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Perhaps the most important window in GCK is the Construct Window. This is the place where you will do the majority of your cloning manipulations and can precisely define how your construct will look.
1. Start GCK.
2. Open the file Bluescript KS+ in the tutorial files folder by choosing File > Open.... This will bring up Figure 1. The tutorial files folder should be in the GCK folder.
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Figure 1: Opening a File
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The buttons on the bottom let you choose to have listed different types of files in the list of files. Since we are opening a construct file, leave the radio button set on Construct. Select the Bluescript KS+ file and press the Open button. You will see Figure 2.
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Figure 2: Bluescript KS+
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3. This construct has a number of segments of DNA indicated in different colors and patterns. In the lower left corner of the Construct window is an indicator of the location of the current insertion point. The insertion point is where new sequence would be placed into the current construct by typing or pasting. Clicking with the mouse anyplace along the DNA will place the insertion point at the closest boundary between two segments.
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Figure 3: Selected Segment
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4. Double-click on the red segment of DNA. This will highlight that segment as shown in Figure 3. Note how the indicator in the bottom left corner now shows the range of nucleotides selected. The range is always shown in the clockwise orientation (or from left to right for linear constructs). You should see 792-625 selected. The origin is defined as position#1.
5. Once an object is selected, you can modify it. Choose Format > Lines > and choose the second line down to change the width of the selected DNA segment to 2 pixels.
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Figure 4: Magnified View
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6. This vector has T3 and T7 promoters and a polycloning site that we want to indicate. The promoters are shown in green and the polycloning site is a striped blue. Let's add directionality to the promoters. Before you can add arrowheads to any segment of DNA it must first be selected. The promoter segments are rather small and might be difficult to select at this magnification. So click the mouse on one of the green segments (between the blue and red segments) to place the insertion point near what we are interested in and then choose Construct > Magnification > Zoom In to enlarge the view. Zoom In again and then select the top green segment by double-clicking. You will see Figure 4. Nucleotides 626-645 will be selected.
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Figure 5: Segment Get Info Box
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7. Choose Construct > Get Info... to see the name of the segment and any associated comments. This is the T7 promoter as shown in Figure 5. Every segment of DNA can have a name and comments associated with it. These comments can be used to store information about the construct and can be searched using the Search Files capability of GCK (Tutorial 8: Finding Comments). For now just press the Cancel button -- you don't want to make any changes at this time.
8. You should still have the T7 promoter selected as shown in Figure 4. If you do not, then select it again by double-clicking on the segment. First, change the line thickness by choosing Format > Lines > and choosing the third line down. Next add an arrowhead pointing in the clockwise direction by choosing Format > Lines > and choosing the rightward pointing arrow in the second section of the Lines menu.
9. Adjust the arrowhead size by choosing Format > Lines > Size Arrowhead.... You will see Figure 6. Click and drag the mouse in the dialog box to resize the arrowhead. Click OK.
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Figure 6: Size Arrowhead
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10. We now need to adjust the T3 promoter segment to point in the counter-clockwise direction. This can be done by following the same steps we just did for the T7 promoter. Select the lower green segment (T3 promoter) by double-clicking it. If you cannot see this segment in the window, use the scroll-bars to bring it into view. Choose Format > Lines > and select the third line down, choose Format > Lines > and select the leftward pointing arrow. This will add an arrowhead that is the same size as the last arrowhead created so you should have symmetrical arrowheads.
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Figure 7: Modified Bluescript KS+
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11. Finally, choose Construct > Magnification > Fit to Window. This will produce Figure 7.
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