journal menu
abstracts
The DNA duplex containing mercury-mediated base pairs (T-Hg(II)-T) is an attractive biomacromolecular nanomaterials. In a recent study, it was confirmed that the Hg(II) ion significantly stabilizes a DNA duplex by binding selectively to a T-T mispair [1]. Based on the phenomenon observed, a DNA-based sensing system that selectively and sensitively detects Hg(II) ions in aqueous solution was developed [2]. In the present study, we have solved the first crystal structure of a B-form DNA duplex containing two consecutive T-Hg(II)-T base pairs [3]. The Hg(II) ion occupies the center between two T residues. The geometry of the T-Hg(II)-T base pair is very similar to that of the canonical Watson-Crick base pairs. The distance of N3-Hg(II) bond is 2.0 Å, suggesting that the N3 nitrogen releases an imino-proton even at neutral pH (pKa of N3 position of T is 9.8) and directly bonds to Hg(II). In the B-form DNA, the helical axis runs through the center of base pairs, and the Hg(II) ions are therefore aligned along the helical axis. The distance between the two neighboring Hg(II) ions is 3.3 Å. The relatively short Hg(II)-Hg(II) distance indicates that the metallophilic attraction could exit between them and may stabilize the B-form duplex. To support this, the DNA duplex is largely distorted and adopts an unusual non-helical conformation in the absence of Hg(II). In conclusion, the Hg(II) ion is essential for maintaining the B-form conformation of the DNA duplex containing T-T mispairs. The structure of the Hg(II)-DNA hybrid duplex itself and the Hg(II)-induced structural switching from the non-helical form to the B-form provide the basis for the structure-based design of metal-conjugated nucleic acid nanomaterials.
abstracts
Crystal structures of several functional non-coding RNAs, such as ribozymes, aptamers, ribosomes and tRNAs, have been reported so far. Unusual structural motifs and non-complementary base pairs are important for their functions. In the present study, we have determined a crystal structure of an unusual RNA duplex containing a strontium ion binding motif. A 19 mer RNA (5'-UUGUCGCUU[Br]CGAAAAAGUC-3') was chemical synthesized and purified by denaturing PAGE. Crystallizations were performed by the sitting-drop vapor diffusion method. The initial phase was solved by the SAD method. Atomic parameters were refined at a resolution of 3.0 Å. The 19 mer RNA forms an unusual antiparallel duplex. At both ends of the duplex, the Watson-Crick G=C and A-U and the Wobble GoU and AoC base pairs are formed. The Wobble C10oA14* pair is available only in acidic condition by protonation of N1 of A14* (* indicates residues of the opposite strand). Two hydrogen bonds, N1-H(A14*)...O2(C10) and N6-H(A14*)...N3(C10), are observed in the base pair. In the center of the duplex, two sheared G11oA13* and G11*oA13 base pairs are formed. The distance between two RNA chains becomes shorter by the GoA base pair and hydrogen bonds between the Watson-Crick edge of G11 and the phosphate group of A12*. Therefore, the central A12 residue cannot make a base pair, but it makes a stacking interaction with A12*. The A12 residue stacks also with A13 of the sheared GoA base pair. As a result, an A13-A12-A12*-A13* stacked column is formed at the minor groove of the duplex, and the G11 base of the sheared GoA base pair is inclined toward the minor groove. By taking such a unique structure, the RNA duplex has a Sr2+ ion binding pocket in the center. A hydrated Sr2+ ion binds to O6 and N7 of G11 and G11*. The Sr2+ ion is surrounded by four phosphate groups of two RNA chains. The Sr2+ ion is tightly captured by eight hydrogen bonds in total.
