A. We have documented Biotin-AA-dCTP (N-5002) incorporating at a very high percent substitution for dCTP, up to 97%, in our white paper: PCR incorporation of modified dNTPs: the substrate properties of biotinylated dNTPs. We do not have analagous PCR data on the efficiency of the N4-Biotin-OBEA-dCTP (N-5004), but since the modification is to the N4 nitrogen, it may interfere with Watson-Crick base pairing. Therefore, while this dCTP analog can be incorporated in PCR, the percent substitution for dCTP may not be as high as for Biotin-AA-dCTP.
As you eluded to, different analogs will incorporate in PCR with varying efficiency and some optimization may be needed. We recommend performing some initial PCR experiments using natural:modified dNTPs in ratios such as 1:0, 3:1, 1:1, 1:3 and 0:1 to identify the best conditions for modified nucleotide incorporation with robust amplicon yield.

We do not detect tritium labels by gel. Our standard radioactive labeling process includes purification by our double HPLC method, PAGE analysis (of the DNA sequence) and isotopic purity as determined by HPLC. We do not use photoimagers. However, this link may be helpful: http://imagers.salk.edu/pimager/pimFAQ.html It contains a section on Westerns, which describes a special screen to use for tritium detection. Tritium is low energy so you cannot do direct autoradiography.

A. CleanAmp™ dNTPs can be used with a broad selection of DNA polymerases including Taq, Pfu, Pfu (exo-), Dynazyme™, Deep VentR™, Tth and Tfi. When using CleanAmp™ dNTPs with these polymerases, all were able to produce the desired amplicon. Learn More…

A. No, CleanAmp™ dNTPs are reverted back to the corresponding standard dNTP prior to being incorporated into the amplicon.  The 3’-hydroxyl modification blocks enzyme incorporation until it is removed during heat activation.  After heat activation, the enzyme efficiently incorporates the corresponding standard dNTP.

A. A phosphoramidite is the actual building block we use to chemically synthesize oligonucleotides. It usually consists of a protected nucleoside with a 3’ phosphitylating reagent, where phosphorus is in the trivalent state and protected with a stable amine and ester. Learn More…

Q. Can I buy linker reagents directly from TriLink?
A. Yes, click here to view the reagents still sold through TriLink. All of our other DNA synthesis reagents are now sold through Glen Research.

Q. Can TriLink label nucleotides with a DNA intercalating dye (e.g. Thiazole Orange)?

A. Yes, we are able to label nucleotides with a DNA intercalating dye. Using TriLink’s custom synthesis service, we can conjugate your dye of choice to dNTPs containing the appropriate linker. Read More…

Q. Does TriLink provide LNA modified oligonucleotides?

A. Yes, we are able to synthesize LNA modified oligonucleotides, however there are a few stipulations. Since this material is under license by Exiqon we require that our customers obtain a license from Exiqon, purchase the LNA amidites and have the material shipped to our facility for synthesis.

Q. Why does the price of trimer modified oligonucleotides vary?

A. Trimer modification requires a highly custom synthesis protocol in which multiple additional factors are taken into account. Each trimer mix job is individually analyzed in order to provide the most cost effective pricing in terms of synthesis cost and trimer amidite usage. Read More…

A. CleanAmp™ dNTPs are able to decrease the formation of primer dimer products while increasing the specificity of the desired product better than unmodified dNTPs. Use of CleanAmp™ dNTPs also reduces data fluctuation, giving a more consistent PCR result.