What is the difference between the hydrogen bonding of thymine/adenine and cytosine/guanine

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Physical Chemistry Chemical Physics , 7 23 , Naumov , M. Quantum-chemical study, IR spectra, and intramolecular hydrogen bonds in dimeric 5- and 6-methyluracils. Russian Journal of General Chemistry , 74 12 , Pair your accounts. Your Mendeley pairing has expired. Notice the angle of the sugar and phosphate groups in relation to the planar nitrogenous base. In double-stranded DNA, two long molecules twist around one another in a double helix. These molecules are d eoxy n ucleic a cids DNA : polymers made up of nucleotides In a DNA double helix, the phosphate and sugar groups make up the outer 'backbones,' and the flat nitrogenous bases are pointed toward the middle of the helix.

Click the buttons below to examine a segment of a DNA double helix from many angles. The first button has colored the backbone sugar and phosphate groups purple to simplify the image.

One key point to notice in the DNA double helix structure is that the planar nitrogenous bases from the two strands are pointing toward each other, in the middle of the helix. Pairs of nitrogenous bases are set in the same plane, and interact with each other via hydrogen bonding. These pairs are often referred to as base pairs , abbreviated 'bp.

Recall that electronegativity values generally increase toward the top and right of the periodic table, as illustrated in the image below. Oxygen and nitrogen are electronegative atoms found in nitrogenous bases. They are represented in models by the color conventions: red for oxygen , and blue for nitrogen. Electronegative O and N atoms with free lone pairs are potential hydrogen bond acceptors. Hydrogen atoms attached to very electronegative atoms like O and N have strong partial positive charge and are potential hydrogen bond donors.

The dotted line in the image below represents the non-covalent attractive force between a hydrogen bond donor H atom with little 'ownership' of its valence electrons and a hydrogen bond acceptor electronegative atom with at least one lone pair of electrons. Many of the oxygen, nitrogen, and hydrogen atoms in the nitrogenous bases are very effective hydrogen bond donors and acceptors, as illustrated in the image below.

Remember: Hydrogen bond donors are only those H atoms bound to an electronegative atom such as N or O. Hydrogen bond acceptors are electronegative atoms with at least one lone pair of electrons. Also notice that potential hydrogen bond donors and acceptors close to the sugar R group are ignored in the image above. This is because those parts of the nitrogenous base close to the sugar-phosphate backbone will be unavailable for hydrogen bonding with the other base in the pair.

Let's examine a single guanine residue to identify potential hydrogen bond donors and acceptors. Guanine will be highlighted in yellow , and the attached sugar and phosphate in the backbone will blink purple. Keeping in mind the point of sugar attachment, we can identify guanine's hydrogen bond donors and acceptors that are available to interact with a paired nitrogenous base.

This property can be attributed to the large number of hydrogen bonds that exists within water. Another unusual property of water is it has a higher density than it's solid counterpart - ice. This is due to the unique formation of the hydrogen bonds forming a lattice structure whereby the strength and relative rigidity of the bonds allow for greater separation between molecules than in its liquid form where the molecules interact at a greater velocity.

In the DNA helix , the bases: adenine , cytosine , thymine and guanine are each linked with their complementary base by hydrogen bonding. Adenine pairs with thymine with 2 hydrogen bonds.

Guanine pairs with cytosine with 3 hydrogen bonds [6]. This creates a difference in strength between the two sets of Watson and Crick bases. Guanine and cytosine bonded base pairs are stronger then thymine and adenine bonded base pairs in DNA. This difference in strength is because of the difference in the number of hydrogen bonds. This allows researchers to figure out the base content of DNA by observing at what temperature it denatures.

The higher the temperature at which DNA denatures the more guanine and cytosine base pairs are present. To ensure both primers anneal proportionally to their binding sites they must be designed such that they produce hydrogen bonds of similar affinity.