Structure of the DNA Coiled Coil Formed by d(CGATATATATAT)

Luchi, Daniela De; Tereshko, Valentina; Gouyette, Catherine; Subirana, Juan A.

doi:10.1002/cbic.200500449

Cited by 19 publications

(34 citation statements)

References 9 publications

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“…Hoogsteen base pairs are not frequently observed in B-DNA although the propensity of A/T base pairs to adopt this geometry was shown by several crystal structures of free DNA fragments that contain sequences of alternating A and T bases 32,33 . However, this conformation appeared to be induced by crystal packing interactions of the free DNA fragments because NMR studies of (dA-dT) n fragments (n=3,4,5) indicated that the Watson-Crick geometry was the dominant one in solution 32 .…”

Section: Discussionmentioning

confidence: 99%

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

Kitayner

Rozenberg

Rohs

et al. 2010

Nat Struct Mol Biol

227

335

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p53 binds as a tetramer to DNA targets consisting of two decameric half-sites separated by a variable spacer. Here we present high-resolution crystal structures of complexes between p53 core-domain tetramers and DNA targets consisting of contiguous half-sites. In contrast to previously reported p53-DNA complexes that display standard Watson-Crick base pairs, the newly reported structures exhibit non-canonical Hoogsteen base-pairing geometry at the central A/T doublet of each half-site. Structural and computational analyses demonstrate that the Hoogsteen geometry distinctly modulates the B-DNA helix in terms of local shape and electrostatic potential which together with the contiguous DNA configuration results in enhanced protein-DNA and protein-protein interactions compared to non-contiguous half-sites. Our results suggest a mechanism, which relates spacer length to protein-DNA binding affinity. Our findings also expand the current understanding of protein-DNA recognition and establish the structural and chemical properties of Hoogsteen base pairs as the basis for a novel mode of sequence readout.

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Section: Discussionmentioning

confidence: 99%

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

Kitayner

Rozenberg

Rohs

et al. 2010

Nat Struct Mol Biol

227

335

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“…Similar HG structures were subsequently reported for related sequences d(ATATATCT) 47 and d(CGATATATATAT). 48 …”

Section: Hg Base-pairs In Naked Duplexesmentioning

confidence: 99%

A historical account of hoogsteen base‐pairs in duplex DNA

et al. 2013

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In 1957, a unique pattern of hydrogen bonding between N3 and O4 on uracil and N7 and N6 on adenine was proposed to explain how poly(rU) strands can associate with poly(rA)-poly(rU) duplexes to form triplexes. Two years later, Karst Hoogsteen visualized such a non-canonical A-T base-pair through X-ray analysis of co-crystals containing 9-methyladenine and 1-methylthymine. Subsequent X-ray analyses of guanine and cytosine derivatives yielded the expected Watson-Crick base-pairing but those of adenine and thymine (or uridine) did not yield Watson-Crick base-pairs, instead favoring ‘Hoogsteen’ base-pairing. More than two decades ensued without experimental ‘proof’ for A-T Watson-Crick base-pairs, while Hoogsteen base-pairs continued to surface in AT-rich sequences, closing base-pairs of apical loops, in structures of DNA bound to antibiotics and proteins, damaged and chemically modified DNA, and in polymerases that replicate DNA via Hoogsteen pairing. Recently, NMR studies have shown that base-pairs in duplex DNA exists as a dynamic equilibrium between Watson-Crick and Hoogsteen forms. There is now little doubt that Hoogsteen base-pairs exist in significant abundance in genomic DNA where they can expand the structural and functional versatility of duplex DNA beyond that which can be achieved based only on Watson-Crick base-pairing. Here, we provide a historical account of the discovery and characterization of Hoogsteen base-pairs hoping that this will inform future studies exploring the occurrence and functional importance of these alternative base-pairs.

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“…Studies have shown 1,3,5,28--32 that A-T Hoogsteen bps are energetically more favorable than G-C + Hoogsteen bps and are more likely to form in duplex DNA. Fewer studies have examined IR and Raman bands of A-T Hoogsteen bps as compared to G-C + in part due to the absence of model duplexes for inducing Hoogsteen such as GC 9 .…”

Section: Resultsmentioning

confidence: 99%

“…The characterization of Hoogsteen bps by X-ray crystallography can also be complicated by potential effects arising due to crystal packing forces. For example, several AT-rich sequences form DNA duplexes composed of Hoogsteen bps by X-ray crystallography 28--32 but predominantly form canonical duplexes composed of Watson-Crick bps when examined using solution NMR. While solution NMR can be used to unambiguously characterize Hoogsteen bps, size limitations hinder application to large protein-DNA complexes.…”

Section: Introductionmentioning

confidence: 99%

Robust IR‐based detection of stable and fractionally populated G‐C⁺ and A‐T Hoogsteen base pairs in duplex DNA

Stelling

Zhou

et al. 2017

FEBS Letters

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Non-canonical G-C+ and A-T Hoogsteen base pairs can form in duplex DNA and play roles in recognition, damage repair, and replication. Identifying Hoogsteen base pairs in DNA duplexes remains challenging due to difficulties in resolving syn versus anti purine bases with X-ray crystallography; and size limitations and line broadening can make them difficult to characterize by NMR spectroscopy. Here, we show how infrared (IR) spectroscopy can identify G-C+ and A-T Hoogsteen base pairs in duplex DNA across a range of different structural contexts. The utility of IR-based detection of Hoogsteen base pairs is demonstrated by characterizing the first example of adjacent A-T and G-C+ Hoogsteen base pairs in a DNA duplex where severe broadening complicates detection with NMR.

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Structure of the DNA Coiled Coil Formed by d(CGATATATATAT)

Cited by 19 publications

References 9 publications

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

A historical account of hoogsteen base‐pairs in duplex DNA

Robust IR‐based detection of stable and fractionally populated G‐C⁺ and A‐T Hoogsteen base pairs in duplex DNA

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Structure of the DNA Coiled Coil Formed by d(CGATATATATAT)

Cited by 19 publications

References 9 publications

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

A historical account of hoogsteen base‐pairs in duplex DNA

Robust IR‐based detection of stable and fractionally populated G‐C+ and A‐T Hoogsteen base pairs in duplex DNA

Contact Info

Product

Resources

About

Robust IR‐based detection of stable and fractionally populated G‐C⁺ and A‐T Hoogsteen base pairs in duplex DNA