DNA recognition

The compiex may be detected by DNA poiy-merase-mediated extension of the oiigonucieotide with radioiabeied precursors. Finaiiy, the compiex may be used for tempiate-direc-ted iigation (cyciization) of an oiigonucieotide, that may resuit in an earring compiex 

Triplex Triplex Invasion Duplex Invasion Double Duplex Invasion Tail-Ciamp 

PNA targeting of duplex DNA is not limited to homopurine sequences. Under special circumstances (high negative superhelical stress) mixed purine-pyrimidine PNA-peptide conjugates can bind by duplex invasion (Fig. 4.7) [31], but such complexes are of limited stability. However, using a set of pseudo-complementary PNAs containing diaminopurine-thiouracil substitutions, very stable double duplex invasion complexes can be formed (Fig. 4.4) and the only sequence requirement is about 50% AT content. Very recently, it was also demonstrated that reasonably stable helix invasion complexes can be obtained with tail-clamp PNA comprising a short ( six bases) homopyrimidine bis-PNA clamp and a mixed sequence tail extension [32] (Fig. 4.7). 

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Eisenstein, M., Shakked, Z.i Hydration patterns and intermolecnlar interactions in A-DNA crystal structures. Implications for DNA recognition. J. Mol. Biol. 248 (1995) 662-678... 

DNA Recognition in Procaryotes by Helix-Turn-Helix Motifs... 

The positions of the DNA recognition helices (5) and the helices (3) that connect the core with the heads are indicated. The approximate position of the side chain of residue 77 is marked as a purple hall (see text for the significance of this residue). (Adapted from R.-G. Zhang et al.. Nature 327 591-597, 1987.)... 

Anderson, W.F., et al. Proposed a-helical super-secondary structure associated with protein-DNA recognition. 

Harrison, S.C., Aggarwal, A.K. DNA recognition by proteins with the helix-tum-helix motif. Anna. Rev. Biochem. 59 933-969, 1990. 

Pabo, C.O., Lewis, M. The operator-binding domain of X repressor structure and DNA recognition. Nature 298 443-447, 1982. 

Most sequence-specific regulatory proteins bind to their DNA targets by presenting an a helix or a pair of antiparallel p strands to the major groove of DNA. Recognition of the TATA box by TBP is therefore exceptional it utilizes a concave pleated sheet protein surface that interacts with the minor groove of DNA. Since the minor groove has very few sequence-specific... 

Pabo, C.O., Sauer, R.T. Transcription factors structural families and principles for DNA recognition. 

Klemm, J.D., et al. Crystal structure of the Oct-1 POU domain bound to an octamer site DNA recognition with tethered DNA-binding modules. Cell 77 21-32, 1994. 

Fairall, L., et al. The crystal structure of a two zinc finger peptide reveals an extension to the rules for zinc finger/DNA recognition. Nature 366 483-487, 1993. 

Marmorstein, R., Harrison, S.C. Crystal structure of a PPRl-DNA complex DNA recognition by proteins containing a Zn2Cys6 binuclear cluster. Genes Dev. 

Pavletich, N.P., Pabo, C.O. Zinc finger-DNA recognition crystal structure of a Zif268-DNA complex at 2.1 A. Science 252 809-817, 1991. 

Synthesis of calicheamicin oligosaccharide dimers and their duplex DNA recognition 97YGK600. 

P.B. Dervan, and K.J. Breslauer The thermodynamics of polyamide-DNA recognition Hairpin polyamide binding in the minor groove of duplex DNA. Biochemistry 1999, 38, 2143-2151. 

Nguyen, D.H., J. W. Szewczyk, E.E. Baird, and P. B. Dervan. Alternative heterocycles for DNA recognition An N-methylpyrazole/N-methylpyrrole pair specifies for A-T/T-A base pairs. Bioorg. 

FIG. 3 Three-dimensional (3D) DNA networks as crystallization matrices for the selective binding of DNA-recognition proteins [8]. The latter, represented by shaded spheres, bind specifically to recognition sites of the six-connected, cubic DNA lattice. For srmphfication, linear double-helical DNA stretches are represented by lines. 

Figure 39-13. A schematic representation of the three-dimensional structure of Cro protein and its binding to DNA by its helix-turn-helix motif. The Cro monomer consists of three antiparallel p sheets (P1-P3) and three a-helices (a,-a3).The helix-turn-helix motif is formed because the aj and U2 helices are held at about 90 degrees to each other by a turn offour amino acids. The helix of Cro is the DNA recognition surface (shaded). Two monomers associate through the antiparallel P3 sheets to form a dimer that has a twofold axis of symmetry (right). A Cro dimer binds to DNA through its helices, each of which contacts about 5 bp on the same surface of the major groove. The distance between comparable points on the two DNA a-helices is 34 A, which is the distance required for one complete turn of the double helix. (Courtesy of B Mathews.)...

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