tRNA cloverleaf

D Loop:

Anticodon loop:

Variable Loop:

TψC Loop:

Acceptor Stem:

5' Terminus:

3' Terminus:

Non-Watson-Crick Base Pairs:
Modified Bases:
Learning Objectives
  1. To understand the correspondence between the cloverleaf diagram and tRNA's three-dimensional structure.
  2. To understand that tRNA structure depends on base pairing and base stacking interactions.
  3. To understand that tRNA contains modified nucleotides and nonstandard base pairs.

Activity Instructions

Explore the three-dimensional structure of tRNA and its relationship to the cloverleaf diagram. The L-shaped 3D structure of tRNAPhe from yeast is shown in the window on the left, and the cloverleaf representation of its secondary structure is shown on the right. Click on any of the labeled buttons to see their locations in three dimensions. When the button for a region of tRNA is clicked, the corresponding region in 3D on the left will be highlighted in a color similar to that of the cloverleaf. Use buttons on the right of the window to display some additional features of tRNA structure: stretches of continuously stacked bases and non-Watson-Crick base interactions (with each set of stacked or interacting bases having a different backbone color), as well as the modified nucleotides of tRNAPhe. Click and drag to rotate the molecule.

  1. Which tRNA stem stacks on top of the acceptor stem?
  2. What region of the tRNA is farthest from the anticodon loop in three dimensions?
  3. Is the TψC loop closer to the D loop or to the anticodon loop in three dimensions?