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DNA-Protein Interactions & Complexes
Prokaryotic promoter Consensus sequence is not present in majority of prokaryotic promoters. Sequence motifs encompassing 6 -10 nucleotides are degenerate; Probability of finding similar sequences in regions other than promoters is quite high. Harley and Reynolds (1987) Nucleic Acids Res. 15(5): 2343 -2361. 6
Sequence logo for B. subtilis, E. coli and M. tuberculosis promoter sequences No sequence conservation 7
Does this indicate that there are other signals which help in positioning RNA polymerase? Hence analysis of structural properties of a DNA sequence to locate signals that are: • Relevant to transcription from a functional/mechanistic/structural point of view. • Unique to the promoter sequences and can be used to differentiate between promoter and non-promoters. • Can be predicted from a given sequence. For example: 1) DNA STABILITY (Ability of DNA to Open up) 2) DNA CURVATURE (Intrinsically curved DNA structure) 3) DNA BENDABILITY (Ability of DNA to bend)
Why Stability? • An important step in transcription is the formation of an open complex which involves strand separation of DNA duplex upstream of the transcription start site (TSS) • This separation takes place without the help of any external energy. • Hence evaluating stabilities of promoter sequences may give some clues.
Stability of base paired dinucleotides based on Tm (melting temp data) on a collection of 108 oligonucleotide duplexes. Santa. Lucia J (1998) Proc. Natl. Acad. Sci. USA 95(4): 1460 -1465.
A representative free energy profile for 1000 nt long E. coli promoter sequence
DNA bendability DNA Protein
TATA-containing promoters show different structural properties from TATA-less promoters The average free energy, Dnase 1 sensitivity, Nucleosome positioning preference and curvature profiles of S. cerevesiae promoters w. r. t TSS. TATAcontaining promoters are less stable (fig a), highly bendable (fig b) and more curved (fig d) as compared to TATA-less promoters. The nucleosome positioning preferences (fig c) are only slightly different.
• Different DNA binding helix turn helix protein motifs