Melt curve

Helicity against temperature for the chain you selected, with its derivative underneath, so a melt is read as a shape rather than as a single melting temperature.

What it doesCopy Anchor Link

A melting temperature is one number taken off a curve. It answers "where is the midpoint" and nothing else — not how sharp the transition is, not whether there is more than one, not how much of the chain is still paired ten degrees below it. Two sequences can share a Tm to a tenth of a degree and melt nothing alike.

This is the curve that number comes from. θ, the fraction of base pairs still formed, is drawn against temperature; −dθ/dT, its slope, is drawn beneath it on the same temperature axis. The midpoint is where θ crosses one half, and it is also the peak of the derivative — a domain that melts in two stages shows two peaks there while θ shows only a step with a shoulder.

The two are stacked rather than overlaid on a shared vertical axis. θ is a probability bounded by 0 and 1; the derivative is a slope whose height depends on the temperature spacing it was sampled at. Drawing them together means rescaling one of them, and a rescaled derivative read against a helicity axis invites treating its height as an amount of pairing, which it is not.

When you'd use thisCopy Anchor Link

• When a Tm looks right and the behaviour does not. A shallow transition and a sharp one at the same midpoint behave differently at every temperature except that midpoint, which is the one temperature a protocol rarely sits at.
• When you are choosing an annealing temperature. What matters is how much of the chain is paired at the temperature you will actually hold, and that is a point on this curve, not the midpoint.
• When a long template may melt in domains. AT-rich stretches open before GC-rich ones, and separate domains appear as separate peaks in the derivative.
• When comparing buffers. Salt shifts the whole curve; changing Na⁺ and watching it move shows whether the shift is enough to matter over your working range.

What this computesCopy Anchor Link

• θ(T), fractional helicity — the fraction of base pairs still formed at each temperature, from a nearest-neighbour statistical model over the chain you selected.
• −dθ/dT, the differential melting curve — the slope of the above. Its peaks are melting transitions; the number of peaks is the number of cooperatively melting domains.
• The melting temperature — the temperature at which θ = 0.5. On a multi-domain chain this is a weighted midpoint and not a description of either domain, which is the case the derivative is there to make visible.
• The transition width — how far in temperature the curve takes to fall, which is the cooperativity the midpoint alone discards.
• The ionic conditions the curve was computed at — the sodium concentration is the same buffer every other melting readout in the editor uses, so changing it here changes them together rather than leaving two answers for one solution.

What it does not doCopy Anchor Link

The model is validated over a bounded chain length, and outside it the panel refuses and names the limit rather than drawing a curve it cannot stand behind. It describes a chain melting at equilibrium: it is not a prediction of a hybridisation rate, and it does not model mismatches, modified bases, or the kinetics of a ramp.