Sequence-specific B-to-Z transition in self-assembled DNA: A biophysical and thermodynamic study

Abstract

The most remarkable conformational transition in nature is the B-to-Z transition of DNA which not only contributes for epigenetic regulation but also is exploited to create several advanced nanomaterials for sensing and nanomechanics. The present communication focuses on the intrinsic factors that control the La3+/Ce3+-induced B-to-Z transition in self-assembled branched DNA (bDNA) nanostructures. The transition is sensitive even to two nucleotide change in the loop length and overhang sequences. Predominantly, bDNA structures having 3 T loop length are more sensitive towards helical switching than the 5 T bearing structures. Particularly, bDNA US-17, US-19 and US-23 having 3 Tin the loop are showing B-Z transition in presence of LaCl3. Interestingly, with 'GATC' overhangs both La3+/Ce3+-induced B-to-Z transition was noticed in bDNA structures US-21 and US-22 (having 3 T and 5 T in the loop, respectively). The lanthanide-induced B-Z transition in bDNA is reversed with treatment of EDTA. Isothermal titration calorimetry (ITC) experiments show that the binding mode of lanthanide salts to bDNA followed an entropically and enthalpically favorable process. Further, for the first time ITC data suggests the B-to-Z transition in bDNA is a cooperative shift from exothermic to endothermic. (C) 2019 Elsevier B.V. All rights reserved.