1JB8

The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation

Summary for 1JB8

• Entry DOI: 10.2210/pdb1jb8/pdb
• Descriptor: 5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3', 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3' (3 entities in total)
• Functional Keywords: dna/dna intercalation, rna/dna hybrid, rna/dna polypurine tract, dna-rna complex, dna/rna
• Total number of polymer chains: 2
• Total formula weight: 6247.04

Authors

Han, G.W.,Kopka, M.L.,Langs, D.,Dickerson, R.E. (deposition date: 2001-06-02, release date: 2003-07-01, Last modification date: 2024-04-03)

Primary citation

Han, G.W.,Kopka, M.L.,Langs, D.,Sawaya, M.R.,Dickerson, R.E.
Crystal structure of an RNADNA hybrid reveals intermolecular intercalation: Dimer formation by base-pair swapping
Proc.Natl.Acad.Sci.USA, 100:9214-9219, 2003

PubMed 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.

PubMed: 12872000
DOI: 10.1073/pnas.1533326100

Experimental method

X-RAY DIFFRACTION (2.38 Å)