The normal course of gene expression involves the production of RNA by a process known as transcription. Messenger RNAs encode proteins, the essential structural and catalytic building blocks required for cell structure, function, and growth. RNA is an ideal target for drug discovery because it is the key regulatory molecule, determining both which proteins will be produced in a cell and the extents to which they will be synthesized.

PTC is developing drugs that modulate the availability or utilization of RNA. To understand the power and scope of this technology, it is necessary to review the central role of RNA in the cellular flow of gene expression.

RNA is an important mediator of gene expression.
Genes, the basic units of inheritance, are encoded in discrete stretches of DNA molecules that reside within chromosomes in the nucleus of a cell. Expression of the information present in genes is an ordered multi-step process that proceeds from DNA to RNA to protein (Figure 1). Proteins are the end products of this process and either provide cells with important structural elements or with catalysts that carry out cellular biochemical reactions. To ensure that the appropriate proteins are always synthesized in the correct cells at the correct times, the information encoded by genes is deciphered by a specialized mechanism. An intermediate form of the genetic information, called messenger RNA (mRNA), is synthesized in a process known as transcription (Figure 1). mRNA then acts as a critical mediator of gene expression, carrying the necessary information from the "library" of genes stored in the cellular DNA to the machinery that makes proteins.



Figure 1. The flow of genetic information to the cell.

RNA utilization: decoding the mRNA to synthesize proteins.
The information in mRNA molecules is "translated" by the ribosome, a specialized cellular apparatus, to produce individual proteins (Figure 2). This protein synthesis machinery is capable of sequentially reading each three-letter genetic code "word" in mRNA and converting its respective encrypted information into a string of protein building blocks called amino acids (Figure 2). The string of amino acids is called a polypeptide and proteins are comprised of one or more polypeptides.

To maintain accuracy, the protein synthesis apparatus must be able to determine the precise sites on the mRNA where decoding should begin and where it should end.

Initiation, the selection of the start site, is delineated by a unique code word comprised of three nucleotides (i.e., AUG). After initiation, the translational apparatus progresses along the mRNA, decoding one "word" (3 bases) at a time. This progression is called "elongation" (Figure 2). The final step in translation, called "termination," occurs when one of three special code words (i.e., UAG, UAA, UGA) is recognized (Figures 2 and 3). These termination signals, or "nonsense codons," comprise a genetic signal to end protein synthesis.

Regulation of mRNA utilization by controlling the translation process is an important step in regulating gene expression. The efficiency with which an mRNA is utilized to synthesize protein is governed both by the precise sequences within the mRNA as well as by factors that interact with these elements. Translational regulation is important for controlling the expression of many cellular genes involved in cancers, inflammatory, and cardiovascular diseases. Moreover, many infectious agents initiate their pathogenic program by usurping a cell's translation machinery. A set of PTC's proprietary platform technologies is based on the Company's expertise in translation.

Figure 2.

RNA availability: the lifespan of an RNA is an important control point.
An mRNA is a transient copy of the cell's permanent genetic information that is used to synthesize a specific protein. After its use as a template for protein synthesis, the mRNA is turned over, or degraded, by cellular enzymes. Since the quantity of a particular protein synthesized in a given time depends on the cellular concentration of its mRNA it follows that the regulation of mRNA decay rates (i.e., the rates of mRNA degradation) provides a powerful means of controlling gene expression. mRNA turnover is a very specific process requiring information contained in coding regions of the mRNA and in non-coding regions, known as "untranslated regions," or UTRs. Specific proteins that regulate mRNA turnover interact with these regions of mRNA and, often, with the translation apparatus. The processes of mRNA decay and translation are often linked, requiring ongoing translation of the mRNA for its appropriate regulation. PTC's founders and scientists have played prominent roles in the development of the scientific basis of these concepts.

RNAs have protein-like properties: they have defined, complex structures and can catalyze enzymatic reactions.
Although RNA is chemically similar to DNA, there are striking differences that make it unique. For example, RNA contains the sugar, ribose, rather than deoxyribose, and the base uracil (U) rather than thymine (T).

While DNA consists of a uniform double-stranded structure, RNA is a single-stranded nucleic acid, a feature that allows it to fold into a rich set of structural conformations. RNAs can even fold into unique structures that carry out chemical reactions. The first enzymes in evolution were probably not proteins, but small RNAs that formed unique structures.

There are a number of cellular RNAs that do not encode proteins, but form structures that are either part of enzyme complexes, or regulate gene expression directly. For example, half of the mass of the ribosome (the entity that catalyzes protein synthesis) consists of RNA and this RNA portion is responsible for carrying out the chemical reaction that synthesizes proteins. Many other complexes that carry out important and necessary cellular functions also have RNA components (e.g., telomerase, RNase P, and Xist). Similarly to proteins, RNAs can form varied and extensive structures that are unique sites to which drugs can bind specifically. This important feature of RNAs underscores several of PTC's core technologies.

Figure 3. The steps in the translation process.