[Polleke]

Hallo all,
I have the following question: how come intramolecular bonds are stronger (more favored) then intermolecular bonds in DNA.

I am working with a scorpion probe and the principle of this probe is that it can bind intramoleculary with complementary DNA (on the same DNA stretch).
Rather then that the complemtary DNA binds with the template DNA (other stretch of DNA) from which it was amplified.

In short: you have 1 sequence that is complentary with template DNA (on another stretch of DNA) and with a small piece of DNA on the same DNA stretch (the scorpion probe).
Now the whole idea behind all of this is that the probe will bind that complementary DNA intramoleculary rather then binding the template DNA intermoleculary.
But why is this? The idea behind it, is based on hydrogen bounds... so what is the difference?

Thanks in advance.

[fledarmus]

In a solution, on average, how far is the complementary DNA strand from an intermolecular species? How far from an intramolecular species?

A large part of the bond strength is that you have removed a portion of the entropy by fixing the complementary strand within a certain distance of the primary.

[Polleke]

In a solution, on average, how far is the complementary DNA strand from an intermolecular species? How far from an intramolecular species?

A large part of the bond strength is that you have removed a portion of the entropy by fixing the complementary strand within a certain distance of the primary.

Ok, I see what you mean.

Thanks

[Nescafe]

I don't get it. Can you elaborate please...

[fledarmus]

Let's say you put tiny spots of the cloth side of a piece of velcro on a lot of ping pong balls, and tiny spots of the hook side on a lot more ping pong balls, then you let them bounce around a room at enormous velocities and see which ones stick together. That would be your intermolecular binding.

If you attach some of the ping pong balls with the cloth side to others with the hook side by a short piece of string, would you expect the ones with the string to be more or less likely to be attached together than to be attached to any of the other wandering ping pong balls? How about if instead of a string, they were attached together by a curved spring that held them so the two patches were facing each other and only a few millimeters apart? That would be your intramolecular binding. The probe is located close enough to the corresponding binding site that the binding site is much more likely to find the probe than the template, which is on a separate stretch of DNA.

[Nescafe]

Let's say you put tiny spots of the cloth side of a piece of velcro on a lot of ping pong balls, and tiny spots of the hook side on a lot more ping pong balls, then you let them bounce around a room at enormous velocities and see which ones stick together. That would be your intermolecular binding.

If you attach some of the ping pong balls with the cloth side to others with the hook side by a short piece of string, would you expect the ones with the string to be more or less likely to be attached together than to be attached to any of the other wandering ping pong balls? How about if instead of a string, they were attached together by a curved spring that held them so the two patches were facing each other and only a few millimeters apart? That would be your intramolecular binding. The probe is located close enough to the corresponding binding site that the binding site is much more likely to find the probe than the template, which is on a separate stretch of DNA.

The last four and a half lines were all that I needed. The while long pong thing was clever but it kind of threw me off a bit.

Appreciate it though

Cheers,

Nescafé.