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. 2002 Dec 1;30(23):5244-52.
doi: 10.1093/nar/gkf661.

A Hoogsteen base pair embedded in undistorted B-DNA

Jun Aishima  1 , Rossitza K Gitti, Joyce E Noah, Hin Hark Gan, Tamar Schlick, Cynthia Wolberger
Affiliations

A Hoogsteen base pair embedded in undistorted B-DNA

Jun Aishima et al. Nucleic Acids Res. .

Abstract

Hoogsteen base pairs within duplex DNA typically are only observed in regions containing significant distortion or near sites of drug intercalation. We report here the observation of a Hoogsteen base pair embedded within undistorted, unmodified B-DNA. The Hoogsteen base pair, consisting of a syn adenine base paired with an anti thymine base, is found in the 2.1 A resolution structure of the MATalpha2 homeodomain bound to DNA in a region where a specifically and a non-specifically bound homeodomain contact overlapping sites. NMR studies of the free DNA show no evidence of Hoogsteen base pair formation, suggesting that protein binding favors the transition from a Watson-Crick to a Hoogsteen base pair. Molecular dynamics simulations of the homeodomain-DNA complex support a role for the non-specifically bound protein in favoring Hoogsteen base pair formation. The presence of a Hoogsteen base pair in the crystal structure of a protein-DNA complex raises the possibility that Hoogsteen base pairs could occur within duplex DNA and play a hitherto unrecognized role in transcription, replication and other cellular processes.

