Inmolecular biology, areading frame is a specific choice out of the possible ways to read thesequence of nucleotides in anucleic acid (DNA orRNA) molecule as a sequence of triplets. Where these triplets equate toamino acids or stop signals duringtranslation, they are calledcodons.
A single strand of anucleic acid molecule has aphosphoryl end, called the5′-end, and ahydroxyl or3′-end. These define the5′→3′ direction. There are three reading frames that can be read in this 5′→3′ direction, each beginning from a different nucleotide in a triplet. In a double stranded nucleic acid, an additional three reading frames may be read from the other,complementary strand in the 5′→3′ direction along this strand. As the two strands of a double-stranded nucleic acid molecule are antiparallel, the 5′→3′ direction on the second strand corresponds to the 3′→5′ direction along the first strand.[1][2]
In general, at the most, one reading frame in a given section of a nucleic acid, is biologically relevant (open reading frame). Some viral transcripts can be translated using multiple, overlapping reading frames. There is one known example of overlapping reading frames in mammalianmitochondrial DNA: coding portions of genes for 2 subunits of ATPase overlap.
DNA encodes protein sequence by a series of three-nucleotidecodons. Any given sequence of DNA can therefore be read in six different ways: Three reading frames in one direction (starting at different nucleotides) and three in the opposite direction. Duringtranscription, the RNA polymerase read the template DNA strand in the 3′→5′ direction, but the mRNA is formed in the 5′ to 3′ direction.[3] The mRNA is single-stranded and therefore only contains three possible reading frames, of which only one istranslated. The codons of the mRNA reading frame are translated in the 5′→3′ direction intoamino acids by aribosome to produce apolypeptide chain.
Anopen reading frame (ORF) is a reading frame that has the potential to betranscribed into RNA andtranslated into protein. It requires a continuous sequence of DNA which may include astart codon, through a subsequent region which has a length that is a multiple of 3 nucleotides, to astop codon in the same reading frame.[4]
When a putative amino acid sequence resulting from the translation of an ORF remained unknown in mitochondrial and chloroplast genomes, the corresponding open reading frame was called an unidentified reading frame (URF). For example, theMT-ATP8 gene was first described as URF A6L when the complete humanmitochondrial genome was sequenced.[5]
The usage of multiple reading frames leads to the possibility ofoverlapping genes; there may be many of these in viral, prokaryote, and mitochondrialgenomes.[6] Some viruses, e.g.hepatitis B virus andBYDV, use several overlapping genes in different reading frames.
In rare cases, a ribosome may shift from one frame to another during translation of an mRNA (translational frameshift). This causes the first part of the mRNA to be translated in one reading frame, and the latter part to be translated in a different reading frame. This is distinct from aframeshift mutation, as the nucleotide sequence (DNA or RNA) is not altered—only the frame in which it is read.