Sequence specific recognition

Figure 7.8 Sequence-specific recognition sites in the major groove of DNA for three restriction enzymes—Eco RI, Bal I, and Sma I. The DNA sequences that are recognized by these enzymes ate represented by tbe color code defined in Figure 7.7.

Seeman, N.C., Rosenberg, J.M., Rich, A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl. Acad. Sci. USA 73 804-809, 1976. 

Figure 8.8 The DNA-binding heiix-turn-helix motif in lambda Cro. Ca positions of the amino acids in this motif have been projected onto a plane and the two helices outlined. The second helix (red) is called the recognition helix because it is involved in sequence-specific recognition of DNA.

B. H. Geierstanger, D. E. Wemmer, and P. B. Dervan. Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin. Proc. Natl. 

Mrksich, M., M.E. Parks, and P.B. Dervan. Hairpin peptide motif A new class of oligopeptides for sequence-specific recognition in the minor-groove of double-helical DNA. J. Am. Chem. Soc. 1994, 116, 7983-7988. 

SwALLEY, S.E., E.E. Baird, and P.B. Dervan. Effects of y-turn and j8-tail amino acids on sequence-specific recognition of DNA by hairpin polyamides. /. Am. 

Dervan. Sequence-specific recognition of DNA in the nucleosome by pyrrole-imidazole polyamides. J. Mol. Biol. 2001,... 

N. T., Lhomme J., Helene C. Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-[alpha]-thymidylate covalently linked to an azidoproflavine derivative. Nucleic Acids Res. 1987 15 7749-7760. 

Allain FH, Bouvet P, Dieckmann T, Feigon J (2000a) Molecular basis of sequence-specific recognition of pre-ribosomal RNA by nucleolin. Embo J 19 6870-6881... 

Thuong N, Helene C (1993) Sequence specific recognition and modification of double helical DNA by oligonucleotides. Angew. Chem Int Ed Engl 32 666-690 Tien Kuo M, Hsu TC (1978) Biochemical and cytological studies of bleomycin actions on chromatin and chromosomes. Chromosoma 68(3) 229-240... 

Tranger JW, Baird EE, Mrksich M, Dervan PB (1996) Extension of sequence-specific recognition in the minor groove of DNA by pyrrole-imidazole polyamides to 9-13 base pairs. J Am Chem Soc 118 6160-6166... 

Lazinski, D., Grzadzielska, E. Das, A. (1989). Sequence-specific recognition of RNA hairpins by bacteriophage antiterminators requires a conserved arginine-rich motif. Cell 59, 207-18. 

Zh. Zhang, Ch-H. Lee, V. Mandiyan, J.-P. Borg, B. Margolis, J. Schlessinger, and J. Kuryan. Sequence-specific recognition of the internalization motif of the Alzheimer s amyloid precursor protein by the XI1 PTB domain. EMBOJ, 16, 6141 6150, 1997. 

V. Petri, M. Hsieh, E. Jamison and M. Brenowitz. DNA sequence-specific recognition by the Saccharomyces cerevisiae "TATA" binding protein promoter-dependent differences in the thermodynamics and kinetics of binding. Biochemistry 37 (1998) 15842-9. 

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