DNAProtein Interactions Complexes Prokaryotic promoter Consensus sequence is

  • Slides: 31
Download presentation
DNA-Protein Interactions & Complexes

DNA-Protein Interactions & Complexes

Prokaryotic promoter Consensus sequence is not present in majority of prokaryotic promoters. Sequence motifs

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

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?

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

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

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

A representative free energy profile for 1000 nt long E. coli promoter sequence

DNA bendability DNA Protein

DNA bendability DNA Protein

TATA-containing promoters show different structural properties from TATA-less promoters The average free energy, Dnase

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

• Different DNA binding helix turn helix protein motifs

DNAprotein interactions DNAProtein interaction Lambda repressor and croDNAprotein interactions DNAProtein interaction Lambda repressor and cro
PROMOTER WHO IS A PROMOTER The promoter isPROMOTER WHO IS A PROMOTER The promoter is
Consensus Algorithms Consensus Algorithms Byzantine Generals Consensus AlgorithmsConsensus Algorithms Consensus Algorithms Byzantine Generals Consensus Algorithms
Drosophila Solexa data analysis Ahsan 325 Promoter PromoterDrosophila Solexa data analysis Ahsan 325 Promoter Promoter
PROMOTERS Who is a Promoter Promoter a personPROMOTERS Who is a Promoter Promoter a person
WELCOME TO BRAND PROMOTER Brand promoter company basedWELCOME TO BRAND PROMOTER Brand promoter company based
Chapter 12 DNAprotein interactions Preparation of nuclear extractsChapter 12 DNAprotein interactions Preparation of nuclear extracts
Footprinting DNAProtein Interactions Powerful and fairly rapid methodsFootprinting DNAProtein Interactions Powerful and fairly rapid methods
Detecting DNAprotein Interactions Xinghua Lu Dept Biomedical InformaticsDetecting DNAprotein Interactions Xinghua Lu Dept Biomedical Informatics
Hybridization Nucleic acid Basics PCR Electrophoresis DNAProtein interactionsHybridization Nucleic acid Basics PCR Electrophoresis DNAProtein interactions
REACTIVITY OF METAL COMPLEXES Lability Inertness Of ComplexesREACTIVITY OF METAL COMPLEXES Lability Inertness Of Complexes
Lecture 5 Triangulations simplicial complexes and cell complexesLecture 5 Triangulations simplicial complexes and cell complexes
CLAUSE COMPLEXES EXPANSION AND PROJECTION PRACTICE Clause ComplexesCLAUSE COMPLEXES EXPANSION AND PROJECTION PRACTICE Clause Complexes
Lecture 5 Triangulations simplicial complexes and cell complexesLecture 5 Triangulations simplicial complexes and cell complexes
Lecture 5 Triangulations simplicial complexes and cell complexesLecture 5 Triangulations simplicial complexes and cell complexes
TRANSITIONS IN COMPLEXES TRANSITIONS IN COMPLEXES Transitions inTRANSITIONS IN COMPLEXES TRANSITIONS IN COMPLEXES Transitions in
Complexes Complexes Compounds in which a metal atomComplexes Complexes Compounds in which a metal atom
Prokaryotic vs Eukaryotic Cells Prokaryotic Primitive Simple DNAProkaryotic vs Eukaryotic Cells Prokaryotic Primitive Simple DNA
Prokaryotic vs Eukaryotic Cells Major Cell Types ProkaryoticProkaryotic vs Eukaryotic Cells Major Cell Types Prokaryotic
Prokaryotic Transcription Both Eukaryotic Transcription Prokaryotic Transcription 1Prokaryotic Transcription Both Eukaryotic Transcription Prokaryotic Transcription 1
Prokaryotic and Eukaryotic Cellular Structure Prokaryotic Eukaryotic CellsProkaryotic and Eukaryotic Cellular Structure Prokaryotic Eukaryotic Cells
ROSLAILI RASYID Mikroorganisme PROKARYOTIC vs EUKARYOTIC STRUCTURE PROKARYOTICROSLAILI RASYID Mikroorganisme PROKARYOTIC vs EUKARYOTIC STRUCTURE PROKARYOTIC
Prokaryotic Gene Control Operons Chapter 18 1 ProkaryoticProkaryotic Gene Control Operons Chapter 18 1 Prokaryotic
Prokaryotic V Eukaryotic Prokaryotic cells pro before karyoteProkaryotic V Eukaryotic Prokaryotic cells pro before karyote