2.1 Dimer formation Primer dimers are formed when primers bind to each other without binding to the target template [12]. Homodimers and heterodimers are the two types of primer dimers [13]. A homodimer is formed when two identical primers bind, whereas a heterodimer is formed when two prim...
Solving Primer Dimer Problems Change all the sequencing reagents and water for a fresh batch. Also clean the pipettors as they can also be the cause of the primer dimer contamination. Raise the annealing temperature and/or use a shorter annealing time. Use different primers for sequencing that ...
Even a small number of primer-dimers can result in false-negatives and/or false-positives. Herein, we demonstrate a new class of primer technology that greatly reduces primer-dimer propagation, showing successful amplification of 60 template copies with no signal dampening in a background of 150,...
AnalysisEnter up to 10 sequences at a time, and the tool returns values for all major physical properties, such as molecular weight, melting temperature, secondary structure, and primer dimer formation (secondary structure and primer dimer formation information provided in simple-t...
The results show tight control of primer-dimer artifacts, even in highly multiplexed assays. Total reaction volumes were 50 µL, with 10 ng of genomic DNA template or no template as controls. RNase H2 was present in all reactions, but has no functional role in PCRs with standard primers...
One major challenge in the design of highly multiplexed PCR primer sets is the large number of potential primer dimer species that grows quadratically with the number of primers to be designed. Simultaneously, there are exponentially many choices for multiplex primer sequence selection, resulting in...
(10 μL) by electrophoresis on a 3.5% high resolution agarose gel in 1X TAE stained with dye for detecting dsDNA. Gene specific sncRNA amplicons should form discrete ~75 bp bands that are easily distinguished from smaller primer-dimer bands that may be seen in the no-template control ...
Gene specific sncRNA amplicons should form discrete ~75 bp bands that are easily distinguished from smaller primer-dimer bands that may be seen in the no-template control reaction. 3. End-point PCR can be used for qualitative determination of differences in the expression of a given sncRNA ...
dimer structures. We have recently shown experimentally that hairpin loops, if present, can greatly reduce the efficiency of the reaction by limiting primer availability and the ability to bind to the target site (Singh et al., 2000). The effect of primer-template mismatches on the PCR has ...
As the value is de- pendent upon the amount of oligos and the amount of template, it is difficult to calculate this value (given cDNA is used as a template). Primer3 claims that the default (50 nM) works well for most applications. Instruction: For the Poplar example, default is ok....