Time-Gel · live simulator · DNA

What does it cost to find the right owner?

UV light leaves dimers in DNA. Searchers (XPC) walk the strand. When one stops, a verifier (TFIIH) checks the spot in steps, and every step burns ATP. A real lesion passes and is cut out. An intact spot should fail; when it passes anyway, the cell cuts good DNA. The energy spent per correct repair is the cost of finding the owner.

lesion (CPD)searcher (XPC)verifying (ATP)correct cutwrong cutRNA polymerase (gene rows)
ATP spent0
Correct cuts0
Wrong cuts0
ATP / correct0
Lesions left0
Error / visit0

Error against energyKinetic proofreading: error per visit = f · (fg)n. Dot = current setting.

What the clock would seeThe Time-Gel question carried into a cell

≈ 10⁻¹¹ s

Time-Gel clock shift per repairing cell (estimate from the application note). Far below anything measurable. This simulator does not test Time-Gel.

Entropy produced by repair: σ ≈ rATP·|ΔGATP|/T. One ATP ≈ 20 kBT at 37 °C, so each ATP here adds about 20 kB of entropy.

Assumptions

What is a choice here. f = 0.2 is chosen so errors are visible; real NER discrimination is far sharper. Steps and timings are compressed. The shape of the result is the point: with no energy (g = 0) extra checks buy nothing; each energised step multiplies the error down by fg. Kinetic proofreading (Hopfield 1974, Ninio 1975; for NER, Reardon & Sancar 2003) predicts the same outcomes without Time-Gel. Paper: Information Looking for Its Owner in DNA Repair v1.0.

Model output, not experimental evidence. This page does not represent the views of Aziz Sancar or his laboratory.