About this experiment
Build a helix from a short DNA sequence, inspect individual base pairs and separate the strands. Sequence controls GC content and the idealized hydrogen-bond count, while geometric twist controls the drawing of the helix. The complementary strand is displayed in the opposite chemical direction.
Learning goals
- Pair A with T and C with G on antiparallel strands.
- Relate GC content to a simple hydrogen-bond count.
- Distinguish geometric helix parameters from a molecular energy calculation.
How to use it
- 1Select several base pairs in three dimensions and compare their partners.
- 2Apply a different six-to-twenty-four-base sequence and inspect its complement.
- 3Unzip the helix and compare the paired-base and bond counts.
- 4Change base pairs per turn, then record contour length and GC content.
The model
Assumptions
- The sequence describes one strand from 5′ to 3′; the aligned complement runs 3′ to 5′. Only standard DNA bases are accepted.
- Axial rise is fixed at 0.34 nm per base pair. Twist is a geometric control around a B-DNA reference of about 10.5 pairs per turn.
- A-T pairs count as two hydrogen bonds and G-C as three. This count is not a binding-energy or melting-temperature model; stacking, solvent and ionic conditions are excluded.
Try this in class
- Q1Why must the displayed complement have the opposite end labels?
- Q2Why is hydrogen-bond count alone insufficient to predict melting temperature?
Frequently asked questions
Does changing twist simulate DNA supercoiling?
No. It redraws a helix with a chosen angular repeat without solving elasticity or topology.
Does unzipping remove nucleotides?
No. It separates complementary bases while retaining both parental backbones.