PrimerDesign

Genetic code Second position | T | C | A | G | ----+--------------+--------------+--------------+--------------+---- | TTT Phe (F) | TCT Ser (S) | TAT Tyr (Y) | TGT Cys (C) | T T | TTC " | TCC " | TAC | TGC | C F | TTA Leu (L) | TCA " | TAA Ter | TGA Ter | A T i | TTG " | TCG " | TAG Ter | TGG Trp (W) | G h r --+--------------+--------------+--------------+--------------+-- i s | CTT Leu (L) | CCT Pro (P) | CAT His (H) | CGT Arg (R) | T r t C | CTC " | CCC " | CAC " | CGC " | C d | CTA " | CCA " | CAA Gln (Q) | CGA " | A P | CTG " | CCG " | CAG " | CGG " | G P o --+--------------+--------------+--------------+--------------+-- o s | ATT Ile (I) | ACT Thr (T) | AAT Asn (N) | AGT Ser (S) | T s i A | ATC " | ACC " | AAC " | AGC " | C i t | ATA " | ACA " | AAA Lys (K) | AGA Arg (R) | A t i | ATG Met (M) | ACG " | AAG " | AGG " | G i o --+--------------+--------------+--------------+--------------+-- o n | GTT Val (V) | GCT Ala (A) | GAT Asp (D) | GGT Gly (G) | T n G | GTC " | GCC " | GAC " | GGC " | C | GTA " | GCA " | GAA Glu (E) | GGA " | A | GTG " | GCG " | GAG " | GGG " | G ----+--------------+--------------+--------------+--------------+----

real time PCR primer design IDT

Alignments (http://molbiol-tools.ca/Alignments.htm)

Oligo calculation(http://www.basic.northwestern.edu/biotools/oligocalc.html)

1) Budovskaya YV et al. PNAS. 102(39):13933-13938, 2005;

(2)Stephan JS et al. PNAS, 106(40): 17049-17054, 2009;

(3) Zheng L, et al. Nucleic Acids Research. 32(14): e115, 2004. An efficient one-step site-directed and site-saturation mutagenesis protocol.

(4)SGD: http://www.yeastgenome.org/

(5) ExPASy translate tool: http://www.expasy.ch/tools/dna.html

(6) Reverse Complement: http://www.bioinformatics.org/sms/rev_comp.html

(7) Restriction enzymes: http://en.wikipedia.org/wiki/Restriction_enzyme

Restriction enzyme list: http://www.genscript.com/cgi-bin/products/enzyme.cgi?op=all_ez

Restriction enzyme: http://www.thelabrat.com/restriction/index.shtml

(8) Restriction site finder: http://www.utmb.edu/scccb/software/sitefind.html

(9) DESIGN PCR PRIMERS: http://molbiol-tools.ca/PCR.htm

(10) Tm calculator: http://www.appliedbiosystems.com/support/techtools/calc/

(11) Reverse complement: http://www.bioinformatics.org/sms/rev_comp.html

(12) webcutter find restriction site: http://rna.lundberg.gu.se/cutter2/

(13) Hydrophobic amino acids: http://www.russell.embl.de/aas/hydrophobic.html

(14) Restriction site finders http://www.restrictionmapper.org/

(15) 10 Tips For Designing PCR Primers That Work

Posted by aliu under SmartNote

Since PCR primer design is one of the most widely used features of DNASIS SmartNote, we did some research and put together a list of the top 10 tips for designing PCR primers that work. When designing oligonucleotide primers for PCR, it is helpful to keep some considerations in mind to optimize the output and specificity of your experiment. Here are some tips gathered from experts to get you started:

1. Design your PCR primers to be 18-30 oligo nucleotides in length. The longer end of this range allows higher specificity and gives you space to add restriction enzyme sites to the primer end for cloning.

2. Make sure the melting temperature (Tm) of the primers used are not more than 5°C different from each other. You can calculate Tm with this formula: Tm = 4(G + C) + 2(A + T)°C

3. Aim for a Tm between 65 and 70°C for each primer over the region of hybridization

4. Use an annealing temperature (Ta) of 10 to 15°C lower than the Tm.

5. The GC content of each primer should be in the range of 40-60% for optimum PCR efficiency.

6. Try to have uniform distribution of G and C nucleotides, as clusters of G’s or C’s can cause non-specific priming.

7. Avoid long runs of the same nucleotide.

8. Check that primers are not self-complementary or complementary to the other primer in the reaction mixture, as this will encourage formation of hairpins and primer dimers and will compete with the template for the use of primer and reagent.

9. If you can, make the 3′ end terminate in C or A, as the 3′ is the end which extends and neither the C or A nucleotide wobbles. This will increases the specificity.

10. You can avoid mispriming by making the 3′ end slightly AT rich.

11. Use the right software. OK, so it’s 11 tips. Using the right software is a great way to automate these steps and minimize errors, especially when you have to design primers for many sequences. DNASIS SmartNote includes several primer design tools and is also a lab notebook that automatically keeps a record of your analysis results. You should definitely give it a try. Click here to sign up a free account.

If you prefer traditional desktop software, take a look at DNASIS Max instead.

References: http://rothlab.ucdavis.edu/protocols/PrimerDesign.html http://www.biochem.ucl.ac.uk/bsm/nmr/protocols/protocols/oligo.html http://www.protocol-online.org/prot/Molecular_Biology/PCR/PCR_Primer/

http://www.mcb.uct.ac.za//pcroptim.htm

(16)quick change mutagenesis PCR kit

WESTERN BLOTTING

The 4 Important Steps for Western Blot Quantification

Reliable Quantification of Western Blot Data

A Defined Methodology for Reliable Quantification of WesternBlot Data

Softwares for Western Blot quantification

Image J; Scion Image Software (Scion, Frederick, MD); Quantity One; LI-COR system; FluorChem FC2 ;

Total protein stains, such as Flamingo Pink, Sypro Ruby, Amido Black, or Ponceau S

How to quantify images of western blot bands?