Hydrogen Bonds – Why we have Two Sets of DNA Bases? /+ Response

This is a diagram showing hydrogen bonds.
http://www.sciencedaily.com/releases/2014/07/140715141755.htm

This shows one of my contentions about why we have 4 bases. The reason is that those 4 bases make two sets.

The two sets are different in that G-C has 3 hydrogen bonds, and A-T two.
That means that each has a slight selection advantage.
The G-C is slightly more stable and will denature at a higher temp.
The A-T is slightly less stable, more active, and will denature at a lower temp

—————–

Someone said that base stacking was important too. Correct.

Both play a part as found in these quotes from across the net. Though even base stacking should be affected by the G-C or A-T content as I suggested

Quotes
The two strands of DNA are bound together mainly by the stacking interactions, hydrogen bonds and hydrophobic effect between the complementary bases.
———-
The stability of the DNA double helix depends on a fine balance of interactions including hydrogen bonds between bases, hydrogen bonds between bases and surrounding water molecules, and base-stacking interactions between adjacent bases.
———–
DNA duplex stability is determined primarily by hydrogen bonding, but base stacking also plays an important role.

Hydrogen bonding
The heterocyclic bases of single-stranded DNA have polar amido, amidino, guanidino and carbonyl groups that form a complex network of hydrogen bonds with the surrounding water molecules. Some of these bonds must be broken during duplex formation as the inter-base hydrogen bonds are formed. The overall process is one of “hydrogen bond exchange” and the net change in enthalpy upon duplex formation is partly due to ∆H(H-bonds formed) − ∆H(H-bonds broken). For duplexes of any significant length this is an exothermic process at ambient temperature. Not surprisingly the coming together of two large oligomeric molecules is entropically unfavourable (∆S is negative).

Base stacking
Inter-strand hydrogen bonding is clearly important in driving the formation of DNA duplexes, but it is by no means the only contributing factor. The individual bases form strong stacking interactions which are major contributors to duplex stability, as base stacking is much more prevalent in duplexes than in single strands (Figure 1). Base-stacking interactions are hydrophobic and electrostatic in nature, and depend on the aromaticity of the bases and their dipole moments. Base-stacking interactions in nucleic acid duplexes are partly inter-strand and partly intra-strand in nature. However, it is probably more informative to consider base pairs rather than individual bases as discrete units in order to visualize the stabilising effects of base stacking.

The degree of stabilization afforded by base stacking depends on the DNA sequence. Some combinations of base pairs form more stable interactions than others, so nearest neighbour base-stacking interactions are important determinants of duplex stability.

Base-stacking interactions increase with increasing salt concentration, as high salt concentrations mask the destabilising charge repulsion between the two negatively charged phosphodiester backbones. DNA duplex stability therefore increases with increasing salt concentration. Divalent cations such as Mg2+ are more stabilising than Na+ ions, and some metal ions bind to specific loci on the DNA duplex.

Tom Hendricks

BIOLOGY HYPOTHESIS http://wp.me/p5S9X-eO
BIOLOGICAL SPECULATIONS Through The Years http://wp.me/P5S9X-Pp
UV PAPER http://www.daviddarling.info/encyclopedia/U/UV_origin_of_life.html
Catabolic and Anabolic evolved, but they did not blend.

============

When this was posted on SBE newsgroup, I got this response and my reply

RESPONSE TO WLH AND TWO REFERENCES

Dr. Moran and I discussed this with you many
years ago if you remember? My source then was the book BIOCHEMISTRY, Abeles, Frey and Jencks 1992,
and nothing has changed since then. But here is a more complete explanation from Moran:
http://sandwalk.blogspot.com/2007/07/measuring-stacking-interactions.html
or from Wiki:
http://en.wikipedia.org/wiki/Nucleic_acid_thermodynamics
Notice in the Wiki article that base stacking contribution to melting can be very different for the same set of bases depending on how they stack, for instance, if a G-C is stacked on top of a G-C or on a C-G.
William L Hunt
But that just adds to my argument. Now we have three selection points
1. G-C content in a single base pair
2. G-C content in stacked base pairs.
3. G-C stacked base pairs are stronger than C-G stacked on G-C

Moran says in that sited article:

The Tm refers to the melting temperature, which is the midpoint of the transition between the double-stranded DNA and the completely denatured molecule with free single strands.
In your second example it’s clear that the A/T rich region would separate first followed by the G/C rich region. (This is why many promoter regions tend to be A/T rich.) But it’s not clear whether the actual Tm of the two molecules would be different.

Wiki article says:

The process of DNA denaturation can be used to analyze some aspects of DNA. Because cytosine / guanine base-pairing is generally stronger than adenosine / thymine base-pairing, the amount of cytosine and guanine in a genome (called the “GC content”) can be estimated by measuring the temperature at which the genomic DNA melts.[1] Higher temperatures are associated with high GC content.

GC content is a real factor, whether in a single pair, or stacked segment.

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2 Responses to “Hydrogen Bonds – Why we have Two Sets of DNA Bases? /+ Response”

  1. musea Says:

    But so what? Mr. Hunt this doesn’t change anything – it adds a slight proviso is all, and that is this: there is a slight difference between G-C stacked on another G-C then stacked on C-G. But even Moran says:

    In your second example it’s clear that the A/T rich region would separate first followed by the G/C rich region. (This is why many promoter regions tend to be A/T rich.) But it’s not clear whether the actual Tm of the two molecules would be different.

    Therefore my fundamental idea is valid for now TWO reasons instead of one
    1. Stacking 2. hydrogen bonds
    .
    G-C or C-G stack is less likely to denature than A-T or T-A AND
    G-C base pairs still have 3 hydrogen bonds over two for A-T.

    I think this concern of yours, adjusts more than changes my idea. I’m glad to add base stacking to my arguments that now seem stronger because of it.

    Then too, perhaps a bigger adjustment in my thinking, than the stacking complaint, is that of how bases respond to UV. See new posts.

  2. musea Says:

    G-C base sections conserve
    A-T base sections change

    Wiki:
    Because cytosine / guanine base-pairing is generally stronger than adenosine / thymine base-pairing, the amount of cytosine and guanine in a genome (called the “GC content”) can be estimated by measuring the temperature at which the genomic DNA melts.[1] Higher temperatures are associated with high GC content.

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