Nucleic Acids: General Properties


Nucleic acids are biological polymers generally composed of four different monomer units termed nucleotides. The unit length of one molecule can be as much as one billion nucleotides. Although the biological roles that nucleic acids fulfil are diverse, the structure and function of each molecule is elaborated from a common set of general properties.

Keywords: DNA; RNA; double helix; hairpin; base pair; hydrogen bond

Figure 1.

Chemical structure of DNA and RNA polymers. The bases are shown in blue while the phosphate and sugar backbone is shown in red. Chemical differences that distinguish RNA structure from DNA structure are shown in parentheses. The nomenclature for each base and its corresponding nucleoside is indicated. Atoms are numbered for one sugar, one purine base and one pyrimidine base. The glycosidic bond (χ) of one nucleoside is labelled, and the base of each nucleoside is shown in an anti conformation. Rotation about the glycosidic bond by 180° would orient the base in a syn conformation. A single phosphodiester linkage is shown between adjacent nucleosides on each strand. Shaded arrows highlight the antiparallel orientation of each polynucleotide strand in a duplex. Dashed lines represent hydrogen bonds in each base pair, and the major andminor groove edges of each base pair are indicated. Note that bond lengths are not proportional and may be exaggerated in the interest of clarity.

Figure 2.

Three‐dimensional space‐filling models of B‐, A‐ and Z‐form helices. Bases are coloured blue and the phosphate and sugar backbones are coloured red. Major (M) and minor (m) grooves are indicated for each double helix.

Figure 3.

Unusual base pairs that may be accommodated in double‐helical structures. Hydrogen bonds are indicated by dashed lines and R groups represent the continuation of polynucleotide structure through the phosphate and sugar backbone. All bases are in an anti configuration unless otherwise specified.

Figure 4.

Specific double‐helical structures. (a) Hairpin formation. An RNA hairpin with a UNCG tetraloop sequence is shown. Self‐complementary regions are indicated by open and filled wedges. (b) Cruciform formation. A DNA duplex containing an inverted repeat sequence is shown. (c) Intrinsic DNA bending. A sequence containing two A‐tracts phased with the helical repeat of B‐DNA is shown. Arrows indicate bends centred on each A‐tract. A schematic representation of the double helix illustrates the cumulative bend affected by each phased A‐tract. Thick lines trace the path of each phosphodiester backbone, while the thin line denotes the helix axis.

Figure 5.

Reactions affecting nucleic acid structure. (a) Cyclizing mechanism of RNA transesterification.(b) Hydrolysis of RNA or DNA.(c) Deamination of cytosine by bisulfite. (d) Deamination of cytosine by nitrous acid. (e) Depurination of guanosine. (f) Hydroxyl radical conversion of guanine to 8‐hydroxyguanine.(g) Hydroxyl radical conversion of thymine to thymine glycol. The participation of a base (B) or acid (A) is shown in the first two reactions. R groups represent the continuation of polynucleotide structure through the phosphate and sugar backbone.

Figure 6.

Three‐dimensional space‐filling models and hydrogen‐bonding patterns for triple and quadruple helices. For the triplex, canonically paired bases and their phosphate and sugar backbones are coloured blue and red, respectively, while the bases and backbone of the third strand are coloured gold and green, respectively. For the quadruplex, bases are coloured blue and the backbone is coloured red. Hydrogen bonds are indicated by dashed lines and R groups represent the continuation of polynucleotide structure through the phosphate and sugar backbone.


Further Reading

Blackburn GM and Gait MJ (eds) (1990) Nucleic Acids in Chemistry and Biology. New York: Oxford University Press.

Bloomfield VA, Crothers DM and Tinoco I (eds) (2000) Nucleic Acids: Structures, Properties and Functions. Sausalito, CA: University Science Books.

Cantor CR and Schimmel PR (1980) Biophysical Chemistry. New York: W.H. Freeman and Company.

Guschlbauer W (1976) Nucleic Acid Structure. New York: Springer‐Verlag.

Saenger W (1984) Principles of Nucleic Acid Structure. Springer Advanced Texts in Chemistry. New York: Springer‐Verlag.

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Soukup, Garrett A(May 2003) Nucleic Acids: General Properties. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0001335]