SUNY at Albany
June 19-23, 2001
X-ray Analysis of a RNA Tetraplex r(cggggc)4
Guanine rich DNA tetraplexes have been done by x-ray crystallography, while no atomic structures are available for RNA tetraplexes. RNA tetraplexes have various biological functions, including telomere functions. We have synthesized, purified, crystallized an RNA oligonucleotide r(cggggc) and collected ultra-high resolution data (0.61 Å, 111,178 unique reflections) using synchrotron radiation at APS. The space group is P4212 and cell contents are: a=b=36.16 Å, and c=74.09 Å. To solve the structure, a set of three wavelength MAD data of the isomorphous bromo-derivative r(Bruggggu) were also collected at 1.7 Å. The native data of r(cggggc) was then refined. There are four strands in the asymmetric unit. Each strand sits on a four fold symmetry axis and forms a parallel RNA tetraplex with symmetry related molecules. The four independent RNA strands are not identical. Each strand has the third and the sixth residues C2? endo puckered sugars while the remaining ones are C3? endo. All the bases are in the anti glycosyl conformation. The G tetrads are approximately planar ( zero inclination angle) and similar to DNA tetraplexes, which are different from the RNA duplexes (average 14º inclination angle). All the 3? side cytosines stack within the tetraplex column, forming a cytosine tetraplex. While the 5? side cytosines swing out and form novel octaplexes with the guanine tetraplexes. The tetraplex molecules stack on each other in opposite polarity (head-to-head /tail-to-tail) to form a pseudo-continuous column. The G tetrads are coordinated to a string of two strontium ions that sit on the four-fold symmetry axis which pass through the pseudo-continuous tetraplex helices. A sodium/water are also found on the same axis.
Research supported by NIH grant GM-17378.
Junpeng Deng , Yong Xiong & Muttaiya Sundaralingam
The Ohio State University