Hydrogen Bonds - Why We Have Two Sets of DNA Bases?

[Tom Hendricks]

his 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

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.

[William L Hunt]

On Fri, 18 Jul 2014 14:10:44 -0400 (EDT), Tom Hendricks <tom-he...@att.net> wrote:

>his 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

In both RNA and DNA the stability and denaturing temperature comes from the base stacking energy
not from hydrogen bonding. While the base stacking energy depends on the neighboring base
configuration, generaly the G-C will stack with more energy than A-T or G-U (in RNA).
William L Hunt

[RSNorman]

On Sat, 19 Jul 2014 19:06:15 -0400 (EDT), wlh...@earthlink.net
(William L Hunt) wrote:

>On Fri, 18 Jul 2014 14:10:44 -0400 (EDT), Tom Hendricks <tom-he...@att.net> wrote:
>
>>his 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

> In both RNA and DNA the stability and denaturing temperature comes from the base stacking energy
>not from hydrogen bonding. While the base stacking energy depends on the neighboring base
>configuration, generaly the G-C will stack with more energy than A-T or G-U (in RNA).

It could also be mentioned that the base pairing notion "proposed" by
Hendricks is about 60 years old, now.

[Tom Hendricks]

Do you have some references for that? Thanks.

[Tom Hendricks]

Both play a part as found in these quotes from across the net. Though even base stacking would be affected by the G-C or A-T content as I suggested, wouldn't it?

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]

> It could also be mentioned that the base pairing notion "proposed" by
>
> Hendricks is about 60 years old, now.

Could you follow up that statement with some more proof or information? Thanks.

[William L Hunt]

On Wed, 23 Jul 2014 00:27:33 -0400 (EDT), Tom Hendricks <tom-he...@att.net> wrote:

>Do you have some references for that? Thanks.
>

First, in your original post, you mention that G-C pair with 3- hydrogien bonds and A-T with 2.
Then you follow by observing that G-C denatures at a higher temperature and A-T at a lower.
While you don't say directly that this is cause of the difference in denaturing temperature there is
this implication. And your implication is incorrect. 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

[Tom Hendricks]

Though this quote is not directly related to hydrogen bonds, it does seem to fit the selection advantage of nucleobases.

"The photostability of nucleobases increases upon their stacking and formation of Watson Crick Pairs (Sobolewski and Domcke 2006)."

This paper sent to me by researcher , Armen Y. Mulkidjanian

Perhaps hydrogen bonds and stacking affects the outcome through their photostability. Though I have not given up the idea that there is selection pressure on the two sets of bases.

[Tom Hendricks]

These quotes from the following paper support selection through UV. I think that would be part of this thread too.

Fundamental Molecules of Life are Pigments which Arose and Evolved to Dissipate the Solar Spectrum, Michaelian, Simeonov
http://arxiv.org/abs/1405.4059

Here are some QUOTES from the lengthy article

The 5 naturally occurring nucleic bases are U-V pigments which absorb in the 240-290 nm UV region.

It has been demonstrated that the G-C Watson Crick base pairs exhibit superior photon dissipation characteristic compared to other possible base pairing. Abo-Riziq et. all 2005

Therefor the coupling of nucleobase photon dissipation to the water cycle and the resulting increase in entropy production can be seen as the thermodynamic driving force for their polymerization into RNA/DNA and the ensuing replication of these polymers through an ultraviolet and temperature assisted RNA/DNA reproduction (UVTAR; Michaelian, 2009;2011

UVC light must have acted as a selective force (Saga, 1973; Mulkidjamian et al,. 2003; Serrano-Andres and Merchan, 2009) not only for stability but for photon dissipation characteristics and this was probably the onset of an evolution through a thermodynamic natural selection.

Compare these ideas with the speculation of many years ago in my paper

UV Paper
http://www.daviddarling.info/encyclopedia/U/UV_origin_of_life.html

[Tom Hendricks]

> First, in your original post, you mention that G-C pair with 3- hydrogien bonds and A-T with 2.
>
> Then you follow by observing that G-C denatures at a higher temperature and A-T at a lower.
>
> While you don't say directly that this is cause of the difference in denaturing temperature there is
>
> this implication. And your implication is incorrect. 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 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.

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.

[RSNorman]

You must be kidding.

Chargaff discovered the base pairing rule, A = T and C = G in 1949 and
in 1953 Watson and Crick used the equal length of the AT and th CG
hydrogen bonding scheme as the basis of their double helix.

Your contention about why we have four bases is that they form two
sets.

[Tom Hendricks]

> 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

This quote from the same 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.

[Tom Hendricks]

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 two 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.

[William L Hunt]

On Sun, 3 Aug 2014 19:26:34 -0400 (EDT), Tom Hendricks <tom-he...@att.net> wrote:

>
>> First, in your original post, you mention that G-C pair with 3- hydrogien bonds and A-T with 2.
>>
>> Then you follow by observing that G-C denatures at a higher temperature and A-T at a lower.
>>
>> While you don't say directly that this is cause of the difference in denaturing temperature there is
>>
>> this implication. And your implication is incorrect. 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 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.

My only point was what is causing the differences in melting temperature in strands, where you
implied it was the 3 versus 2 h-bonds.There are differences between G-C and A-T. One is how they
align with 2 h-bonds or 3 h-bonds, another is the larger planar surface area in the G-C where
larger surface contact beween the stacked pairs increases the stacking energy. Both correlate to the
strand melting temperature although the correlation is much better when adding up the individual
base-stacking energies. This hardly matters in any large strand where the different base-stackings
all average out. But for small strands using a calculation that adds up the actual base stackings
gives a better result than just counting the G-C content.
Moran and I think the base-stacking is the causal factor. It is still not clear to me that you
accept this. Though clearly for your purposes it doesn't matter what is the causal factor, only that
there is a correlation.
William L Hunt