DNA Structure


Deoxyribonucleic acid (DNA) is a polymer of nucleotides that provides the chemical basis for inheritable characteristics of all cellular organisms. The genetic information in DNA is defined by the sequence of individual bases, which are the pyrimidines, cytosine and thymine and the purines, guanine and adenine. Hydrogen bonds form between appropriately positioned donors and acceptors on the bases of each strand, such that A pairs with T and G pairs with C. In the cell, DNA usually adopts a double‐stranded helical form, with complementary base pairing holding the two strands together. The most stable double‐stranded conformation is called B‐form DNA. A high degree of flexibility in DNA molecules means that a wide range of other structures can occur under specific conditions, including some that involve more than two strands of DNA.

Key Concepts:

  • Deoxyribonucleic acid (DNA) is the genetic material of all cellular organisms and provides the chemical basis for inheritable characteristics.

  • DNA is a polymer of nucleotides, each being the phosphate ester of one of four different nucleosides that consist of a five‐carbon sugar and a nitrogen‐containing base; the presence of different chemical groups at opposing ends of the nucleotide means that it has polarity, with sequence details usually defined in the 5′ to 3′ direction.

  • The genetic information contained in DNA is defined by the sequence of individual bases, which are the pyrimidines – cytosine (C) and thymine (T) – and the purines – guanine (G) and adenine (A).

  • Double‐stranded DNA has a 1:1 ratio of purine to pyrimidine bases, known as Chargaff's rules; hydrogen bonds are formed between appropriately positioned donors and acceptors on the bases of each strand, such that A pairs with T and G pairs with C.

  • Base‐pairing rules mean that the sequence of one strand dictates the sequence of the second strand – a fundamental property of DNA in copying this information into new DNA molecules (replication) and for directing the synthesis of RNA molecules (transcription).

  • In 1953 the structure of DNA was shown to consist of two twisted backbone chains of alternating units of phosphoric acid and deoxyribose, linked by crosspieces of purine and pyrimidine bases.

  • In addition to base pairing, DNA helices are stabilised by base‐stacking interactions that occur between neighbouring bases in order to reduce the area of these hydrophobic heterocycles that are exposed to solvent.

  • In Watson–Crick base pairs, the two sugars linked to each base are located on the same side of the helix, meaning that the gap between these sugars forms asymmetric, continuous grooves in the surface, referred to as ‘major’ and ‘minor’.

  • DNA has a remarkably supple structure that can adopt a variety of bends, twists and altered helical and nonhelical conformations that are typically stabilised by the many different hydrogen‐bonding schemes that can form.

  • Many unusual conformations of DNA have been identified in vitro, including some involving more than two strands of DNA, such as triplexes (three strands) and quadruplexes (four strands), although the significance for such structures in biological functions is not yet fully clear.

Keywords: deoxyribonucleic acid; base pair; gene; double helix; Watson–Crick; unusual DNA structures

Figure 1.

Structure of DNA and base pairs. Note that bond lengths are not proportional and some have been exaggerated for clarity. Broken lines represent hydrogen bonds in each base pair. (a) Chemical structure of DNA. The nomenclature for each base and its corresponding nucleoside is indicated. Atoms are numbered for one sugar, one purine base and one pyrimidine base. A single phosphodiester linkage is shown between adjacent nucleosides on each strand. Arrows highlight the antiparallel orientation of each polynucleotide strand in a duplex. The major and minor groove edges of each base pair are indicated. (b) Hoogsteen and reverse Hoogsteen base pairs of dA·dT and dG·dC.

Figure 2.

Three‐dimensional space‐filling models of B‐, A‐ and Z‐form helices. Major (M) and minor (m) grooves are indicated for each double helix.

Figure 3.

Three‐dimensional space‐filling models and hydrogen‐bonding patterns for triplexes and quadruplexes. Broken lines indicate hydrogen bonds and ‘R groups’ represent the continuation of polynucleotide structure through the phosphate and sugar backbone.



Avery OT, Macleod CM and McCarty M (1944) Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. Journal of Experimental Medicine 79: 137–158.

Bacolla A, Wojciechowska M, Kosmider B, Larson JE and Wells RD (2006) The involvement of non‐B DNA structures in gross chromosomal rearrangements. DNA Repair 5: 1161–1170.

Balasubramanian S, Hurley LH and Neidle S (2011) Targeting G‐quadruplexes in gene promoters: a novel anticancer strategy? Nature Reviews Drug Discovery 10: 261–275.

Barbic A, Zimmer DP and Crothers DM (2003) Structural origins of adenine‐tract bending. Proceedings of the National Academy of Sciences of the USA 100: 2369–2373.

Bevilacqua PC and Blose JM (2008) Structures, kinetics, thermodynamics, and biological functions of RNA hairpins. Annual Review of Physical Chemistry 59: 79–103.

Biffi G, Tannahill D, McCafferty J and Balasubramanian S (2013) Quantitative visualization of DNA G‐quadruplex structures in human cells. Nature Chemistry 5: 182–186.

Bochman ML, Paeschke K and Zakian VA (2012) DNA secondary structures: stability and function of G‐quadruplex structures. Nature Reviews Genetics 13: 770–780.

Bowater RP and Wells RD (2001) The intrinsically unstable life of DNA triplet repeats associated with human hereditary disorders. Progress in Nucleic Acid Research and Molecular Biology 66: 159–202.

Brazda V, Laister RC, Jagelska EB and Arrowsmith C (2011) Cruciform structures are a common DNA feature important for regulating biological processes. BMC Molecular Biology 12: 33.

Castel AL, Cleary JD and Pearson CE (2010) Repeat instability as the basis for human diseases and as a potential target for therapy. Nature Reviews Molecular Cell Biology 11: 165–170.

