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Help me out with Primer calculation for point mutagenesis....

Primer concentration

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8 replies to this topic

#1 kartiga natarajan

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Posted 21 February 2013 - 06:28 AM

Can u guys plz help me out in preparing stock & working of primers for doing point mutations....

Herewith i have attached the primer details for your suggestions...

Thanks in advance...Posted Image If possible also suggests me with the annealing temperature...

Attached Files



#2 GNANA

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Posted 21 February 2013 - 07:19 AM

you will get 100 micro molar final conc of each primers if you dissolve in the appropriate volume they have mentioned in volume-pmol/microlitre. this will be your stock.

but how i usually do is for mutagenesis i use 125 ng of primers in total. so i would suggest you to dissolve as they mentioned but calculate like below,

for Primer 1 in ur sheet:
594 microlitres will give you 100micromolar final concentration this is one way.... and the other is ,they also mentioned it is 805 micrograms so now if you dissolve 805 mcirograms in 594 volume (just not to alter the universal primer stock conc_100miromolar) this will give you-1.36 micrograms/microlitre (805/594), so now your stock is 1.36 microgram/microlitre or 100micromolar.

to get 100ng/microlitre (working) - 0.1/1.36x100 (total volume) = 7.35

so to prepare 100 ng/microlitre - 7.35 (stock primer)+ 92.65mcirolitres (H2O).

now you can use 1.25 microlitres of each primers per pcr to get 125ng of each primer for a reaction.

good luck....

note: i would go with 63 or 65 as annealing temp for this primer....try out....
I would prefer being perfectionist rather than a passionist in Research.

I always had an alternate hypothesis....

#3 kartiga natarajan

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Posted 21 February 2013 - 08:37 AM

For that primer i went for 68 &55 as annealing temp but that did not workPosted Image ..I will try now with 63 & 65... Posted Image
Thank u so much Posted Image

#4 kartiga natarajan

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Posted 25 February 2013 - 05:58 AM

HI GNANA....
I tried as per ur suggestions...for that 284D primer & for 353 D primer @ 63 & 65...I got some faint band but i dont know whether its my template (100ng) which i have used for the reaction...Give ur suggestions by seeing the picture...so that i may proceed with Dpn1..If u suggest me to go to Restriction...Also give idea abt the reaction i need to follow...Posted Image

Will be waiting for your replyPosted Image

#5 kartiga natarajan

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Posted 25 February 2013 - 06:00 AM

Sorry i forgot to attach my picture & the reaction details...help me outAttached File  S284 & S353 pcr.ppt   127.5KB   138 downloads

#6 kartiga natarajan

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Posted 25 February 2013 - 06:01 AM

Sorry i forgot to attach my picture & the reaction details...help me outAttached File  S284 & S353 pcr.ppt   127.5KB   138 downloads

Regarding Point mutation......

#7 GNANA

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Posted 25 February 2013 - 06:14 AM

when i see comapring the 63 the 65 degree PCR looks like having a faint PCR band...fine, just proceed with Dpn digestion, i dnt know what Dpn you are using, the kit provided? if KITs jus follow as they suggested for Dpn digestion or NEB enzyme? i use NEBs Dpn, which i directly add 1 microlitre or slight over 1 microlitre in the PCR, incubate an hour at 37 degrees then i do purify and proceed for transformation. but purification is just optional. make sure you have good competent cells.
I would prefer being perfectionist rather than a passionist in Research.

I always had an alternate hypothesis....

#8 kartiga natarajan

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Posted 25 February 2013 - 06:24 AM

Me too using Dpn1 from NEB...So Is this reaction ok?

Reaction for 50 microlitre
Pcr Product- 40microlitre
10X NEB buffer4- 5 microlitre
Dpn1-------------1 microlitre
H20----------------4 microlitre

Incubate at 37 for 1 hour...Is this ok? Thanks in advance for your helping handPosted Image

#9 GNANA

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Posted 25 February 2013 - 06:34 AM

ya sounds fine, but since you added 100ng plasmid i would use like 1.2 Dpn for an hour....otherwise i am ok with urs.

good luck...
I would prefer being perfectionist rather than a passionist in Research.

I always had an alternate hypothesis....





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