Designing DNA Nanostructures

DNA Nanostructures can be created using software known as NanoEngineer-1. NanoEngineer-1 software is really easy to learn and has a 3D workplace. This blog post would help you create DNA Nanostructures from Scratch with the help of NanoEngineer-1. 

Let's make a DNA Triangle

When you start NanoEngineer-1, you will see a layout like this on your screen.

Image 2

Now, click on the "DNA" option and select "Insert DNA"

Image 3

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When you would move your mouse cursor to the white space of the middle, the mouse changes from a pointer to a pencil. 

Now, click anywhere on the white canvas and then move your mouse. You will see that you are creating double-stranded DNA. The farther you move your mouse, the longer would be the strand and vice versa. When you want to stop creating, click once again and you will get double-stranded DNA of a specific length.

Image 5

Now, either you can create two more double-stranded DNA like this or you can copy and paste this strand that you have already created. To show how you can copy-paste it, I would create another two double-stranded DNA by copy-paste.

Now, click on that green tick mark that is given in the panel on the left side. 

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After this, for copy and pasting, right-click on the option of DnaGroup1 and click on "Copy"

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After clicking on "Copy", select the option "Paste from Clipboard" and click on the white canvas two times so that you will get double-stranded DNA. 

Image 8

Thus, after obtaining 3 double-stranded DNA, now we have to arrange them in the shape of a Triangle. So then, click on the "Move" option. After that, you would get options of "Translate" and "Rotate". Right now, click on the option of "Rotate" because we want to rotate a double-stranded DNA to 60 degrees.

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After you click on "Rotate", select a double-stranded DNA out of the three, and then make sure that you have selected "By Specified Angle" in Z-axis in front of "Rotate Around" and type 60.00 as "Rotate By" in the +Rotation as "Direction" in the Move Panel. 

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You will notice that the double-stranded DNA that you selected rotated. Now, select another double-stranded DNA and follow the keep the same settings except "Direction". This time, set -Rotation in Direction. Thus, you will get 2 double-stranded DNA which is rotated by an angle of 60 degrees in the opposite direction.

Now, click on the green tick mark (See image 6). Click on the "Move" option again and this time select "Translate" (See image 9).

Select a double-stranded DNA and make sure the option "Free Drag" is selected. 

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Now you can move your selected double-stranded DNA. Like this, you can move another DNA Strand and make a Triangle.

Click on the green-colored tick mark again (See image 6). Now select the option of "DNA" again and in the same line as "Insert DNA", there is an option of "Join Strands" (See images 3 and 4). Click on "Join Strands".

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You would notice that at the 3' ends and 5' ends, there would be green-colored arrowheads. Click on those arrowheads and join them with the arrowheads of another double-stranded DNA.

Thus, this is how you make a DNA Triangle. Like this, you can create more complex shapes made out of DNA that can be used as DNA Nanodevices.

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