Online
|
Download
|
Store
|
Contact
|
About


Primo In Vitro 3.4: In Vitro Translation / Transcription Design           Click here for more PCR primer design tools.
Applet runs on Java-enabled browsers
PC: Internet Explorer 5.5 or higher and Netscape 4.08 or higher
Mac: Internet Explorer 5.0, IE5.1.4 or higher (IE5.1 will not work because of a bug.)
Need to find better siRNA target sequences? Please visit our SVM RNAi 3.6 for rational siRNA design. Improve your success rate with machine learning.
The Electronic Protocol Book Table of contents BioToolKit 300 Download Trials
     An electronic protocol book with 500 protocols and 100 recipes. A great quick and practical reference for bench scientists as well as for new students.   Get A Copy      A collection of tools frequently used by bench biomedical scientists, ranging from centrifugation force conversion, molecular weight, OD, recipe calculators, to clinical calculators. Include all Primo 3.4, Abie 3.0, Heatmap Viewer, MicroHelper, Godlist Manager, label printing, and grade book.   More info


Primo In Vitro 3.4 --- In Vitro Transcription / Translation Primer Design

Primo In Vitro 3.4 is for designing of oligos/primers for in vitro transcription or in vitro translation. There are three frequently used methods for in vitro transcription / translation.

The first is to PCR amplify the target sequence and attach a bacterial promoter sequence (e.g., T7, T3 or Sp6) to one of the primers. The PCR product is purified. The purification step is optional, but it may limit carry-over contraindications of RNase from template DNA. The PCR product is added to in vitro transcription / translation reaction mixture. Commonly used reagents for in vitro transcription and translation are Rabbit Reticulocyte Lysate and Wheat Germ Extract.

The second is to clone the target sequences into a vector with bacterial promoter (e.g., T7, T3 or Sp6). Usually such vectors (e.g., pBluescript, pGem, and pDP) have two promoters on the opposite ends of their multiple cloning sites (MCS).

The third is for transcribe short sequences ( e.g., siRNA, shRNA). Two oligos are synthesized and annealed. Only the promoter region is double-stranded in the annealed sequences.

How to use Primo In Vitro 3.4 --- In Vitro Transcription / Translation Primer Design (beta-testing)

  • Input your DNA sequences by copy and paste. Numbers and blank spaces will be ignored. Degenerate nucleotide codes can be accepted.
  • Select you promoter (T3, T7, or Sp6) or vector type (pBlueScript, pGEMX, or pDP). The promoter sequence or vector multiple cloning site (MCS) sequence will be shown next to the promoter / vector name. If you would like to modify the promoter sequence or use a different MCS, please change the sequence in this text field.

    Warning: The software will use the sequence from the text field as your desired promoter or vector MCS sequence. If you don't intend to change the default settings, please don't type in the text field.

  • For cloning into a vector, restriction sites may be added to the two ends or the primers. Select appropriate options and restriction enzymes. Enzymes list in the menu are some of the frequently used and most have high activities in PCR reaction buffer.
  • Click on the "Go" button to start.
  • For multiple sequences, please check the "Batch mode" checkbox, and input your sequences in the following format:
    
    >Name of Sequence 1
    
    1 ggccgggcgc ggtggctcac gcctgtaatc ccagcacttt gggaggccga ggcgggtgga
    61 tcacctgagg tcaggagttc gagaccagcc tggccaacat ggtgaaaccc cgtctctact
    121 aaaaatacaa aaattagccg ggcgtggtgg cgggcgcctg taatcccagc tactcgggag
    181 gctgaggcag gagaatcgct tgaacccggg aggcggaggt tgcagtgagc cgagatcgcg
    241 ccactgcact ccagcctggg caacaagagc gaaactccgt ctcaaaaaaa a
    
    >Name of Sequence 2
    aaaaatacaa aaattagccg ggcgtggtgg cgggcgcctg taatcccagc tactcgggag
    gctgaggcag gagaatcgct tgaacccggg aggcggaggt tgcagtgagc cgagatcgcg
    ccactgcact ccagcctggg caacaagagc gaaactccgt ctcaaaaaaa a
    
    >Name of Sequence 3
    61 tcacctgagg tcaggagttc gagaccagcc tggccaacat ggtgaaaccc cgtctctact
    121 aaaaatacaa aaattagccg ggcgtggtgg cgggcgcctg taatcccagc tactcgggag
    181 gctgaggcag gagaatcgct tgaacccggg aggcggaggt tgcagtg
    
    
    Warning: If the "Batch mode" checkbox is not checked, multiple sequences will be treated as one sequence.

  • For in vitro transcription of short sequences (e.g., small interfering RNA -- siRNA), PCR may not be needed. One option is to synthesize two oligos and anneal the two oligos to form a functional promoter.
  • For melting temperature calculation, the nearest neighbor formula is the default.

    For more PCR primer design tools, please visit Primo Home.

    Thanks for using Primo In Vitro 3.4! Please let us know your suggestions and comments.

  • THIS SOFTWARE IS PROVIDED BY CHANG BIOSCIENCE ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL CHANG BIOSCIENCE OR ITS SPONSORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.


    Copyright 2002-2004 Chang Bioscience, Inc. All rights reserved.