Nucleic Acids Research, 2001, Vol. 29, No. 20 4144-4153
© 2001 Oxford University Press
The 1.19 Å X-ray structure of 2'-O-Me(CGCGCG)2 duplex shows dehydrated RNA with 2-methyl-2,4-pentanediol in the minor groove
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznañ, Poland, 1European Molecular Biology Laboratory, c/o DESY, Hamburg, Germany and 2Faculty of Chemistry, Adam Mickiewicz University, Poznañ, Poland
The crystal and molecular structure of 2'-O-Me(CGCGCG)2 has been determined at 1.19 Å resolution, at 100 K, using synchrotron radiation. The structure in space group P3212 is a half-turn right-handed helix that includes two 2-methyl-2,4-pentanediol (MPD) molecules bound in the minor groove. The structure deviates from A-form RNA. The duplex is overwound with an average value of 9.7 bp per turn, characterised as having a C3'-endo sugar pucker, very low base pair rise and high helical twist and inclination angles. The structure includes 65 ordered water molecules. Only a single row of water molecules is observed in the minor groove due to the presence of hydrophobic 2'-O-methyl groups. As many as five magnesium ions are located in the structure. Two are in the major groove and interact with O6 and N7 of guanosine and N4 of cytidine residues through their hydration spheres. This work provides the first example of molecular interactions of nucleic acids with MPD, which was used as a precipitant, cryo-solvent and resolution enhancing agent. The two MPD molecules intrude into the hydration network in the minor groove, each forming hydrogen bonds between their secondary hydroxyl group and exo-amino functions of guanosine residues. Comparison of the 2'-O-Me(CGCGCG)2 structure in the P3212 and P6122 crystals delineates stability of the water network within the minor groove to dehydration by MPD and is of interest for evaluating factors governing small molecule binding to RNA. Intrusion of MPD into the minor groove of 2'-O-Me(CGCGCG)2 is discussed with respect to RNA dehydration, a prerequisite of Z-RNA formation.
* To whom correspondence should be addressed. Tel: +48 61 8528503; Fax: +48 61 8520532; Email: adamiakr{at}ibch.poznan.pl Present address: Wojciech R. Rypniewski, Universitätsklinikum Hamburg-Eppendorf, Institut für Medizinische Biochemie und Molekularbiologie, c/o DESY, Geb. 22a, Notkestraße 85, 22603 Hamburg, Germany This paper is dedicated to Professor Wieslaw Z. Antkowiak on the occasion of his 70th birthday
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  W. Rypniewski, D. A. Adamiak, J. Milecki, and R. W. Adamiak Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex RNA, September 1, 2008; 14(9): 1845 - 1851. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Kierzek, R. Kierzek, W. N. Moss, S. M. Christensen, T. H. Eickbush, and D. H. Turner Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function Nucleic Acids Res., April 1, 2008; 36(6): 1770 - 1782. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Li, R. Liang, D. H. Turner, L. J. Rothberg, and S. Duan Selective quenching of fluorescence from unbound oligonucleotides by gold nanoparticles as a probe of RNA structure RNA, November 1, 2007; 13(11): 2034 - 2041. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-H. Lee and A. Pardi Thermodynamics and kinetics for base-pair opening in the P1 duplex of the Tetrahymena group I ribozyme Nucleic Acids Res., May 14, 2007; 35(9): 2965 - 2974. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. L. Jackson, J. Burchard, D. Leake, A. Reynolds, J. Schelter, J. Guo, J. M. Johnson, L. Lim, J. Karpilow, K. Nichols, et al. Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing RNA, July 1, 2006; 12(7): 1197 - 1205. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Kierzek, A. Ciesielska, K. Pasternak, D. H. Mathews, D. H. Turner, and R. Kierzek The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes Nucleic Acids Res., September 9, 2005; 33(16): 5082 - 5093. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Popenda, J. Milecki, and R. W. Adamiak High salt solution structure of a left-handed RNA double helix Nucleic Acids Res., August 3, 2004; 32(13): 4044 - 4054. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Rozners and J. Moulder Hydration of short DNA, RNA and 2'-OMe oligonucleotides determined by osmotic stressing Nucleic Acids Res., January 9, 2004; 32(1): 248 - 254. [Abstract] [Full Text] [PDF]
|
|