Hydrogen bonds in DNA: Base Pairing & Nature

Deoxyribonucleic acid (DNA) has two helical strands that are connected to each other by hydrogen bonding. Strands of DNA are made up of nucleotides that have phosphate groups, ribose sugar, and nitrogenous bases. They are twisted around each other and form a ladder-like structure known as a double helix. In DNA, hydrogen bonds play an important role in giving intrinsic stability to the molecule.

The genetic information is encoded in the DNA by the specific combination of nitrogenous bases. These are the four nitrogenous bases in DNA:

  • Adenine (A)
  • Thymine (T)
  • Guanine (G)
  • Cytosine (C)

These above base pairs are present in the strands of DNA where they specifically bond with each other by hydrogen bonding and connect the two strands. Adenine (A) always makes two hydrogen bonds with thymine (T), whereas guanine (G) bonds with cytosine (C) by three hydrogen bonds. According to the gas phase experiment, the strength of the hydrogen bond is -12.1kcal/mol for adenine-thymine (AT) while -21.0 kcal/mol for guanine-cytosine (GC).

Hydrogen bonds in DNA

Nature of Hydrogen Bonds in DNA

The nature of hydrogen bonds in DNA is composed of these components:

  • Electrostatic interaction
  • Orbital interaction
  • Charge redistribution

Electrostatic interaction

It is good to understand the hydrogen bonding that holds the base pair together and the importance of electrostatic interaction in the DNA. The bond energy is ΔE is separated into preparation energy ΔEprep and the actual interaction energy ΔEint.

The preparation energy ΔEprep is associated with the breakdown of the equilibrium structure of base pairs into their geometry or individual structures whereas actual interaction energy ΔEint is the energy that is present between these individual structures of base pairs.

ΔE = ΔEprep + ΔEint

Geometrical changes in the DNA base pairs are minor, so the preparation energies ΔEprep are very small 4 kcal/mol or less. On the other hand, interaction energies ΔEint are very essential and analyzed in the Kohn-Sham MO model.

Quantitatively, interaction energy ΔEint is the sum of these:

  • Electrostatic attraction ΔVelstat between the unperturbed charge distribution of base pairs.
  • Pauli repulsive orbital interactions ΔEpauli between orbitals.
  • Bonding orbital interactions ΔEoi (charge transfer).

ΔEint = ΔVelstat + ΔEpauli + ΔEoi

In addition, by examing the charge distribution at the atoms that are responsible for hydrogen bonding between the base pairs. This shows DNA bases have the charge distribution for achieving the electrostatic interaction in the base pairs. All the protons acceptor atoms have a negative charge while corresponding protons have a positive charge.

Orbital Interaction

Orbital interaction due to hydrogen bonding can be studied by considering the orbital electronic structure of DNA bases. Especially 𝛔-electron system, in which orbital interactions like donor-acceptor or charge transfer occur.

According to Molecular Orbital (MO) analysis, the key features that are required for achieving the donor-acceptor orbital interactions are:

  • Lone pair on the oxygen or nitrogen atoms in the base
  • Unoccupied 𝛔* orbital of an N-H group the other base

The result of the above combination is the formation of a weak hydrogen bond. For example, the lone pair on the first nitrogen atom (N1) in the adenine (A) make contact with the 𝛔* orbital on H3-N3 atoms in the thymine (T). Similarly, the lone pair on the O4 atom of the thymine (T) make donor-acceptor interactions with 𝛔* orbitals of N6-H6 of adenine (A).

In the case of the base pair of guanine-cytosine (GC), the above process is repeated in the same way.

Charge redistribution

According to the VDD charge decomposition analysis, it is possible to calculate the changes in atomic charge ΔQA by the formation of base pairs from other bases and to break down them. These results in charge redistribution in the 𝛔 and 𝝅-electron system.


Due to Pauli’s repulsive and bonding orbitals interactions, these components can be further breakdown into charge rearrangement.

ΔQA = ΔQ𝛔A, Pauli + ΔQ𝝅A, Oi

Formation of base pair (AT) from the bases adenine (A) and guanine (T) takes place due to the effect of Pauli’s repulsion. This results in the depletion of the charge density from the central point of overlap and is directed toward the edge of the hydrogen bonds (N6-H6 makes a hydrogen bond with O4 and N1 hydrogen bonded with H3-N3).

This results in a positive charge on the central hydrogen atoms and a negative charge on the edged atom from the hydrogen bond. Due to bonding orbital interaction in the 𝛔-system, atomic charges are also charged.

Electron-donor atoms of hydrogen bonds, such as N6-H6—O4 lose 24 mili-a.u whereas N1—H3-N3 loses 46 mili-a.u. On the other hand, N-H bonds gain 54 mili-a.u. The charge redistribution in the 𝝅-electron system polarizes as a compared 𝛔-electron system where positive or negative charges are canceled or compromised.

Role of Hydrogen bonding in DNA transcription and translation

Transcription and translation are the two chemical reactions that play an essential role in cell growth and gene expression. During these reactions, the double helix of DNA is dissociated and separated into two daughter strands.

One strand acts as a template for the formation of the new complementary strand. This process occurs with high accuracy due to the hydrogen bonding in the complementary base pairs. Besides hydrogen bonding, other factors such as solvation, hydrophobicity, and stacking also contribute to nucleotide insertion in the process.

Concepts Berg

Where are hydrogen bonds found in DNA Quizlet?

Hydrogen bonds can be between the bases of two helical strands of DNA. There are four bases that build up in the form of pairs. For example, Adenine make pairs with thymine with two hydrogen bonds while guanine pair up with cytosine with three hydrogen bonds.

Why does DNA use hydrogen bonds instead of covalent bonds?

DNA uses hydrogen bonds instead of covalent bonds due to their weak properties. However, covalent bonds are stronger than hydrogen bonds. In this way, during transcription and translation, DNA double helix has two strands are separated into daughter strands by the easy breakdown of hydrogen bonds.

Why is hydrogen bonding necessary in DNA?

Hydrogen bonding plays an important role in the stability and connectivity of the strands of DNA together.

In G-C pairing (DNA bases), which one donates more hydrogen bonds?

Both bases guanine (G) and cytosine (C) contribute three hydrogen bonds.

Are there 3 hydrogen bonds between A and T?

No, there are only two hydrogen bonds formed between adenine (A) and thymine (T).

How many hydrogen bonds are between C and G?

During the pairing of cytosine (C) with guanine (G), there are three hydrogen bonds are involved and formed.

How do find the number of hydrogen bonds in 700 DNA nucleotides?

One DNA nucleotide has a total of 5 hydrogen bonds in which AT base pair has 2 while the GC base pair has 3 hydrogen bonds. So, to get the number of hydrogen bonds in 700 DNA nucleotides, just divide the 700 by 2. This results in 350 hydrogen bonds which are present between the AT base pairs. The remaining hydrogen bonds will be between GC base pairs.

Are hydrogen bonds in DNA strong or weak?

Hydrogen bonds present in the molecule of DNA for combing the strands together are very weak.


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