Ribosome Binding Site Design Lab (2D)

Ribosome Binding Site

Shine-Dalgarno strength 70%

Spacer length 8 nt

mRNA secondary structure 20%

Start Codon

Live Readouts

ΔG_total

— kcal/mol

Relative TIR

—

Proteins completed / blocked (queue jams)

0 / 0

How it works

Translation initiation rate follows the thermodynamic RBS model real ribosome-binding-site design tools use (Salis, Mirsky & Voigt, 2009): the total free energy needed to assemble the 30S initiation complex sets the initiation rate exponentially.

ΔG_total = ΔG_spacing + ΔG_structure − ΔG_SD:antiSD
TIR_rel  = exp( −(ΔG_total − ΔG_best) / RT ) · f_codon
RT = 0.616 kcal/mol at 37°C

SD strength — how closely the Shine-Dalgarno sequence matches the 16S rRNA anti-SD (…CCUCC…). A perfect match pairs at ≈ −8.4 kcal/mol; a poor match barely helps at all.
Spacer length — the gap between SD and start codon. ~8 nt aligns the start codon in the ribosome's decoding channel; shorter spacers clash sterically (steeper penalty) and longer ones lose SD-channel alignment.
Secondary structure — a hairpin folded over the RBS must be melted before the ribosome can dock; stronger structure = higher ΔG_structure = slower initiation. Watch the mRNA loop swell and swallow the SD marker on the track.
Start codon — ATG initiates fastest; GTG and TTG use a near-cognate tRNA and initiate ~3× and ~10× slower respectively.
Each initiation attempt that clears the model's rate spawns a ribosome (cyan 30S + magenta 50S) that walks the CDS on the track below, laying down a peptide bead chain. If the ribosome ahead hasn't cleared enough of the transcript, the new one is blocked — real polysome traffic-jam behavior when initiation outruns elongation. The lower gauge panel shows the live ΔG breakdown and the exponential TIR curve.

Shine-Dalgarno Start codon 30S / peptide 50S subunit

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