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

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. Th is method is somewhat similar to the method of using a monoclonal antibody Fab fragment complexed to the molecule of interest in order to obtain cryst als suitable for X-ray crystallographic analysis. Here a novel DNA structur e including two G-A mispairs in a pseudo-hexadecamer determined at 2.3 Angs trom 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 th us composed of a six-base-pair duplex with a four-base single-stranded over hang. In the crystal structure, the bases of the overhang are reciprocally paired (symmetry element -x - 1, -y, z), yielding a doubly nicked pseudo-he xadecamer 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 ana lysis of simulated-annealing omit maps. Although the DNA model here include s nicks in the phosphodiester backbone, modeling of an intact phosphodieste r backbone results in a very similar DNA model and indicates that the struc ture is biologically relevant.