Defining the sequence-recognition profile of DNA-binding molecules

Warren, Christopher L.; Kratochvil, Natasha C. S.; Hauschild, Karl E.; Foister, Shane; Brezinski, Mary L.; Dervan, Peter B.; Phillips, George N.; Ansari, Aseem Z.

doi:10.1073/pnas.0509843102

Cited by 222 publications

(252 citation statements)

References 54 publications

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“…In all four structures the trajectory of the DNA backbone deviates from B-form DNA at the core GA base step within the Exd/Pbx1 binding site. This base step is critical for Exd/Pbx1 binding as observed in the crystal structure (32)(33)(34)(35) as well as our own comprehensive CSI microarray studies (46).…”

Section: Dna Groove Dimensions In Hox-exd/pbx1 Structuresmentioning

confidence: 69%

Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein−DNA Assembly

et al. 2008

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The cooperative assembly of multiprotein complexes results from allosteric modulations of DNA structure as well as direct intermolecular contacts between proteins. Such cooperative binding plays a critical role in imparting exquisite sequence specificity on the homeobox transcription factor (Hox) family of developmental transcription factors. A well-characterized example includes the interaction of Hox proteins with extradenticle (Exd), a highly conserved DNA binding transcription factor. Although direct interactions are important, the contribution of indirect interactions toward cooperative assembly of Hox and Exd remains unresolved. Here we use minor groove binding polyamides as structural wedges to induce perturbations at specific base steps within the Exd binding site. We find that allosteric modulation of DNA structure contributes nearly 1.5 kcal/mol to the binding of Exd to DNA, even in the absence of direct Hox contacts. In contrast to previous studies, the sequence-targeted chemical wedges reveal the role of DNA geometry in cooperative assembly of Hox-Exd complexes. Programmable polyamides may well serve as general probes to investigate the role of DNA modulation in the cooperative and highly specific assembly of other protein-DNA complexes.The physical basis of DNA sequence recognition by its ligands (proteins or small molecules) has been investigated in great detail over the years, and several underlying principles have been defined (1-3). The main contributors to the specificity of DNA sequence recognition are interactions between protein side chains and the edges of the base pairs in the cognate DNA site. Efforts to rationally redesign these direct interactions have yielded some exciting successes (4-8). A major limitation of focusing on re-engineering direct interactions, however, is that recognition of sequence-dependent structural properties of DNA and other modes of indirect readout are also critical specificity determinants (9-15). Often a combination of direct and indirect interactions governs exquisite DNA sequence specificity displayed by its ligands (9,11,(14)(15)(16)(17)(18)(19)(20)(21)(22). Specificity in molecular recognition is also achieved by cooperative binding of multiple proteins to closely appositioned DNA sequences (23). Binding of one protein to its DNA cognate site in the enhancer can alter DNA structure and conformational flexibility of a juxtaposed site, thus allosterically improving the energetics

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Section: Dna Groove Dimensions In Hox-exd/pbx1 Structuresmentioning

confidence: 69%

Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein−DNA Assembly

et al. 2008

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“…37 The chiral substitution of the γ-aminobutyric acid turn residue has been shown to improve binding affi nity and sequence specifi city. 32 For polyamides 14, 16, 19, and 24, the chiral diaminobutyric acid turn residue increases equilibrium association constants for these polyamides by 7-to 50-fold over their achiral variants (Table 2. 5'-TAGTAGT-3' 5'-TAGTGAA-3' 52 We hope that this compilation of polyamide-DNA binding affi nities will serve as a resource for ongoing small molecule gene regulation projects. 8% Gene-PAGE PLUS, 7 M urea, denaturing acrylamide blend was purchased from Amresco.…”

Section: Dna Binding Energetics Quantitative Dnase I Footprint Titramentioning

confidence: 99%

Completion of a programmable DNA-binding small molecule library

et al. 2007

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“…Such have been the advances in microarray technology in terms of cost and feature size that it is possible to probe vast regions of the DNA sequence space systematically and impartially. This ethos was exhibited in a study by Warren et al where the interaction profiles of a transcription factor and a small molecule were determined with every permutation of a duplex DNA sequence 8 bp in length (Warren et al 2006). In the CLADE system described above, the binding affinity of the APC aptamer is strongly dictated by the bases furthest away from the microarray chip surface (Knight et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Analysis of a complete DNA–protein affinity landscape

Rowe

Platt

Wedge

et al. 2009

J. R. Soc. Interface.

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Properties of biological fitness landscapes are of interest to a wide sector of the life sciences, from ecology to genetics to synthetic biology. For biomolecular fitness landscapes, the information we currently possess comes primarily from two sources: sparse samples obtained from directed evolution experiments; and more fine-grained but less authentic information from 'in silico' models (such as NK-landscapes). Here we present the entire protein-binding profile of all variants of a nucleic acid oligomer 10 bases in length, which we have obtained experimentally by a series of highly parallel on-chip assays. The resulting complete landscape of sequence-binding pairs, comprising more than one million binding measurements in duplicate, has been analysed statistically using a number of metrics commonly applied to synthetic landscapes. These metrics show that the landscape is rugged, with many local optima, and that this arises from a combination of experimental variation and the natural structural properties of the oligonucleotides.

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Defining the sequence-recognition profile of DNA-binding molecules

Cited by 222 publications

References 54 publications

Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein−DNA Assembly

Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein−DNA Assembly

Completion of a programmable DNA-binding small molecule library

Analysis of a complete DNA–protein affinity landscape

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