PDBsum entry 1jb8

DNA/RNA

PDB id: 1jb8

Contents

DNA/RNA

Waters ×66

PDB id:

1jb8

Name:

DNA/RNA

Title:

The crystal structure of an RNA/DNA hybrid reveals novel intermolecular intercalation

Structure:

5'-r( Cp Ap Ap Ap Gp Ap Ap Ap Ap G)-3'. Chain: a. Engineered: yes. Other_details: RNA/DNA hybrid of ppt sequence of HIV. 5'-d( Cp Tp Tp Tp Tp Cp Tp Tp Tp G)-3'. Chain: b. Engineered: yes. Other_details: RNA/DNA hybrid of ppt sequence of HIV

Source:

Synthetic: yes. Other_details: synthesized by the solid-phase phosphoramidate method on an eppendorf ecosyn d300 synthesizer.

Biol. unit:

Dimer (from PQS)

Resolution:

2.38Å R-factor: 0.223 R-free: 0.251

Authors:

G.W.Han,M.L.Kopka,D.Langs,R.E.Dickerson

Key ref:

G.W.Han et al. (2003). Crystal structure of an RNA.DNA hybrid reveals intermolecular intercalation: dimer formation by base-pair swapping. Proc Natl Acad Sci U S A, 100, 9214-9219. PubMed id: 12872000 DOI: 10.1073/pnas.1533326100

Date:

02-Jun-01 Release date: 01-Jul-03

DNA/RNA chains

C-A-A-A-G-A-A-A-A-G 10 bases

C-T-T-T-T-C-T-T-T-G 10 bases

DOI no: 10.1073/pnas.1533326100

Proc Natl Acad Sci U S A 100:9214-9219 (2003)

PubMed id: 12872000

Crystal structure of an RNA.DNA hybrid reveals intermolecular intercalation: dimer formation by base-pair swapping.

G.W.Han, M.L.Kopka, D.Langs, M.R.Sawaya, R.E.Dickerson.

ABSTRACT

An intermolecular intercalation of base pairs was found at the CA step in the I222 crystal structure of the RNA.DNA hybrid, r(CAAAGAAAAG).d(CTTTTCTTTG), which contains two-thirds of the polypurine tract sequence of HIV-1 with a substitution of cytosine for the initial adenine. This sequence crystallized in both P212121 and I222 space groups, with an rms difference of only 0.63 A between residues 3 to 18 of the two forms. P212121 and I222 helices are both A-like, but intercalation occurs only in the I222 crystal form. The present structure shows bases stacked in parallel rather than perpendicular as in intercalated DNA (I-DNA). The base intercalation is also different from zipper-like meshing of bases seen in the center of the crystal structure of d(GCGAAAGCT), which does not have Watson-Crick base pairing. The base-step intercalation seen here is reminiscent of domain swapping in proteins; therefore, we call this phenomenon "base-pair swapping." It involves a highly mobile CA step and seems to be sequence-specific and electrostatically stable without disrupting Watson-Crick interactions. It also exhibits a large rise concurrent with unwinding of the helix (low twist). We present a base-pair swapping dimer in nucleic acids.

Selected figure(s)

Figure 3.
Fig. 3. (a) Stereo views of the 2 F[o] - F[c] electron-density map contoured at the 1 level. The RNA·DNA hybrid duplex with rC1·dG20 at the top of the helix. (b) The superposition of the I222 (purple) with the P2[1]2[1]2[1] (blue) structure.

Figure 8.
Fig. 8. Local base-pair stacking without (a) and with (b and c) rC1·dG20 intercalation. (a) CA step: base pairs rC1·G20 (front) and rA2·dT19 (behind). (b) CC* step: base pairs rC1·G20 (front) and 1*·20* (behind; brown). (c) C*A step: base pairs rC1*·dG20* (front; brown) and rA2·dT19 (behind). Note that base-pair overlap is enhanced by intercalation.

Figures were selected by an automated process.