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#consensus sequence

3 public questions tagged with this topic.

Processing of mRNA, rRNA, tRNA

Consensus sequence of branch site is

Branch site consensus in budding yeast Saccharomyces cerevisiae is invariant UACUAAC where central adenosine is nucleophile forming two prime-five prime linkage, highly conserved due to need for base pairing with U2 snRNA GUAGUA and recognition by splicing factors. Mammalian branch point consensus is more degenerate YNYYRAY, specifically CURAY motif where R is purine, Y is pyrimidine, containing bulged adenine. Sequence forms duplex with U2 snRNA positioning adenine for chemistry. Mutations in this motif cause exon skipping, inherited disease such as thalassemia, emphasizing sequence conservation importance.

Ref: Berg et al., Biochemistry, 9th ed., Chapter 28: Consensus branch site UACUAAC; Lodish 9th ed., Yeast vs mammalian branch point sequences

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Transcription in Prokaryotes

Consensus sequence of the -35 element is

Promoter anatomy reveals two conserved hexamers spaced seventeen base pairs apart. Upstream hexamer centered around -35 position consensus sequence TTGACA contacted by sigma70 region 4 helix-turn-helix domain. Downstream Pribnow box at -10 consensus TATAAT recognized by region 2. Spacer length crucial for simultaneous contact of both elements due to helical phasing. TTGACA sequence unambiguously defines -35 element, distinguishing it from -10, UP element recognized by α-CTD, or GC-rich eukaryotic SP1 site GGGCGG. Promoter strength correlates with closeness to TTGACA consensus for -35 interaction optimizing closed complex formation.

Ref: Alberts Chapter 6: -35 consensus TTGACA bacterial promoters; Watson Molecular Biology Gene Promoter table -35 element sequence

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Transcription Basics

Consensus sequence represents

Consensus sequence mathematically summarizes most common nucleotide at each position of alignment of numerous functionally related DNA motifs, such as promoters or transcription factor binding sites. Calculation counts base frequency across aligned examples and chooses majority residue to build idealized pattern that may not exist perfectly in nature. For instance bacterial -10 consensus TATAAT emerges from frequency analysis. Deviations from consensus correlate with reduced binding affinity and promoter strength. Consensus representation provides predictive tool for genome scanning and mutational analysis, distinguishing functional motif conservation from random DNA composition effectively.

Ref: Berg Biochemistry Chapter 28: Consensus idealized common sequence from alignment; Alberts Chapter 6 Promoter consensus construction

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