The crystal structure of an alternating RNA heptamer r(GUAUACA) forming a six base-paired duplex with 3'-end adenine overhangs

Nucleic Acids Res. 2003 Mar 1;31(5):1392-7. doi: 10.1093/nar/gkg226.


The crystal structure of an alternating RNA heptamer r(GUAUACA) has been determined to 2.0 A resolution and refined to an R(work) of 17.1% and R(free) of 18.5% using 2797 reflections. The heptamer crystallized in the space group C222 with a unit cell of a = 25.74, b = 106.58, c = 30.26 A and two independent strands in the asymmetric unit. Each heptamer forms a duplex with its symmetry-related strand and each duplex contains six Watson-Crick base pairs and 3'-end adenosine overhangs. Therefore, two kinds of duplex (duplex 1 and duplex 2) are formed. Duplexes 1 stack on each other forming a pseudo-continuous column, which is typical of the RNA packing mode, while duplex 2 is typical of A-DNA packing with its termini in abutting interactions. Overhang adenine residues stack within the duplexes with C3'-endo sugar pucker and C2'-endo sugar pucker in duplexes 1 and 2, respectively. A Na+ ion in the crystal lattice is water bridged to two N1 atoms of symmetry-related A7 bases.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adenine / chemistry*
  • Base Pairing*
  • Crystallography, X-Ray
  • Hydrogen Bonding
  • Models, Molecular
  • Nucleic Acid Conformation*
  • Oligoribonucleotides / chemistry*
  • Oligoribonucleotides / genetics
  • Water / chemistry


  • Oligoribonucleotides
  • Water
  • Adenine