White Strong & Flexible Plastic, hand painted with watercolor paints. The colors I chose to paint this model:
Protein: Purple ---
Old DNA strand: Green ---
Newly synthesized DNA and incoming NTP: Blue ---
Magnesium ions: Orange
Phi29 Polymerase
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Product Description
Say hello to one of the planet's tiniest copying machines!
The structure you see here is a DNA polymerase from the virus called Φ29 (or Phi29) [1]. This virus is called a bacteriophage, because it makes a living infecting bacteria. Of course its main objective is to make copies of itself, and Φ29 does an remarkable job thanks in part to this remarkable protein.
Every bacterium, fungus, plant, animal, and human on the planet needs to copy its DNA, that famous double-stranded polymer that carries the 4-letter information "coding" for life. Copying is the task of DNA polymerases, a family of proteins that make a new strand of DNA by "reading" one strand and adding complementary letters to the end of its own growing string. In multicellular organisms like people and poinsettias, these proteins are parts of large complexes, with dozens of molecules performing specialized tasks like pulling apart the DNA strands and correcting errors that are bound to happen when copying a 3-billion-letter message. Having many specialized proteins for one task works great in big things like us. But Φ29 is a parasite. A tiny parasite. It can't afford the luxury of big protein complexes. Its survival strategy is to copy as quickly and efficiently as possible, which brings us to our molecule: Φ29 DNA Polymerase.
This protein started showing some surprising properties when Φ29 was being studied in the 1980s. A group of researchers in Madrid [2] wrote a paper on just how resilient this protein is; once it started replicating, nothing could stop it. They threw a battery of tests at the little protein, and in conditions far too cold or too salty for the bacterial DNA polymerase to function, our Φ29 protein would just keep on chugging along. But the most surprising feature was revealed when the researchers had it copy a circular piece of DNA. Starting in one location, the bacterial polymerase would copy around the circle until it got back to where it started. There it would run into the strand it just made on the previous lap and fall off the DNA. But give Φ29 polymerase some circular DNA and it will roll around the circle once... then again... and again... each time pushing the old strand out of the way to make a new one. In this experiment the protein ran around the circle 10 times, copying 70,000 letters of DNA with no signs of slowing down. This strand displacement activity allows Φ29 polymerase to copy its entire genome on its own (once it gets started). Over the next decade it became apparent just how useful this feature makes Φ29 polymerase as a tool for detecting specific DNA sequences inside cells. Work through the 1990s by Drs. Paul Lizardi, Mats Nilsson and others turned this protein into an incredibly sensitive diagnostic tool capable of locating single-letter mutations in DNA [3,4]. Called "Rolling-Circle Amplification", this method has been quickly gaining popularity in molecular biology labs all over the world. You can read an overview of some of the amazing things Φ29 polymerase is being used for here [5].
This 3D printed model comes from X-ray crystallography data from the lab of Dr. Thomas Steitz. The authors managed to crystallize Φ29 polymerase in complex with both the template strand and newly synthesized strand of DNA. You can also see the catalytic center, were two magnesium ions are used to add the next nucleotide onto the growing DNA strand. In the model, I have left the DNA attached to the protein by one small sprue, so you can easily detach it if you like in order to move it around. I recommend printing in White Strong & Flexible plastic so you can hand paint the model and really get a feel for its surfaces and folds. In the images above, I used watercolors to paint the features this way:
Protein: Purple
Old DNA strand: Green
Newly synthesized DNA and incoming NTP: Blue
Magnesium ions: Orange
Thank you for reading, and I hope you get a grip on molecular biology!
Sources for the curious:
[1]* Andrea J. Berman et al., "Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases." The EMBO Journal (2007)
[2]* Luis Blanco et al., "Highly Efficient DNA Synthesis by the Phage Φ29 DNA Polymerase." The Journal of Biological Chemistry (1989)
[3] Paul M. Lizardi et al., "Mutation detection and single-molecule counting using isothermal rolling-circle amplification." Nature Genetics (1998)
[4] Mats Nilsson et al., "Padlock probes: circularizing oligonucleotides for localized DNA detection." Science (1994)
[5] M. Monsur Ali et al., "Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine." Chemical Society Reviews (2014)
*(free full text available)
The structure you see here is a DNA polymerase from the virus called Φ29 (or Phi29) [1]. This virus is called a bacteriophage, because it makes a living infecting bacteria. Of course its main objective is to make copies of itself, and Φ29 does an remarkable job thanks in part to this remarkable protein.
