Hello Bionetters.
It has been recently suggested that a searchable database of primers
for PCR will be set. The basic idea behind this database is that only
___TESTED_&_WORKING___ (!!!) primers should be contained. This may save
many valuable planning and working hours, as well as money. We all know
that even carefully planned primers fail to operate when it comes down
to the tubes...
Dan Jacobson from the Johns Hopkins Univ. GDB, and your humble servant, are
now working on the establishment of this database as a gopher server.
Cited below is the suggested basic form for this database. We now open a
discussion regarding the suggested data fields. We are interested in hearing
your opinions regarding this form.
Please pay attention to the following:
1. This message has been cross posted to several bionet.xxxx groups. It is
suggested however, that the thread will be maintained in bionet.molbio.
methds-reagnts . This will make it easier to read and respond to everyone's
followups.
2. A followup to the newsgroup is prefferred over direct responses in the
Email, so as to keep the thread open. If, for any reason you want to contact
us directly, Dan's address is: danj at gdb.org, my @ is: pc386 at ccsg.tau.ac.il
We hope that this thread will be constructive, and that the database will be
'on the air' as soon as possible.
Greetings,
Dan Jacobson,
Benny Shomer.
This is the suggested form:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Primer Name: ______________________________
Target Gene: ______________________________________________________________
Species: ___________________________
Direction: { FOR / REV }
Matching Primer(s) in this database: _________________________________
Sequence (5' --> 3'): ___________________________
Length: __
Flanking bases ______ to _____ on the target sequence.
Product Length (cDNA):_______
Product Length (genomic):_______
{Lengths are in bp, or 0 for inverse PCR, where length is unknown}
Restriction Site Added: _____________
Mutation presented at base: __
Special Applications: { Inverse/ RT-PCR/ Sequencing/ Cloning/ Mutation/
/ Ligation Mediated}
__________________________________________________________________________
__________________________________________________________________________
******************** Cycle Conditions *********************************
Hot Start: {Yes/No}
Initial Denaturation- Temp: __
Time: ____
Denaturation - Temp: __
Time: ____
Annealing - Temp: __
Time: ____
Extension - Temp: __
Time: ____
Number Of Cycles: __
Final Extension - Temp: __
Time: ____
********************** Buffer Constituents ****************************
(This section basically regards non-standard buffer constituents)
Reaction Volume (ul): __
Used Standard Buffer Supplied By: _______________
MgCl2 Concentration (mM): __
DMSO Concentration (%): __
Formamide Concentration (%): __
Gelatin Concentration (%): __
dNTP's Concentration (uM): __
Primers Concentration (uM): __
Polymerase Type: ___________
Polymerase Concentration (U/Rxn.): ___
Make: _____________
**************************************************************************
Submitting Author.
Name: __________________________________
Institution: ______________________________________________________________
__________________________________________________________________________
Address: _________________________________________________________________
__________________________________________________________________________
E-mail : ________________________________
Fax# : ______________________
References:
__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________
Remarks:
__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
**************************************************************
* Benny Shomer *
* Tel-Aviv University *
* Sackler School of Medicine, Dept.of Embryology and Teratology*
*--------------------------------------------------------------*
* Snail: Ramat-Aviv , Tel-Aviv 69978 , Israel. *
* E-mail : pc386 at ccsg.tau.ac.il *
* Tel : 972-3-640-9238 FAX : 972-3-642-2046 *
* *
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