RNA Structure and Prediction

RNA (ribonucleic acid)

A polymer of ribonucleotides linked together by phosphodiester linkage, which served as the first genetic material.

Thomas R. Cech

The Nobel Prize laureate who in 1982 discovered that unprocessed RNA in $Tetrahymena\text{ }thermophila$ could splice itself, proving RNA has catalytic functions.

Purines

Nitrogenous bases made of a 6-member ring fused to a 5-member ring; specifically Adenine and Guanine.

Pyrimidines

Nitrogenous bases made of a single 6-member ring; in RNA, these are Cytosine and Uracil.

A-like conformation

The structural form adopted by double-stranded RNA because steric clashes between $2'-OH$ groups prevent a B-like conformation.

Primary Structure

The one-dimensional sequence of nucleotide components ($A$, $C$, $G$, and $U$) in an RNA molecule.

Secondary Structure

The two-dimensional base-paired structure of a molecule, such as the local conformation of polymers.

Tertiary Structure

The overall three-dimensional structure of a molecule built on interactions of lower-order secondary structures, such as a pseudoknot.

Stem Loop (Hairpin Loop)

A lollipop-shaped structure formed when a single-stranded nucleic acid loops back on itself to form a complementary double helix (stem) topped by a loop.

Bulge Loop

A structure occurring in helical segments when bases on only one side cannot form base pairs, causing bends in the helix.

Interior Loop

A structure occurring when bases on both sides of a segment cannot form base pairs.

Junction (Multiloop)

A closed structure where two or more double-stranded regions converge.

Pseudoknot

A tertiary structural element formed by base-pairing between an existing secondary structure loop and a free sequence ending.

Messenger RNA (mRNA)

RNA that carries genetic information from the nucleus to the protein-synthesizing machinery (ribosomes).

7-methyl guanosine triphosphate cap

A structure added to the $5'$ terminal end of mRNA that aids in recognition by translation machinery and protects from $5'$ exonuclease.

Poly(A) tail

A polymer of $20$-$250$ Adenylate residues at the $3'$ end of mRNA that prevents attack by $3'$ exonucleases.

Codon

A sequence of $3$ nucleotides on mRNA that carries information for protein synthesis.

hnRNA (heterogeneous nuclear RNA)

The immediate large-sized product of gene transcription in mammalian nuclei; 75\text{%} is degraded while 25\text{%} is processed into mature mRNA.

Transfer RNA (tRNA)

Small RNA molecules ($74$-$95$ nucleotides) that act as adapters by carrying amino acids from the cytoplasm to the protein-synthesizing machinery.

Acceptor Arm

The $7$ base pair arm at the $3'$ end of tRNA with the sequence $CCA$; its $3'$ OH group binds to the carboxyl group of an amino acid.

Anticodon Arm

The arm of tRNA that is complementary to and binds with the triplet codon on mRNA via hydrogen bonds.

DHU arm

The tRNA arm containing DiHydroUracil that serves as the recognition site for aminoacyl tRNA synthetase.

T\text{\psi}C arm

The tRNA arm containing thymidine, pseudouridine, and cytosine, involved in binding tRNA to the ribosome.

Small nuclear RNAs (snRNAs)

RNAs (U1, U2, U4, U5, U6) significantly involved in intron removal and the processing of hnRNA into mature mRNA.

sn