Structure of an RNA/DNA dodecamer corresponding to the HIV-1 polypurine tract at 1.6 Angstrom resolutionDrozdzal, P., Michalska, K., Kierzek, R., Lomozik, L., Jaskolski, M.
(2012) Acta Crystallogr.,Sect.D 68: 169-175
- PubMed: 22281746
- DOI: 10.1107/S0907444911053327
- PubMed Abstract:
- An unusual sugar conformation in the structure of an RNA/DNA decamer of the polypurine tract may affect recognition by RNase H.
Kopka, M.L.,Lavelle, L.,Han, G.W.,Ng, H.-L.,Dickerson, R.E.
(2003) J.Mol.Biol. 334: 653
- Crystal structure of an RNA.DNA hybrid reveals intermolecular intercalation: dimer formation by base-pair swapping.
Han, G.W.,Kopka, M.L.,Langs, D.,Sawaya, M.R.,Dickerson, R.E.
(2003) Proc.Natl.Acad.Sci.USA 100: 9214
- Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA
G Sarafianos, S.,Das, K.,Tantillo, C.,Clark Jr., A.D.,Ding, J.,Whitcomb, J.M.,Boyer, P.L.,Hughes, S.H.,Arnold, E.
(2001) Embo J. 20: 1449
The crystal structure of an RNA/DNA hybrid dodecamer, r(5'-uaaaagaaaagg):d(5'-CCTTTTCTTTTA), which contains three-quarters of the polypurine tract (PPT) sequence of the HIV RNA genome is reported. The hybrid structure was determined at 1.6 Å resoluti ...
The crystal structure of an RNA/DNA hybrid dodecamer, r(5'-uaaaagaaaagg):d(5'-CCTTTTCTTTTA), which contains three-quarters of the polypurine tract (PPT) sequence of the HIV RNA genome is reported. The hybrid structure was determined at 1.6 Å resolution and was found to have the A-form conformation. However, the presence of alternate conformations along the RNA template strand indicated increased flexibility of the PPT sequence. Two segments (at nucleotides 1-2 and 6-8) of the RNA chain have two conformations exhibiting differences in torsion and pseudorotation angles. For conformation I((1-2), (6-8)), 25% of the RNA sugars have the C2'-exo pucker and the rest have the expected C3'-endo pucker. The II(1-2) and II(6-8) conformations of the RNA strand have one sugar with the C2'-exo pucker. None of the ribose rings exist in the C2'-endo form, in contrast to a previous report which postulated a C2'-endo ribose as a key structural element of the PPT. The widths of the minor groove for conformations I((1-2), (6-8)) and II((1-2), (6-8)) of the RNA strand are 9.2-10.5 and 9.4-10.7 Å, respectively. Both ranges are very close to the intervals accepted for A-form RNA duplexes. On the opposing DNA primer strand most of the sugars are C3'-endo, except for the 3'-terminal sugars, which are C2'-endo (T22) or O4'-endo (T23 and A24). The duplex includes a noncanonical u1(anti)·A24(syn) base interaction with only one hydrogen bond between the bases. This noncanonical base interaction at the 5'-end of the template distorts the values of the helical parameters of the adjacent base pair.
Faculty of Chemistry, A. Mickiewicz University, 60-780 Poznan, Poland.