High-Resolution Structure of an Extended A-Tract:  [d(CGCAAATTTGCG)]<sub>2</sub>

Woods, Kristen Kruger; Maehigashi, Tatsuya; Howerton, Shelley B.; Sines, Chad C.; Tannenbaum, Sarah; Williams, Loren Dean

doi:10.1021/ja045207x

Cited by 57 publications

(85 citation statements)

References 30 publications

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“…T n A n sequences do not contain a static bend in solution or in atomic structures, although T-A steps are highly flexible. Most studies show narrow minor grooves over AT-rich segments, but high-resolution structures of some AT sequences, particularly those containing one or more T-A steps, have been reported to display widened minor grooves (Mack et al 2001;Stefl et al 2004;Woods et al 2004). Fis binding to the F1 or F2 sequences containing central A n T n segments generate K d values of 0.2 nM and dissociation rates of 23 and 52 min, respectively (Figs.…”

Section: Fis Binding To Different Dna Sequencesmentioning

confidence: 98%

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

Stella¹,

Cascio²,

Johnson³

2010

Genes Dev.

178

261

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The bacterial nucleoid-associated protein Fis regulates diverse reactions by bending DNA and through DNAdependent interactions with other control proteins and enzymes. In addition to dynamic nonspecific binding to DNA, Fis forms stable complexes with DNA segments that share little sequence conservation. Here we report the first crystal structures of Fis bound to high-and low-affinity 27-base-pair DNA sites. These 11 structures reveal that Fis selects targets primarily through indirect recognition mechanisms involving the shape of the minor groove and sequence-dependent induced fits over adjacent major groove interfaces. The DNA shows an overall curvature of 65°, and the unprecedented close spacing between helix-turn-helix motifs present in the apodimer is accommodated by severe compression of the central minor groove. In silico DNA structure models show that only the roll, twist, and slide parameters are sufficient to reproduce the changes in minor groove widths and recreate the curved Fis-bound DNA structure. Models based on naked DNA structures suggest that Fis initially selects DNA targets with intrinsically narrow minor grooves using the separation between helix-turn-helix motifs in the Fis dimer as a ruler. Then Fis further compresses the minor groove and bends the DNA to generate the bound structure.[Keywords: DNA structure; protein-DNA recognition; DNA bending; nucleoid protein; X-ray crystallography] Supplemental material is available at http://www.genesdev.org.

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Section: Fis Binding To Different Dna Sequencesmentioning

confidence: 98%

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

Stella¹,

Cascio²,

Johnson³

2010

Genes Dev.

178

261

View full text Add to dashboard Cite

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“…Poly(dA:dT) tracts are known to have a different structure, with a shorter helical structure and a narrow minor groove, which may contribute to their low propensity to form nucleosomes (32,119,129,143). In addition, data from crystallography studies suggest the presence of bifurcated hydrogen bonds between an A base and two T's on the opposite strand (32,119,201). However, the existence of these H bonds and their contribution to the structure of poly(dA:dT) remains unclear.…”

Section: At Content Is a Major Cis Factor Influencing Nucleosome Posimentioning

confidence: 99%

Nucleosome Positioning in Saccharomyces cerevisiae

Jansen

Verstrepen

2011

Microbiol Mol Biol Rev

106

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SUMMARY The DNA of eukaryotic cells is spooled around large histone protein complexes, forming nucleosomes that make up the basis for a high-order packaging structure called chromatin. Compared to naked DNA, nucleosomal DNA is less accessible to regulatory proteins and regulatory processes. The exact positions of nucleosomes therefore influence several cellular processes, including gene expression, chromosome segregation, recombination, replication, and DNA repair. Here, we review recent technological advances enabling the genome-wide mapping of nucleosome positions in the model eukaryote Saccharomyces cerevisiae . We discuss the various parameters that determine nucleosome positioning in vivo , including cis factors like AT content, variable tandem repeats, and poly(dA:dT) tracts that function as chromatin barriers and trans factors such as chromatin remodeling complexes, transcription factors, histone-modifying enzymes, and RNA polymerases. In the last section, we review the biological role of chromatin in gene transcription, the evolution of gene regulation, and epigenetic phenomena.

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“…It has been suggested that the difference among these sites is at least partly due to differences in groove width [15][16][17]. Sites such as AATT, for example, have a more narrow groove than TTAA and are in a pre-binding conformation that is better suited to complex formation with unfused heterocyclic compounds such as those discussed above.…”

Section: Introductionmentioning

confidence: 99%

Sequence and length dependent thermodynamic differences in heterocyclic diamidine interactions at AT base pairs in the DNA minor groove

Liu

Kumar

Boykin

et al. 2007

Biophysical Chemistry

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With the goal of developing a better understanding of the antiparasitic biological action of DB75, we have evaluated its interaction with duplex alternating and nonalternating sequence AT polymers and oligomers. These DNAs provide an important pair of sequences in a detailed thermodynamic analysis of variations in interaction of DB75 with AT sites. The results for DB75 binding to the alternating and nonalternating AT sequences are quite different at the fundamental thermodynamic level. Although the Gibbs energies are similar, the enthalpies for DB75 binding with poly(dA)·poly (dT) and poly(dA-dT)·poly(dA-dT) are +3.1 and −4.5 kcal/mole, respectively, while the binding entropies are 41.7 and 15.2 cal/mol·K, respectively. The underlying thermodynamics of binding to AT sites in the minor groove plays a key role in the recognition process. It was also observed that DB75 binding with poly(dA)·poly(dT) can induce T·A·T triplet formation and the compound binds strongly to the dT·dA·dT triplex.

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High-Resolution Structure of an Extended A-Tract: [d(CGCAAATTTGCG)]₂

Cited by 57 publications

References 30 publications

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

Nucleosome Positioning in Saccharomyces cerevisiae

Sequence and length dependent thermodynamic differences in heterocyclic diamidine interactions at AT base pairs in the DNA minor groove

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High-Resolution Structure of an Extended A-Tract: [d(CGCAAATTTGCG)]2

Cited by 57 publications

References 30 publications

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

Nucleosome Positioning in Saccharomyces cerevisiae

Sequence and length dependent thermodynamic differences in heterocyclic diamidine interactions at AT base pairs in the DNA minor groove

Contact Info

Product

Resources

About

High-Resolution Structure of an Extended A-Tract: [d(CGCAAATTTGCG)]₂