RNA

Ribonucleic acid (RNA) is a fundamental biological macromolecule that plays diverse and indispensable roles in the functioning of all known living organisms. As a nucleic acid, it belongs to one of the four major classes of biological macromolecules, alongside proteins, carbohydrates, and lipids. RNA participates both as a carrier of genetic information and as an active cellular effector, contributing to processes ranging from protein synthesis to the regulation of gene expression. Its structural versatility and chemical reactivity allow it to adopt a wide variety of forms, many of which support catalytic and regulatory activities essential for life.

Basic Chemical Composition and Structure

RNA is composed of repeating nucleotide units, each consisting of a ribose sugar, a nitrogenous base, and at least one phosphate group. The ribose sugar contains five carbon atoms, designated 1’ to 5’, with the nitrogenous base attached to the 1’ carbon. RNA contains four primary bases: adenine (A) and guanine (G), which are purines, and cytosine (C) and uracil (U), which are pyrimidines. A distinctive feature of ribose compared to deoxyribose found in DNA is the presence of a hydroxyl group at the 2’ position, which increases the molecule’s chemical reactivity and susceptibility to hydrolysis.
Nucleotides are linked through phosphodiester bonds formed between the 3’ hydroxyl of one ribose and the 5’ phosphate of the next. Because each phosphate group carries a negative charge, RNA functions as a polyanion. Base pairing in RNA commonly follows the canonical rules of cytosine pairing with guanine and adenine pairing with uracil, though non-canonical pairs, such as guanine–uracil, can also occur. These alternative interactions contribute to the structural diversity of RNA, enabling the formation of complex three-dimensional architectures.
RNA is typically single-stranded, although double-stranded RNA (dsRNA) can form in specific biological contexts. Even within single-stranded molecules, regions of internal complementarity often cause the strand to fold back on itself to create short double-helical segments. These segments typically adopt an A-form helix, characterised by a deep, narrow major groove and a shallow, broad minor groove. The 2’ hydroxyl group is central to maintaining this conformation and also facilitates intramolecular reactions that can cleave the RNA backbone under certain conditions.

Structural Organisation: Secondary and Tertiary Forms

RNA molecules often depend on intricate folding patterns to achieve their functional conformations. Secondary structures, stabilised by hydrogen bonding, include elements such as hairpin loops, internal loops, helices, and bulges. These structural motifs form the scaffold for the tertiary configuration of the molecule, which involves long-range interactions and the packing of helical regions into sophisticated three-dimensional shapes.
Metal ions, particularly magnesium, play a crucial role in stabilising RNA structures by counteracting the negative charge of the phosphate backbone and enabling tight folding. Experimental studies on RNA design have demonstrated that a four-base system, as present in nature, is optimal for generating diverse secondary structures. Alternative enantiomers of RNA can also be produced, such as L-RNA constructed from L-ribose, which shows increased resistance to enzymatic degradation compared with naturally occurring D-RNA.
As with proteins, the topology of RNA can be defined in terms of its intramolecular contacts, allowing researchers to analyse folding patterns using concepts such as circuit topology. Complex RNA structures include ribozymes and ribonucleoprotein assemblies, with the ribosome being a notable example. Structural investigations have revealed that the catalytic core of the ribosome is composed entirely of RNA, highlighting the molecule’s capacity for enzymatic function.

Differences Between RNA and DNA

Although RNA and DNA share many characteristics as nucleic acids, they differ in several essential aspects:

• Strandedness: DNA typically exists as a long double-stranded helix, whereas RNA is generally single-stranded and shorter.
• Sugar component: DNA contains deoxyribose, while RNA contains ribose with a 2’ hydroxyl group, contributing to the molecule’s greater chemical lability.
• Base composition: DNA uses thymine as the complement to adenine, whereas RNA uses uracil, a demethylated form of thymine.
• Structural complexity: Unlike the extended, regular double helix of DNA, RNA folds into compact shapes comprising short helices and loops; these configurations support RNA’s catalytic and regulatory functions.

These differences underpin the respective biological functions of DNA as a stable genetic repository and RNA as a versatile molecule suited to transient and reactive cellular roles.

Chemical Modifications of RNA

Although RNA is synthesised using only the four standard nucleotides, extensive chemical modifications often occur during maturation. These post-transcriptional changes affect both the bases and the ribose sugars and contribute to the structural and functional diversity of RNA species.
Prominent modifications include pseudouridine, in which the linkage between uracil and ribose is altered, and 5-methyluridine, commonly found in transfer RNA. Inosine, derived from the deamination of adenine, is of particular significance due to its role in wobble base pairing during translation. More than one hundred modified nucleosides have been identified in naturally occurring RNAs, with tRNA displaying the greatest diversity. Ribosomal RNA (rRNA) also harbours numerous modifications, many located in essential functional regions such as the peptidyl transferase centre, suggesting important roles in structural stability and translational accuracy.

Types of RNA and Their Functions

A wide range of RNA types exist in cellular organisms and viruses, each with specific functional roles.

• Messenger RNA (mRNA): This form carries genetic instructions from DNA to ribosomes, where it directs the synthesis of proteins. mRNA sequences determine the amino acid order of the resulting polypeptide chain.
• Transfer RNA (tRNA): tRNA plays a central role in translation by transporting amino acids to the ribosome. Each tRNA recognises specific codons in the mRNA through its anticodon loop.
• Ribosomal RNA (rRNA): The structural and catalytic core of the ribosome consists of rRNA. It facilitates peptide bond formation, functioning as a ribozyme.
• Non-coding RNAs (ncRNA): Although historically overshadowed by protein-coding RNAs, ncRNAs constitute the vast majority of transcriptional output in eukaryotes. They include tRNA and rRNA but also regulatory molecules such as small nuclear RNA (snRNA), microRNA (miRNA), and long non-coding RNA (lncRNA). Many of these molecules influence gene expression, RNA processing, chromatin dynamics, and cellular signalling.
• Small RNAs: Molecules shorter than 200 nucleotides, including miRNAs and small interfering RNAs (siRNAs), often participate in post-transcriptional gene regulation.
• Long RNAs: Molecules longer than 200 nucleotides, including mRNAs and lncRNAs, are involved in both coding and non-coding functions.

Some RNA species act as catalysts, capable of accelerating chemical reactions such as the cleavage or ligation of other RNA molecules. These catalytic RNAs, known as ribozymes, provide strong evidence for the hypothesis that early life forms may have relied on RNA both for information storage and for catalytic activity.

Biological and Evolutionary Significance

RNA fulfils vital functions across living organisms and viruses. Many viruses, including several human pathogens, utilise RNA genomes, relying on RNA replication mechanisms that differ from those of DNA-based organisms. Within cells, RNA orchestrates protein synthesis, regulates gene activity, and participates in numerous essential biochemical pathways.
A widely supported evolutionary concept, known as the RNA world hypothesis, proposes that early life on Earth employed RNA as both a genetic material and a catalytic agent before the evolution of DNA and protein enzymes. The discovery of catalytic RNA, alongside the RNA-based catalytic core of the ribosome, provides compelling evidence for this scenario, suggesting that RNA may have been the foundation upon which modern biological complexity developed.