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Specific DNA Binding Sites

Structural Features of Specific DNA Binding Sites

Since RNA polymerase must interact at the promoter site of all genes, you might expect that all genes would have a similar nucleotide sequence in the promoter region. This is found to be true for both prokaryotic and eukaryotic genes. You would expect, however, that all transcription factors would not have identical DNA binding sequences. The sequences of DNA just upstream of the start site of the gene that binds protein (RNA polymerase, transcription factors, etc) are called promoters. The table below shows the common DNA sequence motif called the Pribnow or TATA box found at around -10 base pairs upstream from the start site, and another at -35. Proteins bind to these sites and facilitate binding of RNA polymerase, leading to gene transcription.

Prokaryotic  Promoter Sequences

Promoter

-35 Region

Spacer -10 Region Spacer RNA start
trp operon TTGACA N17 TTAACT N7 A
tRNAtyr TTACA N16 TATGAT N7 A
lP2 TTGACA N17 GATACT N6 G
lac operon TTTACA N17 TATGTT N6 A
rec A TTGATA N16 TATAAT N7 A
lex A TTCCAA N17 TATACT N6 A
T7A3 TTGACA N17 TACGAT N7 A
consensus TTGACA   TATAAT    

The TATA box in prokaryotes is also known as the Pribnow box. A similar sequence is found in eukaryotes (consensus TATAAA) located about 25 nucleotides upstream from the transcription start site. It is also called the Goldstein-Hogness box.

In addition, in eukaryotes, sequences further upstream called response elements bind specific proteins (such as CREB or cyclic AMP response element binding protein) to further control gene transcription.

Eukaryotic Response Elements (RE)s

Regulatory agent

Module

Consensus DNA bound Factor Size (daltons)
Heat Shock HSE CNNGAANNTCCNNG 27 bp HSTF 93,000
Glucocorticoid GRE TGGTACAAATGTTCT 20 bp Receptor 94,000
Cadmium MRE CGNCCCGGNCNC . ? .
Phorbol Ester TRE TGACTCA 22 bp AP1 39,000
Serum SRE CCATATTAGG 20 bp SRF 52,000
Antioxidant ARE GTGACTCAGC      
Pheromone (fungus)   ACAAAGGGA      
Hypoxia HRE

CCACAGTGCATACGT

GGGCTCCAACAGGTC

CTCTCCCTCCCATGCA

  Hypoxia Inducible Factor 826 aa
Peroxisome Proliferator Activated Receptor (PPAR) PPRE aGG_CAAAGGT(CG)A   PPAR 59,000
Steroid (general) (progesterone, androgen, mineralcorticoids, glucocorticoids)  

AGAACAxxxACAAGA

(inverted repeat)

     
  • Eukaryotic Promoter Database - annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally

Figure: Eukaryotic promoters and regulatory regions

10 eukpromoterNatREv0703.jpg

Figure: Eukaryotic multisubunit general transcription apparatus

11 txnregNatRev0703.jpg

"The multi-subunit general transcription apparatus: identification of tissue-specific and gene-selective subunits. Diversified metazoan transcription initiation complexes. a, The eukaryotic transcriptional apparatus can be subdivided into three broad classes of multi-subunit ensembles that include the RNA polymerase II core complex and associated general transcription factors (TFIIA, -B,-D,-E,-F and -H), multi-subunit cofactors (mediator, CRSP, TRAP, ARC/DRIP, and so on) and various chromatin modifying or remodelling complexes (SWI/SNF, PBAF, ACF, NURF and RSF). b, c, Metazoan organisms have evolved multiple gene-selective and tissue-specific TFIID-like assemblies by using alternative TAFs (TBP-associated factors such as the ovarian-specific TAF105) as well as TRFs (TBP-related factors such as TRF2 in Drosophila and mice) to mediate the formation of specialized RNA polymerase initiation complexes that direct the transcription of tissue-specific and gene-selective programmes of expression." (Nature reference in figure above.)

Proteins can interact specifically with DNA through electrostatic, H-bond, and hydrophobic interactions. AT and GC base pairs have available H bond donors and acceptors which are exposed in the major and minor groove of the ds DNA helix, allowing specific protein-DNA interactions.

Figure: AT and GC base pairs have available H bond donors and acceptors

12 Hbondmajmingrove.gif