What is RNA?

Ava: Dr. Rivera, I’ve been struggling with RNA extractions in the lab. No matter how careful I am, something always seems to go wrong. Do you have any advice?

Dr. Rivera: You’re not alone, Ava. RNA extraction can be tricky, especially with RNA being prone to degradation. But with the proper techniques and tools, you can make it almost foolproof. 

Ava: That’s exactly what I need to hear! But I feel overwhelmed; there are so many steps and variables. How do I know I’m doing it right? 

Dr. Rivera: Start by understanding the science behind each step. Then, learn the best practices for handling and storing your samples and how you can optimize yields for different tissues. Come and let’s level up your skills!

RNA is a single-stranded molecule made up of smaller building blocks called nucleotides. Each nucleotide contains:

• Nitrogenous base: Adenine (A), uracil (U), cytosine (C), and guanine (G). RNA uses uracil instead of thymine (T), which is found in DNA.
• Ribose sugar: This five-carbon sugar (also called pentose) includes an additional hydroxyl (-OH) group compared to the deoxyribose in DNA.
• Phosphate group: This forms the backbone of the RNA strand, linking the nucleotides together.

The single-stranded structure of RNA allows it to fold into diverse three-dimensional shapes necessary for its various functions.

RNA and DNA are considered nucleic acids, a group of biomolecules that store and transmit genetic information. However, the two differ in structure and function. RNA is typically single-stranded, while DNA is double-stranded, forming a double helix. RNA contains a ribose sugar, whereas DNA uses deoxyribose, which lacks one oxygen atom. Additionally, RNA replaces thymine (T) with uracil (U) as a nitrogenous base. Functionally, RNA is more versatile, acting as a messenger, adapter, catalyst, and regulator, while DNA primarily serves as a stable, long-term storage of genetic information.

RNA is also more transient and dynamic, often operating within the cytoplasm and nucleus to facilitate immediate cellular processes like protein synthesis or gene regulation. RNA is also found in different subcellular compartments. In contrast, DNA (particularly genomic DNA) resides in the nucleus (or nucleoid in prokaryotes) and is tightly packed to protect its integrity.

RNA is synthesized through a process called transcription, which occurs in three steps:

1. Initiation: Transcription begins when the enzyme RNA polymerase binds to a specific region of the DNA called the promoter. This region signals the starting point for RNA synthesis. Next, RNA polymerase unwinds the DNA double helix to expose the template strand, which will be used to synthesize the RNA molecule.
2. Elongation: During elongation, RNA polymerase moves along the DNA template strand, adding complementary RNA nucleotides to the growing RNA chain. The RNA sequence is complementary to the DNA template strand, except that uracil (U) replaces thymine (T).
3. Termination: Transcription continues until RNA polymerase encounters a termination signal in the DNA sequence. This signal indicates the end of the RNA transcript. Upon reaching this signal, RNA polymerase releases the newly synthesized RNA molecule and detaches it from the DNA.

RNA molecules are usually single-stranded because only one of the DNA strands is used as a template for transcription.

The single-stranded structure of RNA enables it to perform diverse functions. It serves as a template for protein synthesis, folds into complex three-dimensional shapes to interact with other molecules, and binds to complementary RNA sequences (e.g., miRNA) to regulate gene expression. Below is a table that summarizes the functions of different types of RNA, including their roles in the cell.

RNA molecules are distributed across various subcellular compartments, where their location dictates their function and relevance in biological processes, including their biomedical applications. Determining the spatial location of RNA, its distribution within the cell, and the dynamic change in their location helps researchers better understand the regulation of cellular processes, gene expression, and disease mechanisms.

It also enables the identification of different types of RNA that are crucial for specific biological functions and guides the development of targeted therapies for various diseases. This knowledge is critical for optimizing RNA extraction methods, as different RNA populations require tailored protocols to ensure integrity and accurate analysis for both basic research and clinical applications.

In most research applications, such as gene expression analysis, total RNA isolates that do not discriminate between subcellular locations are sufficient. However, for other applications, such as when studying the functions of mitochondrial RNA, isolating RNA for structural elucidations, or characterizing the functions of organelle-specific RNAs (e.g., snoRNAs), several considerations for extracting RNA should be noted for optimal recovery.

RNA is involved in a wide array of cellular processes that are crucial to the proper functioning of an organism. As we have seen, RNA exists in different forms, each with distinct functions and localized to specific subcellular compartments. The dynamic roles and distributions of RNA make them a valuable tool for researchers who are aiming to explore and manipulate genetic information.

• RNA biomarker research – one of the most prominent research applications of RNA is in the study of diseases. RNA’s involvement in regulating gene expression means that alterations in RNA molecules can have profound implications for various diseases, including cancer, genetic disorders, and neurodegenerative diseases. For example, in cancer research, RNA can reveal how tumors evade the immune system or resist treatment, providing relevant data on how to develop more effective therapies.
• Biotechnology – one of the most notable applications of RNA research is in the development of RNA vaccines, such as the COVID-19 mRNA vaccines, which have demonstrated the potential of RNA to trigger immune responses and combat infectious diseases. Beyond vaccines, RNA is being explored as a therapeutic tool to treat a wide range of conditions, including viral infections, genetic disorders, and even some cancers.
• Pathology – the presence and patterns of RNA expression provide crucial information about the health status of an individual. Through techniques like RNA sequencing (RNA-seq), scientists can analyze gene expression profiles and detect abnormalities that may indicate disease or other health conditions.
• Environmental and agricultural research – RNA studies in plants, for example, help researchers understand how plants respond to environmental stressors, such as drought or disease, and how they can be engineered for improved resilience or yield. In animal research, RNA studies help scientists explore genetic traits, disease susceptibility, and the effects of environmental factors on gene expression.