In nucleic acid thermodynamics, TM (melting temperature) refers to which specific condition for a DNA duplex?

Introduction / Context:
TM, or melting temperature, is a fundamental parameter in DNA hybridization, PCR primer design, and nucleic acid biophysics. It captures the temperature at which a DNA duplex is half melted and half intact under specified ionic and sequence conditions.

Given Data / Assumptions:

• We are discussing DNA (or RNA–DNA) duplex stability.
• Salt concentration and sequence composition affect TM.
• Equilibrium conditions are assumed for the definition.

Concept / Approach:
As temperature rises, hydrogen bonding and base-stacking interactions that stabilize the double helix weaken. The melting temperature is defined where the fraction of base pairs that are paired equals the fraction that are unpaired, i.e., 0.5 duplex fraction at equilibrium.

Step-by-Step Solution:

Verification / Alternative check:
Hyperchromic shift at 260 nm shows a characteristic S-shaped melting curve; TM corresponds to its midpoint. Predictive formulas incorporate GC content, length, and salt corrections and should agree with measurements within reasonable error.

Why Other Options Are Wrong:

• Membrane 50% fluid: TM can also denote membrane transition temperature in lipid biophysics, but in nucleic acid questions it specifically refers to DNA duplex melting.
• Protein 50% unfolded: That concept describes protein melting temperature, not DNA TM.
• All of the above: These definitions are domain-specific and not simultaneously applicable here.
• RNA polymerase binding maximum: TM is unrelated to transcription factor binding optima.

Common Pitfalls:
Ignoring ionic strength and sequence length when comparing TM values across experiments. Another pitfall is assuming TM is a single universal property independent of context.

Final Answer:
50% of a DNA duplex is denatured (single-stranded) at equilibrium.