THE CRYSTAL STRUCTURE OF THE RNA/DNA HYBRID r(GAAGAGAAGC).d(GCTTCTCTTC)
Gordon
Leonard1, Tom Brown2
and Graeme Conn2
1Joint
ESRF/EMBL Structural Biology Group, European Synchrotron
Radiation Facility.
2Department of Chemistry, University of Southampton.
RNA/DNA hybrid formation is a crucial step in a number of important biological processes such as transcription, the replication of DNA and reverse transcription. When such hybrids are formed, the RNA strand is a substrate for Rnase H which does not hydrolyse RNA when either single or double stranded. In the absence of detailed structural information of Rnase H/hybrid complexes, quite how the enzyme recognises DNA/RNA hybrids is not clear.
NMR analyses of hybrid structures indicate that that the resulting double helices are intermediate between A and B forms with the DNA strand having sugar puckers which are either in a C3í-endo/C2í-endo (N/S) [1] equilibrium or and overall O4í-endo (E) [2,3] conformation. In either case the resulting average structure of the duplex is the same and their major characteristic is that they have a narrower minor groove than found for all A-form duplexes. This narrow minor groove in RNA/DNA hybrids has been proposed as the major structural parameter enabling the discrimination between these and RNA/RNA duplexes by Rnase H [2]
In contrast to the solution
structures of hybrids, the crystal structure of
r(GAAGAGAAGC).d(GCTTCTCTTC) shows the resultant duplex to be Aí
in form with all sugars except one adopting a C3í-endo (N)
conformation. The detailed conformation of the crystal structure
will be presented and the implications for hybrid recognition by
Rnase H will be discussed.