SELEX: In Vitro Aptamer Selection

Selection Round

Round 0 — naive library

Selection Parameters

Target concentration [T] 100 nM

Wash stringency 0.40

PCR mutation rate 0.12

Auto-run interval 1.2 s

Library Statistics

Mean K_d (geo.)

31.6 µM

Best K_d

— nM

Last round survival

—

Enrichment vs round 0

1.0×

How it works

SELEX (Systematic Evolution of Ligands by EXponential enrichment) starts from a library of ~10¹⁴–10¹⁵ random-sequence single-stranded oligonucleotides and, over repeated rounds, converges on the small subset that folds into a shape binding a chosen target tightly. Each simulated aptamer carries a dissociation constant K_d; at equilibrium the bound fraction follows the Langmuir isotherm:

θ = [T] / ([T] + K_d)
survival probability p = θ^(1 + 4·stringency)

Raising θ to a power sharper than 1 models a stringent wash step: it preferentially keeps sequences whose K_d is well below [T], discarding weak or non-specific binders even though they were nominally "bound". Every round proceeds as:

Partition — each sequence's fate is drawn stochastically from its survival probability (a real gel-shift / column-partition step is itself imperfect and probabilistic).
Amplify (PCR) — surviving strands are cloned back up to full library size; each copy accumulates polymerase error, nudging log₁₀(K_d) by a Gaussian step scaled by the mutation-rate slider — this reseeds diversity and occasionally improves affinity further.
[T] — lowering target concentration between rounds (as real SELEX protocols do) raises the bar, since only sequences with K_d ≲ [T] bind appreciably.

In the visualization, distance from the target sphere maps to each aptamer's current affinity (tight binders orbit close; the naive library sits in a diffuse cloud) and color runs blue → gold as K_d drops. After enough rounds, the cloud collapses into a tight, gold shell — the point at which real SELEX protocols stop and clone/sequence the survivors.

Weak binder (high K_d) Tight binder (low K_d)

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