Crystal Structure of d(gcGXGAgc) with X = G: a Mutation at X is Possible to Occur in a Base-Intercalated Duplex for Multiplex Formation

DNA fragments with the sequences d(gcGX[Y]_n Agc) (n = 1, X = A, and Y = A, T, or G) form base-intercalated duplexes, which is a basic unit for formation of multiplexes such as octaplex and hexaplex. To examine the stability of multiplexes, a DNA with X = Y = G and n = 1 was crystallized under conditions different from those of the previously determined sequences, and its crystal structure has been determined. The two strands are coupled in an anti-parallel fashion to form a base-intercalated duplex, in which the first and second residues form Watson-Crick type G:C pairs and the third and sixth residues form a sheared G:A pairs at both ends of the duplex. The G₄ and G₅ bases are stacked alternatively on those of the counter strand to form a long G column of G₃-G₄-G₅*-G₅-G₄*-G₃*, the central four Gs being protruded. In addition, the three duplexes are associated to form a hexaplex around a mixture of calcium and sodium cations on the crystallographic threefold axis. These structural features are similar to those of the previous crystals, though slightly different in detail. The present study indicates that mutation at the 4th position is possible to occur in a base-intercalated duplex for multiplex formations, suggesting that DNA fragments with any sequence sandwiched between the two triplets gcG and Agc can form a multiplex.

Keywords:

• DNA
• Base-intercalated duplex
• DNA hexaplex
• X-ray structure
• Repetitive DNA sequence

Acknowledgments

We thank Atsushi Nakagawa for facilities and help during data collection. This work was supported in part by Grants-in-Aid for Scientific Research (No. 12480177 and 14035217) from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

This article is dedicated to Professor Eiko Ohtsuka on the occasion of her 70th birthday.

Present address for Jiro Kondo Institut de Biologie Moléculaire et Cellulaire du CNRS, Université Louis Pasteur, 15 rue René Descartes, Strasbourg, France.

Notes

* Small and underlined characters indicate that they can form Watson-Crick G:C and sheared G:A base pairs, respectively, when the fragments are aligned in an anti-parallel fashion for self-assembly or folding.

^aNumber of dsDNA in the asymmetric unit.

^bR_merge = 100 × Σ_hklj | I_hklj - ⟨I_hklj⟩ |/Σ_hklj⟨I_hklj⟩.

^cR-factor = 100 × Σ‖F_o|-|F_c‖/Σ|F_o|, where |F_o| and |F_c| are the observed and calculated structure factor amplitudes, respectively.

^d Calculated using a random set containing 10% of observations that were not included throughout refinement.[ ⁹ ]