LAMP primer designing software [PrimerExplorer] Loop-mediated Isothermal Amplification HOME
PrimerExplorer
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Eiken GENOME SITE
EIKEN CHEMICAL CO., LTD.
PrimerExplorer Instrucitons
[1]Introduction (operating environment)
[2]Operation of each screen (designing regular primers/designing loop primers)
[3]Appendix
2. Operation of each screen (designing loop primers)
to designing regular primers
1. Enter the primer information file
Select the primer information file for the loop primer designing, which was saved in the regular primer designing.
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2. Loop primer design

Basic procedure for the loop primer design is as follows.

  1. Click on [Generate] button to generate the loop primer candidates.
  2. Select the page number for the display of primer list and click on [Display] button.
Loop primer designing page
(1) [Generate] Generate the primer sets.
(2) [Display] List the generated primer sets in a new window.
(3) Page Select the page number for the display of primer list, in which up to 100 primer candidates can be listed in one page.
Specify the parameter setting by inputting the appropriate number or clicking on [-] or [+] button beside the number entry field to change the input value.
Loop Primer Setting
(4) Length Minimum and maximum length of the loop primer
(5) Tm Minimum and maximum Tm value of the loop primer
(6) Limitations Maximum number of combinations when primer set is generated.
LF/LB
The number of LB (LF) candidates which can combine with each LF (LB) when generating LF and LB sets.
Sets
Number of the finally generated primer sets.
(7) GC rate(%) Acceptable value for GC rate
(8) dG threshold Generated primers that meet the following criteria are selected as candidates
Dimer check
the primer's dimer forming potential (dG)
(stability between the combined primers) is more than this value.
3'stability
its 3' stability value (dG) is below this value.
(9)
 Reset Parameter Reset parameter value to the default condition.
Primer Setting
(10) Experimental
Conditions		 Concentration of
oligo[microM]
Oligo-nucleotide (µM)
Na+[mM]
Sodium ion (mM)
Mg2+[mM]
Magnesium ion (mM)
(11) dG threshold
[Kcal/mol]		 dG threshold
5'stability
5' stability
3'stability
3' stability
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3. Loop primer list
Up to 100 generated loop primers sets will be listed in each page.

Each row stands for one loop primer set, and each loop primer fragment's location refers to the target sequence above directly.
Check the box (left-side each loop primer set) and click on [Details] button (top of the page), then the detail information of the selected loop primers will be displayed.
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4. Detail information of the loop primer sets

The loop primer's information below is shown.

  • LF
  • LB

The following information is shown with each loop primer fragment.

  • Name
  • The position of 5' end on the target sequence
  • The position of 3' end on the target sequence
  • Length
  • Tm value
  • Stability of 5' end
  • Stability of 3' end
  • GC rate
  • Loop Primer sequence
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[1]Introduction (operating environment)
[2]Operation of each screen (designing regular primers/designing loop primers)
[3]Appendix
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