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Figures

Figure 1
Figure 1
(A) Crystal structure of the α2 homeodomain contains four α2 proteins bound to two α2 binding sites in the DNA. Base pair A7-T37 (red box) is a Hoogsteen base pair. Figure produced with SETOR (37). (B) The oligonucleotide duplex used in the crystal structure contains two α2 binding sites (box) with a 5′ overhanging base at each end. (C) The DNA fragment used in the NMR experiments is blunt-ended and contains five fewer base pairs. (D) The DNA fragment used in the molecular dynamics simulations.
Figure 1
Figure 1
(A) Crystal structure of the α2 homeodomain contains four α2 proteins bound to two α2 binding sites in the DNA. Base pair A7-T37 (red box) is a Hoogsteen base pair. Figure produced with SETOR (37). (B) The oligonucleotide duplex used in the crystal structure contains two α2 binding sites (box) with a 5′ overhanging base at each end. (C) The DNA fragment used in the NMR experiments is blunt-ended and contains five fewer base pairs. (D) The DNA fragment used in the molecular dynamics simulations.
Figure 1
Figure 1
(A) Crystal structure of the α2 homeodomain contains four α2 proteins bound to two α2 binding sites in the DNA. Base pair A7-T37 (red box) is a Hoogsteen base pair. Figure produced with SETOR (37). (B) The oligonucleotide duplex used in the crystal structure contains two α2 binding sites (box) with a 5′ overhanging base at each end. (C) The DNA fragment used in the NMR experiments is blunt-ended and contains five fewer base pairs. (D) The DNA fragment used in the molecular dynamics simulations.
Figure 1
Figure 1
(A) Crystal structure of the α2 homeodomain contains four α2 proteins bound to two α2 binding sites in the DNA. Base pair A7-T37 (red box) is a Hoogsteen base pair. Figure produced with SETOR (37). (B) The oligonucleotide duplex used in the crystal structure contains two α2 binding sites (box) with a 5′ overhanging base at each end. (C) The DNA fragment used in the NMR experiments is blunt-ended and contains five fewer base pairs. (D) The DNA fragment used in the molecular dynamics simulations.
Figure 2
Figure 2
The Hoogsteen base pair is stabilized by intra-DNA and protein–DNA interactions in the crystal structure of the α2 homeodomain–DNA complex. (A) Simulated annealing omit map of the A7-T37 base pair. The two hydrogen bonds between the N7 of base A7 and N3 of base T37, as well as between the N6 of A7 and the O4 of T37 characterize a Hoogsteen base pair. The same base pair modeled in the Watson–Crick configuration (green) clearly does not fit the electron density. Figure prepared with Pymol (38). (B) The A7 N6 group makes a bifurcated hydrogen bond with both T37 and T36. Base stacking interactions between T6 and A7, as well as A8 and T9, may contribute to stabilization of the Hoogsteen base pair. (C) The Arg4 residue of the α2D homeodomain packs against the sugar–phosphate backbone at bases A7 and T6. (B) and (C) prepared with VMD (39).
Figure 2
Figure 2
The Hoogsteen base pair is stabilized by intra-DNA and protein–DNA interactions in the crystal structure of the α2 homeodomain–DNA complex. (A) Simulated annealing omit map of the A7-T37 base pair. The two hydrogen bonds between the N7 of base A7 and N3 of base T37, as well as between the N6 of A7 and the O4 of T37 characterize a Hoogsteen base pair. The same base pair modeled in the Watson–Crick configuration (green) clearly does not fit the electron density. Figure prepared with Pymol (38). (B) The A7 N6 group makes a bifurcated hydrogen bond with both T37 and T36. Base stacking interactions between T6 and A7, as well as A8 and T9, may contribute to stabilization of the Hoogsteen base pair. (C) The Arg4 residue of the α2D homeodomain packs against the sugar–phosphate backbone at bases A7 and T6. (B) and (C) prepared with VMD (39).
Figure 2
Figure 2
The Hoogsteen base pair is stabilized by intra-DNA and protein–DNA interactions in the crystal structure of the α2 homeodomain–DNA complex. (A) Simulated annealing omit map of the A7-T37 base pair. The two hydrogen bonds between the N7 of base A7 and N3 of base T37, as well as between the N6 of A7 and the O4 of T37 characterize a Hoogsteen base pair. The same base pair modeled in the Watson–Crick configuration (green) clearly does not fit the electron density. Figure prepared with Pymol (38). (B) The A7 N6 group makes a bifurcated hydrogen bond with both T37 and T36. Base stacking interactions between T6 and A7, as well as A8 and T9, may contribute to stabilization of the Hoogsteen base pair. (C) The Arg4 residue of the α2D homeodomain packs against the sugar–phosphate backbone at bases A7 and T6. (B) and (C) prepared with VMD (39).
Figure 3
Figure 3
NMR studies of the DNA clearly show a Watson–Crick base pair in solution. (A) The NOESY-D2O spectrum was easily assignable in the H1′–H6/H8 region. The weak A7 H1′–A7 H8 NOE correlation peak is consistent with A7 in the anti conformation. (B) The NOESY-H2O spectrum was assignable in the amino–imino region. The A7 H2-T37 H3 NOE correlation (red box) is strong, consistent with a Watson–Crick base pair at A7-T37. (C) In the NOESY-D2O spectrum, the A7-H2 peak is shifted upfield and is broader than other adenine H2 peaks, consistent with a flexible A7 base.
Figure 3
Figure 3
NMR studies of the DNA clearly show a Watson–Crick base pair in solution. (A) The NOESY-D2O spectrum was easily assignable in the H1′–H6/H8 region. The weak A7 H1′–A7 H8 NOE correlation peak is consistent with A7 in the anti conformation. (B) The NOESY-H2O spectrum was assignable in the amino–imino region. The A7 H2-T37 H3 NOE correlation (red box) is strong, consistent with a Watson–Crick base pair at A7-T37. (C) In the NOESY-D2O spectrum, the A7-H2 peak is shifted upfield and is broader than other adenine H2 peaks, consistent with a flexible A7 base.
Figure 3
Figure 3
NMR studies of the DNA clearly show a Watson–Crick base pair in solution. (A) The NOESY-D2O spectrum was easily assignable in the H1′–H6/H8 region. The weak A7 H1′–A7 H8 NOE correlation peak is consistent with A7 in the anti conformation. (B) The NOESY-H2O spectrum was assignable in the amino–imino region. The A7 H2-T37 H3 NOE correlation (red box) is strong, consistent with a Watson–Crick base pair at A7-T37. (C) In the NOESY-D2O spectrum, the A7-H2 peak is shifted upfield and is broader than other adenine H2 peaks, consistent with a flexible A7 base.
Figure 4
Figure 4
(A) Energetics of the A7 base calculated from glycosidic angle χ in molecular dynamics simulations. The presence of bound α2 proteins stabilizes the χ angle at 52°, while free DNA is free to rotate over a broad range. (B) The fluctuations of the χ angle around the A7 base (red box) decrease significantly when the α2 proteins are bound to the DNA.
Figure 4
Figure 4
(A) Energetics of the A7 base calculated from glycosidic angle χ in molecular dynamics simulations. The presence of bound α2 proteins stabilizes the χ angle at 52°, while free DNA is free to rotate over a broad range. (B) The fluctuations of the χ angle around the A7 base (red box) decrease significantly when the α2 proteins are bound to the DNA.
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References

    1. Wang A.H., Ughetto,G., Quigley,G.J., Hakoshima,T., van der Marel,G.A., van Boom,J.H. and Rich,A. (1984) The molecular structure of a DNA-triostin A complex. Science, 225, 1115–1121. - PubMed
    1. Gilbert D.E., van der Marel,G.A., van Boom,J.H. and Feigon,J. (1989) Unstable Hoogsteen base pairs adjacent to echinomycin binding sites within a DNA duplex. Proc. Natl Acad. Sci. USA, 86, 3006–3010. - PMC - PubMed
    1. Patikoglou G.A., Kim,J.L., Sun,L., Yang,S.H., Kodadek,T. and Burley,S.K. (1999) TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev., 13, 3217–3230. - PMC - PubMed
    1. Hoogsteen K. (1963) The crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine. Acta Crystallogr., 16, 907–916.
    1. Rice P.A., Yang,S., Mizuuchi,K. and Nash,H.A. (1996) Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell, 87, 1295–1306. - PubMed

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