Using Vector NTI Advance™ 10.

¾ Opening Vector NTI Advance™ 10.0

1. On your Windows® desktop, click on the Start button.
2. Select Programs > Invitrogen > Vector NTI Advance 10 to open the menu of
Vector NTI Advance™ modules.
3. Select Vector NTI Explorer to open the Explorer or Vector NTI to open the
Molecule Viewer,as shown in Figure 1.

Molecule Viewer

Vector NTI Explorer

Figure 1. Opening the Molecule Viewer and Vector NTI Explorer.

¾ Vector NTI Explorer
Vector NTI Explorer is the main tool for accessing the information in your local Vector
NTI Advance™ database. Using the Explorer, you can import, open, export, and organize
molecules and other database items, and launch other Vector NTI Advance™ modules (Figure 2).
To launch Vector NTI Explorer:

• In the Molecule Viewer, click on the Local Database icon ( ), or

• From the Windows® Start menu, select Programs > > Invitrogen > Vector NTI
Advance 10 > Vector NTI Explorer.

Local/Shared Copy
Data Exchange Paste
Search New
Edit
Dismiss subset
Rename
New subset Delete
Forward Properties
Back View mode

List of subbases Camera

Database object
type

List of
database
records

Figure 2. Vector NTI Explorer Window

Figure 3. List of object types.
¾ Molecule Viewer
The Molecule Viewer displays information about DNA, RNA, and protein molecules. To
launch the Molecule Viewer:

• From the Windows® Start menu, select Programs > Invitrogen> Vector NTI
Advance 10 > Vector NTI, or
• Double-click on a molecule name in the Vector NTI Explorer.
To open a molecule from within the Molecule Viewer, click on the Open button ( ) on
the main toolbar and select the molecule name from the dialog box.

The molecule will be loaded into the Molecule Viewer.

Pane-specific
Text Pane Graphics Pane
(info about
features,
restriction
site, etc.)

Sequence Pane

Figure 4. Molecule Viewer window

Graphics Pane Sequence Pane

Display Setup
Text Pane
View Molecule
Fragment

Figure 5. Pane-specific
 Expand Branch

Expand Folder Collapse Branch

Link Panes Delete Annotation

Find Add to Oligo list

Figure 6. Text Pane

Zoom In Zoom Out

Linear Display Fit to Window

Circular Display Standard Arrangement

Translate Direct
Find
Translate Complementary
Graphics Display
Setup Edit Picture
Add Feature Add Annotation

Figure 7. Graphics Pane

Show Both Strands Translate Direct

Paste Translate Complementary

Erase Translations
Copy
Bold
Cut
Italic
Graphics Display Underline Background
Setup Font Color
Font Size
Add Feature
Font Name Font Color

Figure 8. Sequence pane

¾ Create a Molecule Display Window
There are 2 different ways of creating new DNA/RNA in Vector NTI:

• Importing from GenBank/GenPept, EMBL/SWISS-PROT and FASTA formats.

The sequence and Feature map are converted from the file, and the new
molecule becomes part of the Vector NTI database.
1. Open the Vector NTI Explorer.

2. Select the
DNA/RNA Molecules
(Main) within the
database table
combo box.

3. Select the Import

and click the Molecule
from Text file…

4. Import molecules from

GenBank/GenPept,
EMBL/SWISS-PROT 5. Click OK.
and FASTA formats.

6. Choose the file that

you want to import and
click Open.

7. Create a new Subset Name

and click OK.
8. On General page, create the 9. Select the molecule type on DNA/RNA
name of vector in this box. molecule page and click OK.

10. Double click the created file to open.

11. The result is showed

in Molecule Viewer.
 • Creating new molecules from user-defined nucleotide sequences. These can be
manually entered or pasted from the clipboard and the sequence entered as a
new molecule.

1. Open File > Create New Sequence >

Using Sequence Editor (DNA/RNA)…
within the Molecule Viewer.

2. On General page, create the

name of vector in this box.

3. On Sequence and Maps, click Edit

sequence…to add the nucleotide sequences.

4. Paste nucleotide sequences

in this area.

5. Click OK to create
new molecule.
 ¾ Working with a Molecule’s Graphical Representation

Vector NTI also lets you manually format graphical maps and change the predefined
display style for elements of feature and restriction maps. You can also change the shape
and drawing style of features, move and format text, add text annotations, etc.

A. Add features within molecule

1. Select Graphics Pane. 2. Click Add Feature.

3. Choose the Feature.

4. Create the Feature Name.

5. Add the Position of Feature.

6. Select Complementary
when you want to change the
direction of the feature in the
molecule.

7. Click OK.
Show the information of each
feature in the Feature Map.

Show graphical maps in the Graphics Pane.

 B. Change the Graphics Display

There are 2 different ways of Change the Graphics Display in Vector NTI:

• Change the Graphics Display, click on the Graphics Display Setup ( ) on

the main toolbar.
1. Select the feature that you want to
2. Click Graphics Display Setup. change the graphics display.

