Title
Sequence preference and structural heterogeneity of BZ junctions
Author
Doyoun Kim, Jeonghwan Hur, Ji Hoon Han, Sung Chul Ha, Donghyuk Shin, Sangho Lee, Soyoung Park, Hiroshi Sugiyama, Kyeong Kyu Kim
Year
2018
Journal
Nucleic Acids Research
Abstract
BZ junctions, which connect B-DNA to Z-DNA, are necessary for local transformation of B-DNA to ZDNA in the genome. However, the limited information on the junction-forming sequences and junction structures has led to a lack of understanding of the structural diversity and sequence preferences of BZ junctions. We determined three crystal structures of BZ junctions with diverse sequences followed by spectroscopic validation of DNA conformation. The structural features of the BZ junctions were well conserved regardless of sequences via the continuous base stacking through B-to-Z DNA with A-T base extrusion. However, the sequence-dependent structural heterogeneity of the junctions was also observed in base step parameters that are correlated with steric constraints imposed during Z-DNA formation. Further, circular dichroism and fluorescencebased analysis of BZ junctions revealed that a base extrusion was only found at the A-T base pair present next to a stable dinucleotide Z-DNA unit. Our findings suggest that Z-DNA formation in the genome is influenced by the sequence preference for BZ junctions.
Instrument
J-710
Keywords
Circular dichroism, DNA structure, Chemical stability, Biochemistry