Use of an N-terminal fragment from moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-mer DNA molecule containing G-A mispairs

Acta Crystallogr D Biol Crystallogr. 2000 Sep;56(Pt 9):1120-31. doi: 10.1107/s0907444900008246.


Complexation with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase offers a novel method of obtaining crystal structures of nucleic acid duplexes, which can be phased by molecular replacement. This method is somewhat similar to the method of using a monoclonal antibody Fab fragment complexed to the molecule of interest in order to obtain crystals suitable for X-ray crystallographic analysis. Here a novel DNA structure including two G-A mispairs in a pseudo-hexadecamer determined at 2.3 A resolution in a complex with the N-terminal fragment is reported. This structure has an asymmetric unit consisting of the protein molecule bound to the blunt end of a DNA 6/10-mer, which is composed of a six-base strand (5'-CTCGTG-3') and a ten-base strand (3'-GAGCACGGCA-5'). The 6/10-mer is thus composed of a six-base-pair duplex with a four-base single-stranded overhang. In the crystal structure, the bases of the overhang are reciprocally paired (symmetry element -x - 1, -y, z), yielding a doubly nicked pseudo-hexadecamer primarily B-form DNA molecule, which has some interesting A-like structural features. The pairing between the single strands results in two standard (G-C) Watson-Crick pairs and two G-A mispairs. The structural DNA model can accommodate either a standard syn or a standard anti conformation for the 5'-terminal adenine of the ten-base strand of the DNA based on analysis of simulated-annealing omit maps. Although the DNA model here includes nicks in the phosphodiester backbone, modeling of an intact phosphodiester backbone results in a very similar DNA model and indicates that the structure is biologically relevant.

Publication types

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

MeSH terms

  • Adenine / chemistry
  • Base Pair Mismatch*
  • Carbohydrate Conformation
  • Crystallization
  • Crystallography, X-Ray
  • DNA / chemistry*
  • Deoxyribose / chemistry
  • Guanine / chemistry
  • Models, Molecular
  • Moloney murine leukemia virus / enzymology*
  • Nucleic Acid Conformation
  • Peptide Fragments / chemistry*
  • Protein Conformation
  • RNA-Directed DNA Polymerase / chemistry*


  • Peptide Fragments
  • Deoxyribose
  • Guanine
  • DNA
  • RNA-Directed DNA Polymerase
  • Adenine

Associated data

  • PDB/1D1U