Show the
Feature type

3. To modify a feature, click More…

4. Change Font, Font style, Size and

Color of Font, click Font…

5. Click OK.
 9. Click OK to close the dialog box.

7. On the Fill page, select a

color from the color menu.

6. To change the Symbol style,

click the More…
8. Click OK.
 • The other way, click on the Edit Picture ( ) on the main toolbar.

1. Click Edit Picture.

2. Select the feature that you want to change the

graphics display and right click to choose Properties.

3. On the Fill page, select a color

from the color menu.

5. Click OK. to close the dialog box.

4. On the Shape page,

select a shape from the
shape menu.
 Show the result.

¾ Generating Restriction Maps

Restriction maps of DNA/RNA molecules can be quickly generated in Vector NTI. For
unsequenced molecule regions, you may enter the known positions of restriction sites. All
the molecule descendants inherit these sites.

There are 2 different ways of Generating Restriction Maps in Vector NTI:

• Generating Restriction Maps, select Analyses > Restriction Analyses >

Restriction Site…to open the Restriction Map Setup dialog box.
 • Click on the Display Setup ( ) on the main toolbar to open the Molecule
Display Setup dialog box.

1. Click Display Setup.

2. Select RMap Setup… to open

Restriction Map Setup dialog box.

3. Click <Add… to choose

the restriction enzyme.
4. Choose the restriction
enzyme and click OK.

5. Click OK > OK
to close the dialog
box.

Show the NdeI

restriction enzyme
that you chose
Show the information of each restriction
enzyme in the Restriction Map.

Display the Restriction Map

within the molecule on the
Graphic Pane.

Restriction site is shown

on the Sequence pane.
 ¾ Primers Design and PCR Analysis
Vector NTI can design PCR primers, sequencing primers and hybridization probes and
save them to the database for future use. Using parameters you have defined, Vector NTI
can analyze those primers and probes or those you have defined yourself to determine the
best ones for optimal experimental results.

3. Select Analyses > Primer Design > Find PCR Primers…to

open the Find Primers in Selected Region of DNA template
dialog box.

1. Open DNA template file

from the Local Database.

4. Edit the Product Length 2. Choose the gene of

(for example, up to maximum). interest to design primers.

5. Click More >> to attach to 5’terminus of primers.

 7. Choose the restriction enzyme to
design Sense Primer and Antisense
Primer and then click OK.

6. Click … to open the Choose Database Enzyme dialog box.

8. Click OK to close the box.

 Vector NTI generates a number of primer options that satisfy
the conditions previously defined in the PCR Analysis.

10. Select View> PCR Product > Save All

PCR Products to Database…to enter the
prefix for PCR Product(s) name(s) box.

9. Highlight the PCR product.

11. Create the PCR product name.

12. Click OK.

13. Insert the molecule into subset

in the Local Database and click OK.
 14. Open the Local Database.

15. Double click this file to open

on Molcule Viewer.

Show the information of each The PCR product is displayed

primer in the Feature Map > on Graphics Pane.
Primer.

The Sequence of PCR product is displayed on Sequence Pane.

 ¾ Molecule Construction
Construction means creating a DNA molecule from fragments that are completely defined
and made compatible by the user.

1. Open the first fragment 2. Then open the second molecule

from Local Database. from Local Database again.

Two display windows are now open.

3. Select List > Show Lists to

open the Lists dialog box.
 • Define the First Fragment.

4. Press Add > Add Fragment > of the name of the molecule of interest
(First Fragment) to open the Fragment Wizard dialog box.

5. Select the Construction Fragment option,

leave the Insert Inverted option unchecked
and click the Next > to proceed.

6. Define the 5’ terminus of the

new fragment, click on the
restriction site label in the
Graphics Pane and click the
Next> in the dialog box to
proceed.

7. Define the 3’ terminus of the new fragment,

hold down the SHIFT key and click on the
restriction site label in the Graphics Pane and
click the Finish in this screen to complete the
definition of the fragment.

8. Click the Add to List to add the first fragment to the list.
 • Define the Second Fragment.

9. Press Add > Add Fragment > of the name of the molecule of interest
(Second Fragment) to open the Fragment Wizard dialog box.

10. Select the Construction Fragment

option, choose the Insert Inverted option
checked, and click the Next> to proceed.

11. Define the 5’ terminus,

click on the restriction site
label in the Graphics Pane and
click the Next> in the dialog
box to proceed.

12. Define the 3’ terminus, hold down the SHIFT

key and click on the restriction site label in the
Graphics Pane and click the Finish in this
screen to complete the definition of the
fragment.

13. Click the Add to List to add the second fragment to the list.
 15. Click Run to create the new DNA molecules.

14. Select the two fragments.

17. Check this part to create all possible

constructs with compatible fragment.

18. Click Construct to create

the new DNA molecules.

16. Create the name of the construct molecules.

20. Click Yes to create constructs.

19. Insert the molecule into subset in

the Local Database and click OK.
 The two fragments that you used to make this molecule are listed in the Component
Fragments. Their subfolders describe the left and right termini of each fragment.

The new molecule is displayed and changed graphic display on the Graphics Pane.