Base Sequence

The nucleic acids of living organisms (DNA and RNA) are composed of a sequence of repeating units, with each unit composed of three subunits: a sugar (deoxyribose or ribose), a phosphate group, and a nitrogen-containing structure called a base. A base sequence is the specific order in which those nitrogen-containing bases appear in a particular section of nucleic acid and, for each gene in an individual, determine the genotype of that individual.

DNA encodes information on genotype using four bases: adenine, thymine, cytosine, and guanine. Although DNA is a double helix, the existence of base pairs allows full communication of the information in a DNA double helix from one strand (called the coding or sense strand). RNA encodes the information on the relevant coding strand using a similar set of bases as DNA, only substituting uracil for thymine.

When reported in the literature or by a laboratory, base sequences adhere to a simple set of rules allowing [Page 214]universal interpretation of findings. Unless otherwise specified, a reported base sequence is for either the coding strand of a segment of DNA or the equivalent sequence of RNA and is read from left to right. When indicated, the length of the sequence will be given in base pairs (bp), acknowledging the fact that although only one strand is shown, the underlying DNA exists as a pair of complementary strands.

The first letter of each base is commonly used to abbreviate the name of the base in reporting base sequences, as a given sequence may be many hundreds or thousands of bases pairs in length. Sequences are typically written using all upper-case or all lower-case letters, although mixed usage is sometimes used when comparing two sequences to make it easier for the reader to determine differences between sequences.