Every bacterium, fungus, plant, animal, and human on the planet needs to copy its DNA, that famous double-stranded polymer that carries the 4-letter information "coding" for life. Copying is the task of DNA polymerases, a family of proteins that make a new strand of DNA by "reading" one strand and adding complementary letters to the end of its own growing string. In multicellular organisms like people and poinsettias, these proteins are parts of large complexes, with dozens of molecules performing specialized tasks like pulling apart the DNA strands and correcting errors that are bound to happen when copying a 3-billion-letter message. Having many specialized proteins for one task works great in big things like us. But Φ29 is a parasite. A tiny parasite. It can't afford the luxury of big protein complexes. Its survival strategy is to copy as quickly and efficiently as possible, which brings us to our molecule: Φ29 DNA Polymerase.
This protein started showing some surprising properties when Φ29 was being studied in the 1980s. A group of researchers in Madrid [2] wrote a paper on just how resilient this protein is; once it started replicating, nothing could stop it. They threw a battery of tests at the little protein, and in conditions far too cold or too salty for the bacterial DNA polymerase to function, our Φ29 protein would just keep on chugging along. But the most surprising feature was revealed when the researchers had it copy a circular piece of DNA. Starting in one location, the bacterial polymerase would copy around the circle until it got back to where it started. There it would run into the strand it just made on the previous lap and fall off the DNA. But give Φ29 polymerase some circular DNA and it will roll around the circle once... then again... and again... each time pushing the old strand out of the way to make a new one. In this experiment the protein ran around the circle 10 times, copying 70,000 letters of DNA with no signs of slowing down. This strand displacement activity allows Φ29 polymerase to copy its entire genome on its own (once it gets started). Over the next decade it became apparent just how useful this feature makes Φ29 polymerase as a tool for detecting specific DNA sequences inside cells. Work through the 1990s by Drs. Paul Lizardi, Mats Nilsson and others turned this protein into an incredibly sensitive diagnostic tool capable of locating single-letter mutations in DNA [3,4]. Called "Rolling-Circle Amplification", this method has been quickly gaining popularity in molecular biology labs all over the world. You can read an overview of some of the amazing things Φ29 polymerase is being used for here [5].
This 3D printed model comes from X-ray crystallography data from the lab of Dr. Thomas Steitz. The authors managed to crystallize Φ29 polymerase in complex with both the template strand and newly synthesized strand of DNA. You can also see the catalytic center, were two magnesium ions are used to add the next nucleotide onto the growing DNA strand. In the model, I have left the DNA attached to the protein by one small sprue, so you can easily detach it if you like in order to move it around. I recommend printing in White Strong & Flexible plastic so you can hand paint the model and really get a feel for its surfaces and folds. In the images above, I used watercolors to paint the features this way:
Protein: Purple
Old DNA strand: Green
Newly synthesized DNA and incoming NTP: Blue
Magnesium ions: Orange
Thank you for reading, and I hope you get a grip on molecular biology!
Sources for the curious:
[1]* Andrea J. Berman et al., "Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases." The EMBO Journal (2007)
[2]* Luis Blanco et al., "Highly Efficient DNA Synthesis by the Phage Φ29 DNA Polymerase." The Journal of Biological Chemistry (1989)
[3] Paul M. Lizardi et al., "Mutation detection and single-molecule counting using isothermal rolling-circle amplification." Nature Genetics (1998)
[4] Mats Nilsson et al., "Padlock probes: circularizing oligonucleotides for localized DNA detection." Science (1994)
[5] M. Monsur Ali et al., "Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine." Chemical Society Reviews (2014)
*(free full text available)
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Phi29 Polymerase
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