A consequence of this is that by raising the temperature of a solution, we can increase the forces pushing molecules apart from one another. Indeed, the temperature at which a pair of DNA strands comes apart is a measure of the number of hydrogen bonds holding it together. When we speak of 'molecular recognition', we mean that two molecules have a significant affinity for one another. However, the thousands of contributions from individual bonds and the millions of alternative positions and interactions that can take place render predictions about molecular state largely incalculable with current techniques. Nonetheless, the answers aren't unknowable, just out of reach right now.
Nothing is forever.
In our discussions of single molecules, we create dangerous illusions about events at the molecular level. Since molecular matchmaking involves only a few types of interactions, ANY two molecules will have SOME affinity for one another. Further, the capriciousness of the Molecular Wind dictates that even the strongest non-covalent interactions will break periodically. In this fashion, any given molecule of protein X may be off on a donut break at any given time, but there is a reasonable probability that another molecule of protein X will take up residence on the DNA after a small time interval. It's important to keep in mind that there's nobody running the cell's life.