this is my first post and this might be a bit strange question, and I seem to be the only one having problem comprehanding that but...

 

Is DNA melting temperature (Tm - temperature when 50% of DNA molecules is denatured) of DNA "sequence1" the same as Tm of sequence1-sequence1-sequence1,that is longer DNA molecules with completely the same GC content).

 

The system I am thinking about has heating rate slow enough not to affect longer molecules denaturation, and heat input is not limiting factor (is provided as much as needed in order to assure constant temperature increase)?

 

The way I see it, you need energy to denature a bond (2 or 3), for this reason GC content has the highest impact on Tm, eg seq1 has a Tm of 60, and if energy input is not limiting factor than longer sequences (with same GC content) should have the same Tm?

 

What am I missing?

 

Is DNA melting temperature (Tm - temperature when 50% of DNA molecules is denatured) of DNA "sequence1" the same as Tm of sequence1-sequence1-sequence1,that is longer DNA molecules with completely the same GC content).

 

No, Tm is length dependent . The more nucleotides are involved, the more energy is needed. The way to look at it is that it is a stochastic process and with increasing temperature the likelihood of a bond being dissolved (or formed) increases (decreases). However, for more bonds (i.e. bases) you need more successive events. It gets a bit more complicated due to the fact that neighboring interactions factor in as well. I.e. if a bond is present it stabilizes the neighboring bond.

If the CG are surrounded by more GC - higher TM

if GC are surrounded or interrupted by A or T - Lower TM

Another factor associated with TM