Chargaff E, Zamenhof S and Green C (1950) Composition of human desoxypentose nucleic acid. Nature 165: 756–757.

Dahm R (2008) Discovering DNA: Friedrich Miescher and the early years of nucleic acid research. Human Genetics 122: 565–581.

Declais AC and Lilley DM (2008) New insight into the recognition of branched DNA structure by junction‐resolving enzymes. Current Opinion in Structural Biology 18: 86–95.

Dickerson RE, Drew HR, Conner BN et al. (1982) The anatomy of A‐, B‐, and Z‐DNA. Science 216: 475–485.

Drew HR, Wing RM, Takano T et al. (1981) Structure of a B‐DNA dodecamer: conformation and dynamics. Proceedings of the National Academy of Sciences of the USA 78: 2179–2183.

Fathalla M, Lawrence CM, Zhang N, Sessler JL and Jayawickramarajah J (2009) Base‐pairing mediated non‐covalent polymers. Chemical Society Reviews 38: 1608–1620.

Frank‐Kamenetskii MD and Mirkin SM (1995) Triplex DNA structures. Annual Review of Biochemistry 64: 65–95.

Franklin RE and Gosling RG (1953) Molecular configuration in sodium thymonucleate. Nature 171: 740–741.

Hagerman PJ (1990) Sequence‐directed curvature of DNA. Annual Review of Biochemistry 59: 755–781.

Haran TE and Mohanty U (2009) The unique structure of A‐tracts and intrinsic DNA bending. Quarterly Reviews of Biophysics 42: 41–81.

Hershey AD and Chase M (1952) Independent functions of viral protein and nucleic acid in growth of bacteriophage. Journal of General Physiology 36: 39–56.

Hoogsteen K (1963) The crystal and molecular structure of a hydrogen‐bonded complex between 1‐methylthymine and 9‐methyladenine. Acta Crystallographica 16: 907–916.

Hunter CA (1993) Sequence‐dependent DNA structure. The role of base stacking interactions. Journal of Molecular Biology 230: 1025–1054.

Huppert JL (2010) Structure, location and interactions of G‐quadruplexes. FEBS Journal 277: 3452–3458.

Kalish JM and Glazer PM (2005) Targeted genome modification via triple helix formation. Annals of the New York Academy of Sciences 1058: 151–161.

Kitayner M, Rozenberg H, Rohs R et al. (2010) Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nature Structural and Molecular Biology 17: 423–429.

Lilley DM and White MF (2001) The junction‐resolving enzymes. Nature Reviews Molecular Cell Biology 2: 433–443.

Lilley DMJ (1988) DNA opens up: supercoiling and heavy breathing. Trends in Genetics 4: 111–114.

Lipps HJ and Rhodes D (2009) G‐quadruplex structures: in vivo evidence and function. Trends in Cell Biology 19: 414–422.

Mergny JL (2012) Alternative DNA structures: G4 DNA in cells: itae missa est? Nature Chemical Biology 8: 225–226.

Nikolova EN, Kim E, Wise AA et al. (2011) Transient Hoogsteen base pairs in canonical duplex DNA. Nature 470: 498–502.

Packer MJ and Hunter CA (1998) Sequence‐dependent DNA structure: the role of the sugar‐phosphate backbone. Journal of Molecular Biology 280: 407–420.

Rich A and Zhang S (2003) Timeline: Z‐DNA: the long road to biological function. Nature Reviews Genetics 4: 566–572.

SantaLucia J Jr and Hicks D (2004) The thermodynamics of DNA structural motifs. Annual Review of Biophysics and Biomolecular Structure 33: 415–440.

Travers AA (1989) DNA conformation and protein binding. Annual Review of Biochemistry 58: 427–452.

Varani G (1995) Exceptionally stable nucleic acid hairpins. Annual Review of Biophysics and Biomolecular Structure 24: 379–404.

Watson JD and Crick FC (1953) Molecular structure of nucleic acids: a structure for deoxyribose nucleic acids. Nature 171: 737–738.

Wilkins MH, Stokes AR and Wilson HR (1953) Molecular structure of deoxypentose nucleic acids. Nature 171: 738–740.

Wojciechowski F and Leumann CJ (2011) Alternative DNA base‐pairs: from efforts to expand the genetic code to potential material applications. Chemical Society Reviews 40: 5669–5679.

Further Reading

Blackburn GM and Gait MJ (1996) Nucleic Acids in Chemistry and Biology, 2nd edn. Oxford: Oxford University Press.

Calladine CR, Drew HR, Luisi B and Travers AA (2004) Understanding DNA: The Molecule and How it Works, 3rd edn. London: Academic Press.

Crick FHC (1989) What Mad Pursuit: A Personal View of Scientific Discovery. London: Weidenfeld & Nicolson.

Mirsky AE (1968) The discovery of DNA. Scientific American 218(6): 78–88.

Neidle S (2002) Nucleic Acid Structure and Recognition. Oxford: Oxford University Press.

Neidle S (2008) Principles of Nucleic Acid Structure. London: Academic Press.

Neidle S (2011) Therapeutic Applications of Quadruplex Nucleic Acids. London: Academic Press.

Saenger W (1984) Principles of Nucleic Acid Structure. New York, NY: Springer‐Verlag.

Sayre A (1975) Rosalind Franklin and DNA. New York: Norton.

Watson JD (1997) The Double Helix: A Personal Account of the Discovery of the Structure of DNA. London: Weidenfeld & Nicolson.

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Bowater, Richard P, and Waller, Zoë AE(Apr 2014) DNA Structure. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0006002.pub2]