DNA and RNA Structure and Function

Double Helix

The structural architecture of DNA consisting of two polynucleotide strands twisted together around a common axis in a spiral-staircase pattern.

Pitch (DNA)

The vertical length of one complete turn of the DNA double helix, measuring approximately $3.4\,\text{nm}$ and encompassing about $10.4$ base pairs in B-DNA.

Rise (DNA)

The distance between two adjacent, successive base pairs along the helical axis, measuring $0.34\,\text{nm}$.

Chargaff's Rule

The principle that DNA from many organisms contains an equal proportion of adenine and thymine ($\text{A} = \text{T}$) and an equal proportion of guanine and cytosine ($\text{G} = \text{C}$).

Base Stacking

The arrangement in DNA where the flattened ring regions of adjacent bases face one another, stabilizing the double helix by repelling water molecules.

Melting Temperature ($\text{T}_\text{m}$)

The specific temperature at which half ($50\%$) of a double-stranded DNA sample denatures into two single strands.

Intercalating Agent

A chemical agent that inserts between stacked base pairs of DNA, distorting helical structure and interfering with replication and transcription (e.g., ethidium bromide and doxorubicin).

Histones

Positively charged DNA-binding proteins containing abundant lysine and arginine residues that neutralize the negative charge of the DNA backbone to compact it into nucleosomes.

Antiparallel

The orientation of double-stranded DNA in which one strand runs in the $5' \rightarrow 3'$ direction while the complementary strand runs in the opposite $3' \rightarrow 5'$ direction.

Leading Strand

The template-directed DNA strand that is replicated continuously in the $5' \rightarrow 3'$ direction toward the replication fork, requiring only one primer.

Lagging Strand

The DNA strand that is synthesized discontinuously away from the replication fork in the $5' \rightarrow 3'$ direction via Okazaki fragments, requiring multiple primers.

Okazaki Fragments

Short segments of newly synthesized DNA formed discontinuously on the lagging strand during DNA replication.

DNA Origami

A method in DNA nanotechnology where a long single strand of DNA is folded into custom 2D or 3D nanostructures using numerous short synthetic staple strands.

B-DNA

The standard, right-handed Watson–Crick DNA double helix under physiological hydrated conditions, characterized by ~$10.4$ base pairs per turn, a pitch of ~$3.4\,\text{nm}$, and prominent major and minor grooves.

A-DNA

A right-handed helical conformation of DNA formed under dehydrated conditions, in RNA–DNA hybrids, or in dsRNA, featuring ~$11$ base pairs per turn, a pitch of ~$2.8\,\text{nm}$, and a deep major groove.

Z-DNA

An elongated, left-handed double helix containing ~$12$ base pairs per turn and a pitch of ~$4.5\,\text{nm}$, occurring under high salt conditions, negative supercoiling, or alternating GC repeats.

Major Groove

The wider groove of the DNA double helix where the edges of the base pairs are exposed and accessible to regulatory proteins and transcription factors.

Minor Groove

The narrower groove of the DNA double helix where nitrogenous bases are comparatively hidden.

Triplex DNA

A triple-helical nucleic acid structure formed when a third synthetic strand (TFO) binds into the major groove of double-stranded DNA via specific base pairing (T to AT and protonated C to GC).

Messenger RNA (mRNA)

A single-stranded RNA transcript that encodes proteins and acts as the template for protein synthesis during translation.

Transfer RNA (tRNA)

An adaptor RNA molecule responsible for delivering specific amino acids to the ribosome during translation according to its anticodon sequence.

Ribosomal RNA (rRNA)

A structural and catalytic RNA component that combines with proteins to form the large and small subunits of ribosomes.

Ribozyme

An RNA molecule that possesses catalytic activity and accelerates biochemical reactions.

Small Nuclear RNA (snRNA)

Non-coding nuclear RNAs that function in RNA processing events, particularly mRNA splicing.

Small Nucleolar RNA (snoRNA)

Small non-coding RNA molecules that participate in the chemical modification of ribosomal RNAs.

MicroRNA (miRNA)

Small non-coding RNA molecules that regulate gene expression post-transcriptionally.

Small Interfering RNA (siRNA)

Short double-stranded non-coding RNA molecules involved in the RNA interference pathway that silences gene expression.

Long Non-Coding RNA (lncRNA)

Non-coding RNA transcripts longer than 200 nucleotides that regulate diverse cellular processes such as chromatin remodeling and gene expression.