Primer

Part:BBa_K4712086

Designed by: Ke Zhang   Group: iGEM23_SMS-Shenzhen   (2023-09-29)
Revision as of 12:56, 12 October 2023 by AvA0607 (Talk | contribs)


Cd-F1

The primers were designed using NCBI BLAST and SanpGene to achieve efficient and specific amplification. This primer in RPA serves as the initial binding point for the amplification process, ensuring the specificity of the reaction by targeting the desired Corynebacterium diphtheria DNA or RNA sequences. The primers provided data for mathematical modeling for further primer design.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Protocol: Apparatus: Thermal Cycler, Centrifuge, Fluorescence Quantitative PCR Instrument (Ya Rui), 2mL reaction tube, Pipette and Pipette Tip Materials: 1. DNA Isothermal Amplification Reagent Kit (EasyGene Biotechnology) 2. ddH2O 3. Isothermal Amplification Specific Primers: 

 <tr>
   <th>H5N1-F1</th>
   <th>H5N1-R1</th>
   <th>H5N1-F2</th>
   <th>H5N1-R2</th>
   <th>H5N1-F3</th>
   <th>H5N1-R3</th>
   <th>H5N1-F4</th>
   <th>H5N1-R4</th>
 </tr>

 <tr>
   <td>H5N6-F1</td>
   <td>H5N6-R1</td>
   <td>H5N6-F2</td>
   <td>H5N6-R2</td>
   <td>H5N6-F3</td>
   <td>H5N6-R3</td>
   <td>H5N6-F4</td>
   <td>H5N6-R4</td>
 </tr>
 <tr>
   <td>Mtu-F1</td>
   <td>Mtu-R1</td>
   <td>Mtu-F2</td>
   <td>Mtu-R2</td>
   <td>Mtu-F3</td>
   <td>Mtu-R3</td>
   <td>Mtu-F4</td>
   <td>Mtu-R4</td>
 </tr>
 <tr>
   <td>NME-F1</td>
   <td>NME-R1</td>
   <td>NME-F2</td>
   <td>NME-R2</td>
   <td>NME-F3</td>
   <td>NME-R3</td>
   <td>NME-F4</td>
   <td>NME-R4</td>
 </tr>
 <tr>
   <td>SARS-CoV-F1</td>
   <td>SARS-CoV-R1</td>
   <td>SARS-CoV-F2</td>
   <td>SARS-CoV-R2</td>
   <td>SARS-CoV-F3</td>
   <td>SARS-CoV-R3</td>
   <td>SARS-CoV-F4</td>
   <td>SARS-CoV-R4</td>
 </tr>
 <tr>
   <td>SARS-CoV-F5</td>
   <td>SARS-CoV-R5</td>
   <td>SARS-CoV-F6</td>
   <td>SARS-CoV-R6</td>
   <td>SARS-CoV-F7</td>
   <td>SARS-CoV-R7</td>
   <td>SARS-CoV-F8</td>
   <td>SARS-CoV-R8</td>
 </tr>
 <tr>
   <td>Cd-F1</td>
   <td>Cd-R1</td>
   <td>Cd-F2</td>
   <td>Cd-R2</td>
   <td>Cd-F3</td>
   <td>Cd-R3</td>
   <td></td>
   <td></td>
 </tr>
 <tr>
   <td>SP-F1</td>
   <td>SP-R1</td>
   <td>SP-F2</td>
   <td>SP-R2</td>
   <td>SP-F3</td>
   <td>SP-R3</td>
   <td>SP-F4</td>
   <td>SP-R4</td>
 </tr>
 <tr>
   <td>HAdV-B-F1</td>
   <td>HAdV-B-R1</td>
   <td>HAdV-B-F2</td>
   <td>HAdV-B-R2</td>
   <td>HAdV-B-F3</td>
   <td>HAdV-B-R3</td>
   <td>HAdV-B-F4</td>
   <td>HAdV-B-R4</td>
 </tr>
 <tr>
   <td>HAdV-C-F1</td>
   <td>HAdV-C-R1</td>
   <td>HAdV-C-F2</td>
   <td>HAdV-C-R2</td>
   <td>HAdV-C-F3</td>
   <td>HAdV-C-R3</td>
   <td></td>
   <td></td>
 </tr>

</tbody> </table>

4. DL500 marker 5. Test Sample: DNA Template（pUC57-M1）Concentration：1000cps/μL Storage: -20℃ Methods: 1. For a 20μL reaction system: 

 <tr>
   <th>Reagent</th>
   <th>Stock Concentration</th>
   <th>Volume Added（μL）</th>
 </tr>

 <tr>
   <td>Forward Primer</td>
   <td>10μM</td>
   <td>1</td>
 </tr>
 <tr>
   <td>Reverse Primer</td>
   <td>10μM</td>
   <td>1</td>
 </tr>
 <tr>
   <td>Rehydration Buffer (2X)</td>
   <td></td>
   <td>10</td>
 </tr>
 <tr>
   <td>DNA Template</td>
   <td>10nM/L</td>
   <td>2</td>
 </tr>
 <tr>
   <td>ddH2O</td>
   <td></td>
   <td>To 18</td>
 </tr>
 <tr>
   <td>Starter (10X)</td>
   <td></td>
   <td>2</td>
 </tr>

</tbody> </table>

2. Gently tap to mix several times, briefly centrifuge, repeat 3 times (mix gently to avoid vigorous vortexing). 3. Incubate at 37°C for 20 minutes. 4. After heating at 65°C for 10 minutes, proceed to gel electrophoresis. Results:

fig7g.png

(g) Electrophoresis of RPA Primer Screening for Corynebacterium diphtheriae (Cd)

fig9d.png

The figure above correspond to the fluorescence intensity of crRNA targeting Severe acute respiratory Corynebacterium diphtheriae after CRISPR reaction under Bright and UV illumination. The figure utilize pseudocolor to facilitate analysis using software (Image Lab 6). No crRNA is added into negative control. The concentration of DNA template is 10nM/L.

fig8d.png

The linear graphs sequentially correspond to the efficiency verification of crRNAs targeting the DNA sequences of Corynebacterium diphtheriae pathogen. No crRNA is added into negative control. The concentration of DNA template is 10nM/L.

fig10e-right.png

Linear graphs and figure correspond to the fluorescence intensity of crRNAs targeting Corynebacterium diphtheriae pathogen after one-tube reaction of RPA and CRISPR under Bright and UV illumination. The figures utilize pseudocolor to facilitate analysis using software (Image Lab 6). No crRNA is added into negative control. The concentration of DNA template is 10nM/L.

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