RNA Polymerase Identifies and Transcribes Genes

This is the structure of RNA polymerase from the bacteriophage T7. This polymerase is 883 amino acids long and it has a molecular mass of 99,000 grams per mole. The polymer forming reaction catalyzed by RNA polymerase is similar to that catalyzed by DNA polymerase and there are many similarities in their structures. For instance, both types of polymerase have a "right hand" structure with the DNA lying across the palm of the hand and with thumb and finger domains. The thumb is shown above in purple and the fingers are colored red and medium blue.

Like DNA polymerase, RNA polymerase uses one strand of DNA as a template or model which guides the synthesis of a new strand of nucleic acid. The template DNA strand is shown in yellow and the non-template strand is gray, blue, pink and red. However, RNA polymerase is different from DNA polymerase in that it makes a new strand of RNA which is peeled off the DNA template and translated into protein. This process of copying the DNA sequence as an RNA sequence is known as TRANSCRIPTION.

RNA polymerase transcribes specific genes that are found in the DNA. The polymerase recognizes these genes because they have PROMOTERS.

A PROMOTER is an RNA polymerase binding site in the DNA which comes just before a gene. For T7 RNA polymerase, the DNA sequence that makes up the promoter is TATAGTGAGTCGTATTA in the template strand.

For clarity, only short segments of the polymerase and the promoter are shown above. RNA Polymerase recognizes the promoter sequence by hydrogen bonds: Arginine 756 makes two hydrogen bonds to Guanine-9, Glutamine 758 makes two hydrogen bonds to Adenine-8, and Arginine 746 makes two hydrogen bonds to Guanine-7. These are only a few of the protein-DNA interactions involved in promoter recognition.

Once a gene is recognized, it cannot be transcribed from DNA into RNA until the double stranded DNA is melted into two single strands. This is a close-up view of a segment of RNA Polymerase which plays a crucial role in melting and separating the DNA strands. The single stranded portion of the template strand is yellow, the single stranded non-template strand is magenta, and the double stranded DNA duplex of template and non-template strands is gray, blue, red, and pink.

The bases in DNA are non-polar or hydrophobic, somewhat like benzene. To separate the strands, RNA Polymerase has an Alanine - Glycine - Valine - Valine - Glycine segment which is very hydrophobic and which is shown here in green. Hydrophobic molecules bind to other hydrophobic molecules just like drops of oil floating in water bind and merge. In this case, the green, hydrophobic protein segment binds to the hydrophobic bases in DNA, allowing the DNA to melt apart so that the template strand can be transcribed.

The animation above shows a wider angle view of the hydrophobic domain of RNA polymerase that helps melt apart the DNA strands. Again, only the single stranded portion of the template strand is colored yellow. Notice how the template strand reaches into the active site of RNA polymerase, in the center of the palm domain. As you can see, the non-template strand (in magenta) is pushed off around the side of the polymerase.

The process of transcribing a gene sequence from DNA into RNA takes place in the active site of RNA polymerase. Ribonucleoside-triphosphates (NTPs) diffuse into the active site, bind to the template DNA strand (in yellow), and are linked to form a longer and longer RNA chain. This process creates a temporary RNA-DNA duplex with the new RNA strand bound to the template DNA strand. After synthesis, the RNA is peeled off the DNA strand so that it can be translated into protein by the ribosomes.

The crystallographic structure shown was determined by G. M. T. Cheetham, D. Jeruzalmi, and T. A. Steitz at Yale University. This structure is MMDB 10243 in the database of structures maintained at the National Institutes of Health (NIH) by A. Marchier Bauer, K. J. Addess, C. Chappey, L. Geer, T. Madej, Y. Matsuo, Y. Wang and S. H. Bryant. (Nucleic Acids Research 27: 240-243 (1999))

All displays of the three-dimensional structure were generated using the Cn3D viewer developed by C. W. Hogue at the NIH (Trends Biochem. Sci. 22: 314-316 (1997)). Both the MMDB Database and Cn3D program are used by permission of the NIH.

Animations on this page were created with GIF Construction Set (V 2.0a) which was registered 10/22/99.

This page was developed by Dr. John Barnard at the State University of New York at Buffalo Dept. of Microbiology (Jbarnard@acsu.buffalo.edu).


Disclaimer: The contents and link identifiers of this web page are not monitored, reviewed, nor endorsed by the State University of New York at Buffalo. All opinions expressed are my own.