PDBsum entry 1nxr

DNA-RNA hybrid

PDB id: 1nxr

Contents

DNA/RNA

PDB id:

1nxr

Name:

DNA-RNA hybrid

Title:

HIV-1 polypurine hybrid, r(gaggacug):d(cagtcctc), nmr, 18 structures

Structure:

DNA (5'-d( Cp Ap Gp Tp Cp Cp Tp C)-3'). Chain: a. Synonym: RNA/DNA hybrid. Engineered: yes. RNA (5'-r( Gp Ap Gp Gp Ap Cp Up G)-3'). Chain: b. Synonym: RNA/DNA hybrid. Engineered: yes

Source:

Synthetic: yes. Synthetic: yes

NMR struc:

18 models

Authors:

O.Y.Fedoroff,Y.Ge,B.R.Reid

Key ref:

O.Y.Fedoroff et al. (1997). Solution structure of r(gaggacug):d(CAGTCCTC) hybrid: implications for the initiation of HIV-1 (+)-strand synthesis. J Mol Biol, 269, 225-239. PubMed id: 9191067 DOI: 10.1006/jmbi.1997.1024

Date:

21-Feb-97 Release date: 07-Jul-97

DNA/RNA chains

C-A-G-T-C-C-T-C 8 bases

G-A-G-G-A-C-U-G 8 bases

DOI no: 10.1006/jmbi.1997.1024

J Mol Biol 269:225-239 (1997)

PubMed id: 9191067

Solution structure of r(gaggacug):d(CAGTCCTC) hybrid: implications for the initiation of HIV-1 (+)-strand synthesis.

O.Y.Fedoroff, Y.Ge, B.R.Reid.

ABSTRACT

The three-dimensional solution structure of the hybrid duplex r(gaggacug):d(CAGTCCTC) has been determined by two-dimensional NMR, distance geometry (DG), restrained molecular dynamics (rMD) and NOE back-calculation methods. This hybrid, consisting of a purine-rich RNA strand and a pyrimidine-rich DNA strand, is related to the polypurine (+)-strand primer formed after (-)-strand DNA synthesis and RNase H degradation of the viral RNA strand and contains the site of a specific cleavage by reverse transcription (RT) RNase H at the end of the HIV-1 polypurine tract. This polypurine primer is an important intermediate in the formation of virally encoded double-stranded DNA prior to HIV-1 retrovirus integration. The correct processing of this primer is vital in the life cycle of the human immunodeficiency virus type (HIV-1) retrovirus. The structure of the r(gaggacug):d(CAGTCCTC) hybrid, as determined in solution by NMR, is intermediate between canonical A-type and B-type double helices, and has mixed structural characteristics. It is quantitatively different from the previously determined solution structures of other RNA-DNA hybrids, particularly in the width and shape of the major groove, which is wider than the major groove of other hybrids and is close to the dimension of the major groove of B-type DNA duplexes. The structure of this hybrid duplex contains a prominent bend in the double helix with a magnitude and direction similar to the bend in Okazaki fragments. The structural features of the present duplex may explain the unique interactions of this sequence with HIV-1 RT during both (-)-strand and (+)-strand DNA synthesis.

Selected figure(s)

Figure 6.
Figure 6. Comparison of the solution structure of r(gaggacug):d(CAGTCCTC) with the published solution structures of the d(GTCACATG):r(caugugac) [Fedoroff et al 1993] and d(GCTATAATGG):r(ccauuauagc) [Gonzalez et al 1995] hybrids. Dotted lines show the interstrand phosphate-phosphate separation across the major grooves in these hybrids. The major groove width can be calculated by subtracting 5.8 Å from the measured distances.

Figure 8.
Figure 8. Distribution analysis of the pseudo-rotation phase angles of non-terminal sugar residues using molecular dynamics simulations with time-averaged restraints (continuous lines) and with conventional restraints (broken lines). The phase parameter plotted on the abscissa is the pseudo-rotation phase angle in degrees, with 18° corresponding to C3′-endo and 162° corresponding to C2′-endo.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 269, 225-239) copyright 1997.

Figures were selected by an automated process.