I am wondering if the primer could spontaneously be detached from its target (either RNA or DNA) if the concentration of unbound primers drops. In other words, is there an equilibrium between bound and unbound molecules?
I think the conc.does not influence much the target DNA binding on slight change in concentraion,as pico mole conc.is sufficient,its dtection is not so easy if it happens due to this.....
Yes, there is always equilibrium between bound and unbound primers. At Tm of the duplex roughly half of your primer is bound to the RNA/DNA. So, if the Tm of the duplex is low,you'll do yourself a favor by increasing the concentration of the primer.
The stability is a function of the dissociation constant (Dc), and varies with the concentration of the two interacting molecules. The longer, and more G:C rich your interaction is, the lower you Dc, and the more stable your dimer will be. Of course, temperature affects the dissociation constant, so the higher the temperature the less bound primer you'll have for the same sequence.
Of course, there is an equilibrium but it depends on temperature. For example, for the DNA/primer hybrids (100% complementary) 20 nucleotides long you will not affect binding by lowering the concentration of primers. But for short DNA/primer fragments at physiological temperature you can. Principle of Le Chatelier. But you will not affect much, the equilibrium is shifted very much to the right.
Yes, concentration can matter, but it doesn't always.
So, when you have two things binding to each other, the association (binding event) is bimolecular and depends on the concentrations of the two components. The amount of binding is determined by the component in excess (this is sometimes counterintuitive - the maximum physical number of bound molecules is of course determined by the molecule in trace, but the percent bound is determined by the component in excess). If one or both of the components is saturating (say 5-10 times greater than the Kd), then you should be all set and happy.
For dissociation, the reaction is unimoleclar (one thing falling apart), so it does not depend on concentration at all.
So, if your primer/target interaction is extremely stable, the concentrations of target and primer can affect how much of your target is bound, but whatever is bound should essentially stay bound during the time of your experiment.
If your primer/target interaction is very weak and dissociates quickly, you can favor binding by having a high concentration of primer to drive rebinding. This means at equilibrium, you would have more bound.
You can modify the stability of your interaction by changing salt concentrations too. Many Tm calculators will ask you the concentration of your primer and the salt concentration to give you a better estimate of the Tm. Try oligoanalyzer from IDT for example. Make sure you specify whether you are using DNA or RNA as DNA/DNA < DNA/RNA < RNA/RNA in terms of stability.
Of course LeChatlier's principal holds sway here: increase the cocentration of your primer, and you drive the rx to products. Some subtleties exist, not too much to worry about.
This reminds me of a friend that drove everyone crazy in grad school. He refused to fuss over his primer additions; he just dipped his autopipetter into the primer and didnt measure anyrhing out. While everyone fretted that he wasnt being exact and scientific, he never had any failures!
Given a guess, if your primer can self associate or dimerize, higher concentrations can drive this to aggregation and reduce the available primer concentration, but the primer companiea check this when you submit the otder, right?
The biggest effect of concentration is on the speed of formation of a complex. If you use fluorescent probes and follow the reaction by spectroscopy, then the minimum amount of probe necessary to see gives you a very fast reaction, but if you use radioactivity or use the probe as a PCR primer at low concnetration (less than 0.1 µM) it may take more than several seconds for reassociation to occur and so you might not see it for that reason.