINRAZATM resulted from a research collaboration between scientists at Ionis and Cold Spring Harbor. In earlier published research, we and our collaborators at Cold Spring Harbor demonstrated the feasibility of using our antisense technology to control splicing for the treatment of SMA.

In addition to antisense mechanisms, we are also interested in the therapeutic opportunities of other RNA targets, such as microRNAs.


MicroRNAs are small naturally occurring RNA molecules that are created inside cells. There are many different types of RNA that exist within the body, including mRNA. MicroRNAs are important because they appear to have critical functions in controlling processes or pathways of gene expression.

There are nearly 700 microRNAs that have been identified in the human genome, and these are believed to regulate the expression of approximately one-third of all human genes. Targeting microRNA to inhibit disease-causing pathways is an exciting development in RNA-based therapeutics.

To fully exploit the therapeutic opportunities of targeting microRNAs, we and Alnylam jointly established Regulus as a company focused on the discovery, development, and commercialization of microRNA-based therapeutics.

Learn more about Regulus »