Watery Spine Tutorial

This tutorial has two purposes:

1) To help you learn about the structure of the watery spine in the minor groove of B-DNA.

2) To help you learn about the RasMol program.

In order to use this tutorial you will need to install RasMol and properly configure it, if you have not already done so. Click here to go to a site where you can obtain instructions on how to do this.

Once you have installed RasMol, CLICK HERE to open the application and display the structure of a piece of B-DNA. Now resize and/or move this window as well as the RasMol windows so that you can see the structure, while still reading this window. Alternatively, you can print out this tutorial so that you can devote your entire computer screen to the RasMol windows.

RasMol displays two windows: the main window in which you see the structure, and the command line window in which you can enter commands to modify the structure. There are also a series of menus at the top of the screen that you can use to execute a limited set of commands. In the follow tutorial, whenever you are instructed to "enter" a command, you should type the command shown in boldface at the "RasMol" prompt in the command line window and then press return. Altenatively, if you prefer you can use the copy and paste commands to paste the commands into the command line window.

This is the structure of the central 4 basepairs of the Dickerson dodecamer (residues 5-8 of each strand). Enter the command show sequence to see the sequence of each strand.

Select the command sticks from the display menu to thicken the bonds.

Enter the command zoom 150 to magnify the image to 150% of its original size.

Right now, we are looking at the molecule from a funny angle, so it's hard to see what's going on. You could rotate the molecule with the mouse, but instead let's do it by entering the following three commands:

rotate z 109 (rotates the molecule 109° about the z axis)
rotate y -15
rotate x 89

Now you should be looking into the minor groove of the duplex.

"Where's the watery spine?" you may be wondering. Well its not visible in this wireframe model. Why is that? It's because all the hydrogen atoms have been left out of this structure, including the water hydrogen atoms. So the only thing remaining of each water molecule is an oxygen atom. In a wireframe model, we're just looking at the bonds connecting the atoms, and not the atoms themselves. So a single atom that's not covalently bonded to anything else is invisible. To make the water molecules visible, enter the following two commands:

select water (now subsequent commands will only be applied to the water molecules)
dots on

You should now see dots outlining the oxygen atoms of five water molecules. The size of the outlines reveals the Van der Waal's radii of the atoms. Enter the command: color dots yellow. This will change the color of the dots, making them stand out more against the black background.

To add labels to the water molecules enter the following two commands:

label %n%r
color labels white

The "%n" term in the argument of the "label" command specifies the residue name, while the "%r" term specifies residue number. The second command just changes the color of the labels to make them a little easier to see. For water molecules the RasMol residue name is "HOH", so the oxygen atoms of the water molecules should now be labeled HOH1, HOH2, HOH3, HOH4, and HOH5. Now let's save this view, in case you want to come back to it. Enter the command:

write script nice_view

You have now created a text file in your RasMol folder called nice_view containing most of the commands necessary to recreate this view of the molecule. To invoke this series of commands enter:

script nice_view

[Sometimes, the script generated by the write script command doesn't contain all the necessary settings to regenerate a view precisely. For example, after invoking the nice_view script, it will probably be necessary to select the water molecules again (select water) and turn dots back on (dots on).]

To get a feel for how nicely the water molecules fit the minor groove of B- DNA, let's change to a spacefilling model. Enter the following commands:

select all
spacefill on
select water
color magenta
select backbone
color yellow

To go back to the previous view, just invoke the nice_view script, select the water molecules, and turn the dots back on as described above.

Now see if you can answer the following questions:

1) Which water molecules are "first-layer" water molecules, and which water molecules are "second-layer" water molecules?

2) To which specific atoms in the minor groove are each of the first layer water molecules bonded?


a) It may be necessary to rotate the molecule in various ways to get a better feel for the position of the water molecules relative to one another and relative to various functional groups in the minor groove. For example try rotating the molecule 90° about the x axis.

b) If you want to identify an atom, use the mouse to position the cursor right over that atom and click the mouse button. The identity of the atom will appear in the command line window. To learn more about RasMol, you can refer to the online RasMol instruction manual

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voh@chem.ucla.edu // Last revision: October 21, 1996