Every Coding Sequence Has Three Possible Reading Frames

KEY CONCEPT
- Usually only one of the three possible reading frames is translated and the other two are closed by frequent termination signals.

If the genetic code is read in nonoverlapping triplets, there are three possible ways of translating any nucleotide sequence into polypeptide, depending on the starting point. These are called reading frames. For the sequence

A C G A C G A C G A C G A C G A C G
the three possible reading frames are
ACG ACG ACG ACG ACG ACG ACG
CGA CGA CGA CGA CGA CGA CGA
GAC GAC GAC GAC GAC GAC GAC
A reading frame that consists exclusively of triplets encoding amino acids is called an open reading frame (ORF). A sequence that is translated into polypeptide has a reading frame that begins with a special initiation codon (AUG) and then extends through a series of triplets encoding amino acids until it ends at one of three termination codons (UAA, UAG, or UGA).
A reading frame that cannot be read into polypeptide because termination codons occur frequently is said to be closed, or blocked. If a sequence is closed in all three reading frames, it
cannot have the function of encoding polypeptide.
When the sequence of a DNA region of unknown function is obtained, each possible reading frame can be analyzed to determine whether it is open or closed. Usually no more than one of the three possible reading frames is open in any single stretch of DNA. FIGURE 1. shows an example of a sequence that can be read in only one reading frame because the alternative reading frames are closed by frequent termination codons. A long ORF is unlikely to exist by chance; if it had not been translated into polypeptide, there would have been no selective pressure to prevent the accumulation of termination codons. Therefore, the identification of a lengthy open reading frame is taken to be prima facie evidence that the sequence is (or until recently has been) translated into a polypeptide in that frame. An ORF for which no protein product has been identified is sometimes called an unidentified reading frame (URF).

FIGURE 1. An open reading frame starts with AUG and continues in triplets to a termination codon. Closed reading frames can be interrupted frequently by termination codons.