DNA melting during transcription initiation occurs mainly at
Promoter melting nucleation occurs predominantly at AT-rich Pribnow box TATAAT centered -10 relative to start site. This element intrinsically low thermodynamic stability due to only two hydrogen bonds per AT base pair and weak stacking facilitates unwinding. Sigma70 region 2 binds non-template strand exposing bases, flipping Adenine -11 into protein pocket initiating bubble formation. Footprinting using potassium permanganate reacting with single-stranded thymines shows maximal reactivity at -10 region not -35. Structural studies confirm -10 melting propagates toward +1, generating thirteen base transcription bubble. Thus DNA melting during initiation localized to -10 region primarily.
Ref: Berg Biochemistry Section 28.2: DNA melting at -10 region during initiation; Alberts Chapter 6: Pribnow box AT-rich melting nucleation site