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Watson–Crick Base Pairs and Nucleic Acids Stability

  1. Luis A Marky1,
  2. Hui-Ting Lee1,
  3. Angel Garcia2

Published Online: 19 MAY 2010

DOI: 10.1002/9780470015902.a0003126.pub2



How to Cite

Marky, L. A., Lee, H.-T. and Garcia, A. 2010. Watson–Crick Base Pairs and Nucleic Acids Stability. eLS. .

Author Information

  1. 1

    University of Nebraska Medical Center, Omaha, Nebraska, USA

  2. 2

    Rensselaer Polytechnic Institute, Troy, New York, USA

Publication History

  1. Published Online: 19 MAY 2010


Watson–Crick base pairs are crucial in the formation of double-helical deoxyribonucleic acid (DNA) and in the storage of genetic information. They comprise two of the most common geometries involving the pairing of deoxyadenosine (dA) with deoxythymidine (dT) and deoxyguanosine (dG) with deoxycytidine (dC) through the formation of two and three hydrogen bonds, respectively. The complementarity of the antiparallel strands forming a double helix is crucial in DNA replication since the complementary strand is synthesised by adding the Watson–Crick complementary bases of the parent strand. The hybridisation of DNA or DNA–RNA (ribonucleic acid) strands is widely used in biotechnology and molecular biology for multiple purposes. The stability of a nucleic acid helix depends on its sequence, conformation, hydration and solution conditions, and it is measured by temperature-dependent techniques, such as UV (ultraviolet) melting. Examples of oligonucleotide helices with chemical modifications are provided to indicate how these modifications affect the overall stability of a DNA molecule.

Key Concepts:

  • Base pairs are two nucleotide bases interacting via hydrogen bonding.

  • Bulge is a nonpaired nucleotide base in a double-stranded nucleic acid.

  • Hybridisation is a process where two complementary strands interact via base pairing.

  • Nucleic acid conformation is the three-dimensional structural arrangement of a double-helical nucleic acid.

  • Nucleic acid modification is the incorporation, removal or substitution of a chemical group on the natural occurring nucleic acids.

  • Melting curves are the optical changes of a nucleic acid or protein-like molecules as a function of temperature.

  • Stability of nucleic acids is the resistance of nucleic acid duplex to undergo unfolding, proportional to the magnitude of ΔG.

  • Thermal stability is the ability of a nucleic acid duplex to resist temperature denaturation.

  • Unfolding thermodynamic profile is the free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) parameters associated with the unfolding of a nucleic acid or protein molecule.

  • Cooperativity refers to the number of base pairs that are broken simultaneously in the unfolding of a nucleic acid or protein.


  • Watson–Crick base pairs;
  • hybridisation;
  • DNA melting curves;
  • UV spectroscopy;
  • circular dichroism spectroscopy;
  • nucleic acid conformation;
  • unfolding thermodynamic profiles;
  • transition temperature (Tm);
  • free energy and stability