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PDBsum entry 1jb8
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References listed in PDB file
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Key reference
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Title
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Crystal structure of an RNA.Dna hybrid reveals intermolecular intercalation: dimer formation by base-Pair swapping.
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Authors
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G.W.Han,
M.L.Kopka,
D.Langs,
M.R.Sawaya,
R.E.Dickerson.
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Ref.
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Proc Natl Acad Sci U S A, 2003,
100,
9214-9219.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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.
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Headers
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