Differential structural status of the RNA counterpart of an undecamer quasi-palindromic DNA sequence present in LCR of human beta-globin gene cluster

作者：Kaushik Mahima; Kukreti Shrikant^*

来源：Journal of Biomolecular Structure & Dynamics, 2015, 33(2): 244-252.

DOI：10.1080/07391102.2013.877402

• UV-thermal denaturation
• structural studies of RNA oligonucleotide
• RNA hairpin
• structural polymorphism
• RNA duplex
• circular dichroism spectroscopy

Our previous work on structural polymorphism shown at a single nucleotide polymorphism (SNP) (A -> G) site located on HS4 region of locus control region (LCR) of beta-globin gene has established a hairpin -> duplex equilibrium corresponding to A -> B like DNA transition (Kaushik M, Kukreti, R., Grover, D., Brahmachari, S.K. and Kukreti S. Nucleic Acids Res. 2003; Kaushik M, Kukreti S. Nucleic Acids Res. 2006). The G-allele of A -> G SNP has been shown to be significantly associated with the occurrence of beta-thalassemia. Considering the significance of this 11-nt long quasi-palindromic sequence [5 '-TGGGG(G/A)CCCCA; HP(G/A)11] of beta-globin gene LCR, we further explored the differential behavior of the same DNA sequence with its RNA counterpart, using various biophysical and biochemical techniques. In contrast to its DNA counterpart exhibiting a A -> B structural transition and an equilibrium between duplex and hairpin forms, the studied RNA oligonucleotide sequence [5 '-UGGGG(G/A)CCCCA; RHP(G/A)11] existed only in duplex form (A-conformation) and did not form hairpin. The single residue difference from A to G led to the unusual thermal stability of the RNA structure formed by the studied sequence. Since, naturally occurring mutations and various SNP sites may stabilize or destabilize the local DNA/RNA secondary structures, these structural transitions may affect the gene expression by a change in the protein-DNA recognition patterns.

• 出版日期2015-2-1