11.3 RNA structure and types

RNA is the versatile cousin of DNA, playing crucial roles in gene expression and cellular processes. From messenger RNA carrying genetic instructions to regulatory RNAs fine-tuning gene activity, these molecules are essential for life.

RNA's structure is a masterpiece of molecular origami. Single-stranded RNA folds into intricate shapes, forming hairpins, loops, and bulges. These structures enable RNA to perform its diverse functions, from protein synthesis to gene regulation.

RNA Types

Functional RNA Molecules

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• Single-stranded RNA molecules play diverse roles in cellular processes and gene expression
• Messenger RNA (mRNA) carries genetic information from DNA to ribosomes for protein synthesis
• Transfer RNA (tRNA) adaptor molecules deliver amino acids to the ribosome during translation (protein synthesis)
• Ribosomal RNA (rRNA) forms the structural and catalytic core of ribosomes, enabling protein synthesis
• Small nuclear RNA (snRNA) molecules are involved in RNA splicing, a process that removes introns from pre-mRNA to generate mature mRNA
• MicroRNA (miRNA) short, non-coding RNA molecules that regulate gene expression by targeting mRNA for degradation or translational repression (silencing)

Regulatory RNA Molecules

• RNA molecules can also function as regulators of gene expression without being translated into proteins
• Small interfering RNA (siRNA) molecules are involved in RNA interference (RNAi), a process that silences gene expression by degrading complementary mRNA
• Long non-coding RNA (lncRNA) molecules are over 200 nucleotides long and have various regulatory roles, such as modulating chromatin structure and gene expression
• Riboswitches are regulatory RNA elements found in the untranslated regions of some mRNAs that can directly bind metabolites and alter gene expression in response to changes in metabolite concentration
• CRISPR RNA (crRNA) guides the CRISPR-Cas system in prokaryotes to cleave foreign nucleic acids (viral DNA or plasmids) as a form of adaptive immunity

RNA Structure

Secondary Structure Elements

• Secondary structure of RNA refers to the base-pairing interactions within a single RNA molecule that form local structural elements
• Stem-loop structures, also known as hairpins, form when complementary sequences within an RNA molecule base-pair, creating a double-stranded stem and a single-stranded loop
• Internal loops occur when unpaired nucleotides are present on both strands of a double-stranded region, interrupting the stem structure
• Bulges are formed when unpaired nucleotides are present on only one strand of a double-stranded region, causing a bulge in the RNA structure

Higher-Order Structures

• Tertiary structure of RNA refers to the three-dimensional folding of an RNA molecule, stabilized by interactions between secondary structure elements and long-range base-pairing
• Pseudoknots are tertiary structure elements formed when nucleotides in a loop region base-pair with complementary sequences outside the stem-loop, creating a knot-like structure
• Kissing loops occur when the unpaired nucleotides in two hairpin loops base-pair with each other, forming a tertiary interaction between the loops
• RNA G-quadruplexes are stable tertiary structures formed by stacking of G-tetrads, which are planar arrangements of four guanine bases held together by Hoogsteen hydrogen bonding
• RNA molecules can also form complex tertiary structures through interactions with proteins, such as the ribosomal RNA in the ribosome or the snRNA in the spliceosome