Posts tagged dna
Posts tagged dna
Lots of people wanted to know where we got our DNA models from so here’s the link!
Here’s a video of Katherine explaining the DNA motor on the Mini Motors stand.
They borrowed it for the intro to the genetic maps stand.
When we had stopped playing with models of DNA Jon took them home and made a stop frame animation of the DNA mini motor that he builds in the lab with real DNA.
Imagine that the orange strands of DNA are tethered at one end to keep them in place. These are the stators of the motor. The blue cargo is loaded on to the left stator.
In a real experiment an ezyme cuts the top off the stator. As this is only weakly held on by a few base pairs if quickly falls off and floats away. This means the top of the blue cargo is free to bind to the next stator.
The cargo “steps” to the new stator by strand displacement. As this stator is full length all the bases can bind which is more energetically favourable than staying on the old stator.
The whole process of enzyme cutting, short piece of DNA falling off and stepping by strand displacement is repeated to move the cargo to the stator on the right.
The furthest a real DNA motor has gone 16 steps but the motor is very unlikely to fall off so it would make more steps if we could build longer tracks with a greater number of stators.
Recreating the Watson & Crick eureka moment with models of DNA!
When you are designing your DNA walker it is important to remember that the backbones form a double helix. The exact position of the backbone can have a big effect on how the walker behaves! It can be hard to visualise what is going on without a model. We have used everything from bendy straws and pipecleaners to bits of dowling rod but here is a paper model which makes a great double helix. The instructions are here and there are lots more DNA activities on the Wellcome Trust Sanger Institute’s yourgenome.org project page.
The filaments that E.coli use to swim are approximately 0.00001 metres long. In scientific notation this can be written as 10×10-6 metres or 10 µm. To show you how small this is we have taken a series of zoomed in pictures of a Lego brick covered with beads that are 1 µm in diameter. A line of ten beads is the same length as a bacterial filament. The rotary motor which spins the filament is approximately 20 times smaller than the beads in the video. It is 0.000000045 metres in diameter which is normally written as 45×10-9 metres or 45 nanometres.
Kinesin is an even smaller mini motor. It takes steps of 0.000000008 metres (8 nanometres) so it would have to take 125 steps to walk 1 µm. This is the average number of steps a single kinesin motor can take before the feet are no longer co-ordinated and as a consequence it falls off the track.
The DNA motors that we make take steps which are slightly smaller (6 nanometres) than kinesin. So far the longest track that they have travelled along is 16 steps but the motor is very unlikely to fall off so it would travel greater distances if we could build longer tracks.
At the end of the video you can see some of the same beads in water. The centre of one of the beads is marked in blue. As the water molecules bump into the bead there is a transfer of momentum and the bead changes direction. This random jiggling is known as Brownian motion. All the mini motors experience effects of Brownian motion.
We can order the DNA for our experiments online and it arrives in tubes like these. We are planning to give them away at the exhibition, but unfortunately the QR code only works when it is flat. Guess we’ll just have to write the blog address in full! http://mini-motors.tumblr.com/
Two strands of DNA are described as ‘complementary’ if every base on the first strand can pair with the corresponding base on the second strand. Pairing is highly specific, which means that mismatched bases do not generally bond to each other (see previous post).
When two complementary strands of DNA are bound together but one is longer than the other, the overhang is known as a toehold. If a third strand of DNA is introduced which can bind to the toehold and is fully complementary to the longer of the two bound strands, the new strand can quickly displace the shorter strand. This mechanism allows DNA strands to be exchanged, a key step in the operation of DNA motors.
Important lesson on denaturing gels
Naturally occurring mini motors, such as the bacterial flagellar motor, are typically made from proteins. Proteins are very complicated. They have twenty different kinds of subunit (amino acids), and the forces which determine their three-dimensional structure are exceedingly complex. This makes it very difficult to design proteins from scratch. However, DNA is comparatively simple to work with, since there are only four types of subunit, which pair up in a highly predictable fashion. As a result there are a number of scientists – including several in the Mini Motors team - working on DNA motors, tiny locomotive devices made out of DNA. Here, we are taking DNA out of its usual biological context and using it to perform a different function. Rather than acting as an information store for a living organism, here DNA is the material out of which the motors are made, and also the fuel to drive them.
In living cells DNA acts as the store for the genetic information which is the ‘blueprint’ of the organism. It is a comparatively large molecule, consisting of two strands intertwined to form a double helix (see other post). Each strand is formed from a series of subunits called nucleotides, bonded together along the backbone of the strand. Every nucleotide contains a ‘base’, which projects into the centre of the helix and pairs with a complementary base on the other strand. Base-pairing is highly specific: adenine pairs with thymine, guanine pairs with cytosine, and this means that by designing the sequences of a set of DNA strands it is possible to control how they bond to each other and what structure they form. This is the basis of DNA Nanotechnology, the use of DNA to build nanostructures – both dynamic (mini motors!) and static.
DNA: the phosphate backbone of two strands twist around each other to make the familiar double-helix structure with a ladder of hydrophobic bases stacked on the inside.
Here’s a link to a paper from our group that was recently published in Nature Nanotechnology. It explains how you can give a DNA motor instructions to choose which path to take as it walks along a branched track.
Great image of DNA model from thepaperwall.com (but spot the deliberate mistake :p)