MadSci Network: Biochemistry

Re: why don't free nuclotides in the cell pair up?

Date: Wed Feb 28 11:00:43 2001
Posted By: Michael Onken, Admin, MadSci Network
Area of science: Biochemistry
ID: 982992258.Bc

The answer can be seen if we examine the "Wallace rule" for determining the melting points of short DNA double helices based on their lengths - this ignores base-stacking and other nearest-neighbor interactions, which are obviously not important for single nucleotide interactions:

Tm = 2C (A + T) + 4C (G + C)1
(Where each letter represents the number of times each base is present in one strand)

As you can see from the equation, any double-stranded DNA fragment with a GC content around 50% must be at least 13 basepairs long to be stable at a normal body temperature of 37°C. That being the case, the melting point for a single basepair in the absence of other interactions is far below normal body temperature, such that stable hydrogen-bonding between free nucleotides would be the equivalent of ice spontaneously forming in a glass of room temperature water. That is not to say that these interactions never occur, but they are too short- lived to play a substantial role in the cell, especially considering the competing interactions of proteins and other molecules, including water.

1. Wallace, R.B., Shaffer J., Murphy, R.F., Bonner, J., Hirose, T., and Itakura, K. (1979) Nucleic Acids Research 6: 3543- 3547.

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