Gene Designer by DNA 2.0 Tutorial
Prepared by: Angela Dixon
Table of Contents
Getting Started (2)
Library Explorer (2)
New Elements (2)
Design Toolbox (4)
Vectors (5)
Codon Table Library (6)
Codon Optimization (8)
Find Panel (9)
Motifs (10)
Restriction Sites (10)
ORF’s (10)
Icon View (11)
Sequence View (11)
Designing (14)
Tools (14)
Back Translate (14)
Cloning Tool (15)
Design sequencing oligos (17)
Order gene/Request quote (17)
Configure (18)
Restriction Sites (18)
Back Translation Profiles (19)
Motifs (19)
Default Codon Table (20)
1
Getting Started
-Go to www.dna20
-Under the tab Scientific Resources, select Gene Designer
-Click on the Download Now icon
-Create an Account
-
Click on the Install Now icon
-An activation key will be sent to your email address.
-Once you have it installed and activated, open Gene Designer
Library Explorer
The Library Explorer should automatically pop up when you open Gene Designer.  It is a floating icon.
New Elements
Under the New Elements tab you have the options to add:
∙New DNA Element
∙New AA Element
∙New ORF
∙New Design Construct
∙New Folder/Group
∙New Codon Usage Table
3
Add New DNA Element:
1. Click and drag icon from Library
Explorer onto desired window pane
2. Name your new DNA Element
3. Pick a color for your DNA
4. Input the DNA sequence (GATC)
5. Select Orientation
6. Add any notes
7. Click OK
Add New AA Element:
pane1. Click and drag icon from Library
Explorer onto desired window pane
2. Name your new Amino Acid Element
3. Pick a color for your AA sequence
4. Input the AA sequence (GAVLIPMFYWSTCNQKHRDE)
5. Select Orientation
6. Add any notes
7. Click OK
Add New ORF Element:
1. Click and drag icon from Library
Explorer onto desired window pane
2. Name your new Open Reading Frame
Element
3. Pick a color for your ORF
4. Input the DNA sequence (GATC)
5. Select which frame to start reading
6. The corresponding AA sequence will
appear
7. Select whether or not to keep the
original DNA sequence
8. Select Orientation
9. Add any notes
10. Click OK
Add New Construct:
1.Click and drag icon from Library Explorer onto desired window pane
2.Name your new construct
3.Choose if you want it to be circular or linear
4.Add any notes
5.Click OK
6.Your new construct will appear in a new window pane.
Add New Folder/Group:
1.Click and drag icon from Library Explorer onto desired window pane
2.Name your new folder
3.Choose a color
4.Click OK
5.Your new folder will appear under the construct you placed it in. Design Toolbox
The design toolbox has built-in DNA elements available for your projects. Prokaryotic Regulatory Elements
>Transcription
>Promoters
>Operators
>Terminators
>Translation
>RBS
>Replication
Eukaryotic Regulatory Elements
>Transcription
>Enhancers
>Promoters
>Terminators
>Polyadenylation signal sequence
>Translation
>5’UTR
>Initiation Context
>IRES
>Replication
5
Fusion Tags
>Expression of Membrane Proteins (N-terminal Fusion Tags)
>Epitope Tags
>Solubility and Purification Tags
>Protease Cleavage Sites
>Secretion Signals
>Imaging TAGS
Vector Components
>Regulatory Proteins
>Antibiotic Resistance Markers
>Counter-Selectable Markers
Vectors
Under the Vectors tab in the Library Explorer, built-in vectors are available for your use. pT7-SNAP
pT7-SNAP is an E. coli  expression plasmid encoding
SNAP26b, a SNAP-tag protein, which can be expressed
under the T7 promoter. This plasmid is intended to be
used for the expression of SNAP-tag protein fusions for
tighter control of protein expression. It can also be used
as a control plasmid expressing the SNAP-tag alone. The
fusion partner should be cloned as a fusion to the C-
Terminus of the SNAP-tag.
pMCPm™
pMCPm ™ is a mammalian expression plasmid encoding
MCP, an MCP-tag polypeptide, which is expressed under
the CMV promoter. This plasmid is intended for the
cloning and expression of MCP-tag protein fusions in
mammalian cells. pMCPm contains two multiple cloning
sites to allow cloning of the fusion partner as a fusion to
the C-Terminus of the MCP-tag and an appropriate
signal peptide to the N-Terminus of the MCP-tag.

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