RNA Shape and Function

Connect a sequence to its base pairs and a folded molecular shape.

Experimental yeast phenylalanine transfer RNA shown as a pink folded backbone with paired bases and gold resolved metal ions.

Structural referencePDB 1EHZ

Experiment · A 14-nucleotide hairpin

Change the sequence. Inspect the pairing.

Disrupt a stem pair, then make a second change that restores complementarity. Follow the same numbered bases between the pairing map and a spatial schematic.

Sequence variant

Same sequence · same numbered pairs

The backbone is one continuous RNA strand. Lines across the stem mark contacts between bases; the four loop bases are unpaired in this teaching map.

Select a stem base to inspect its partner

Sequence shown 5′ → 3′

Selected contact

G–C

Nucleotides 1 and 14

Canonical pairs in this map

5 / 5

A–U and G–C contacts only

Pairing at positions 3–12

Original A–U

A controlled sequence comparison

Pair 1–14: G–C

These bases can form a canonical Watson–Crick pair in the displayed alignment. Switch variants to inspect a single-base change and its compensatory partner.

1 / 5

Authored pairing and spatial schematics, not a folding simulation or experimental structure. Playback tours the contacts; it does not show a folding pathway. Real RNAs can form wobble and other noncanonical contacts, alternative structures and tertiary interactions. Pair counts do not predict stability or activity.

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Quick reference

One strand can pair with itself

Complementary regions of an RNA can pair within the same strand. Stems, loops and other interactions contribute to a folded structure. RNA can have structural, catalytic and regulatory roles as well as carrying a message.

Sequence and pairing

A base substitution can disrupt a pair in a stem. A second substitution at the paired position may restore compatible pairing. That alone does not prove that the complete RNA has recovered its original structure or function.

Three ways to see one molecule

A sequence, a secondary-structure diagram and a 3D model reveal different information. Moving between those views is a change in representation. It does not show an experimentally observed folding trajectory.

Check your understanding Optional

A second mutation restores pairing in a stem. What does this demonstrate?

Every function of the RNA is definitely restored.RNA always forms a DNA-like double helix along its whole length.The two selected positions can form a compatible pair again.

At the bench

See transfer and ribosomal RNA at work inside the translation machinery.

Open Cell

Sources and model notes

Structure-based views of resolved experimental coordinates. Cutaways, category colours, camera choices and guided highlights are authored for teaching. Coordinates remain fixed; highlights are not experimental trajectories or simulation outputs.

RCSB PDB · Yeast tRNA 1EHZ

Experimental structure of a functional folded RNA.

RCSB PDB · Adenine riboswitch 1Y26

RNA recognition of a small molecule.