posters 5th Asia-Pacific NMR Symposium 2013

NMR Study on the B-Z Junction Structure of 20-bp DNA Duplexes Induced by Z-DNA Binding Proteins: Implication for Z-DNA Formation in a Long Genomic DNA (#162)

Ae-Ree Lee 1 , Hee-Eun Kim , Yeon-Mi Lee , Minjee Jeong , Geum-Hee Hong , Joon-Hwa Lee
  1. GyeongSang National University, Junju GyeongNam, South Korea

Z-DNA, the left-handed form of the double helix, can be formed by alternating purine and pyrimidine bases. Z-DNA is able to be stabilized by interaction with Z-DNA-specific binding proteins with high affinity. Most important advances in recent Z-DNA research is the crystal structure of a junction between the right-handed B-DNA and the left-handed Z-DNA forms of the double helix. The structure of the B-Z junction is important because such a junction should be formed each time a double-helical DNA segment turns into Z-DNA. The handedness of the DNA duplex is completely reversed at the junction by breaking only one base pair and projecting the bases out of the duplex. Base pairs of the B-DNA and Z-DNA segments are continuously stacked across the junction. Our previous NMR study on a 13-bp DNA in complex with the Z-DNA binding protein demonstrates the initial contact conformation as an intermediate structure during B-Z junction formation induced by ADAR1, in which the ADAR1 protein displays unique backbone conformational changes, but the 13-bp DNA duplex maintains the B-form helix. In order to confirm this suggestion and generalize the pathway of the B-Z junction formation, we performed hydrogen exchange studies of various 20-bp DNA duplexes complexed with ADAR1 and backbone perturbation study of ADAR1 upon binding to various DNA. Our study suggest a three-step mechanism of B-Z junction formation: (i) ADAR1 specifically interacts with a CG-rich DNA segment maintaining B-form helix via a unique conformation; (ii) the neighboring AT-rich region becomes very unstable, and the CG-rich DNA segment is easily converted to Z-DNA; and (iii) the AT-rich regions are base-paired again, and the B-Z junction structure is formed.