Hairpin–duplex equilibrium reflected in the A→B transition in an undecamer quasi‐palindrome present in the locus control region of the human β‐globin gene cluster

Our recent work on an A→G single nucleotide polymorphism (SNP) at the quasi‐palindromic sequence d(TGGGG[A/G]CCCCA) of HS4 of the human β‐globin locus control region in an Indian population showed a significant association between the G allele and the occurrence of β‐thalassemia. Using UV‐thermal denaturation, gel assay, circular dichroism (CD) and nuclease digestion experiments we have demonstrated that the undecamer quasi‐ palindromic sequence d(TGGGGACCCCA) (HPA11) and its reported polymorphic (SNP) version d(TGG GGGCCCCA) (HPG11) exist in hairpin–duplex equilibria. The biphasic nature of the melting profiles for both the oligonucleotides persisted at low as well as high salt concentrations. The HPG11 hairpin showed a higher T m than HPA11. The presence of unimolecular and bimolecular species was also shown by non‐denaturating gel electrophoresis experiments. The CD spectra of both oligonucleotides showed features of the A‐ as well as B‐type conformations and, moreover, exhibited a concentration dependence. The disappearance of the 265 nm positive CD signal in an oligomer concentration‐dependent manner is indicative of an A→B transition. The results give unprecedented insight into the in vitro structure of the quasi‐palindromic sequence and provide the first report in which a hairpin–duplex equilibrium has been correlated with an A→B interconversion of DNA. The nuclease‐dependent degradation suggests that HPG11 is more resistant to nuclease than HPA11. Multiple sequence alignment of the HS4 region of the β‐globin gene cluster from different organisms revealed that this quasi‐palindromic stretch is unique to Homo sapiens. We propose that quasi‐palindromic sequences may form stable mini‐ hairpins or cruciforms in the HS4 region and might play a role in regulating β‐globin gene expression by affecting the binding of transcription factors.