Question

I understand that there are three stop codons: UAG, UGA, UAA. Please explain why are there 6 possible reading frames (stretches that do not have any stop codons) when detecting an open reading frame (ORF) and how can cDNA help confirm the correct reading frame? Thanks!

Answer 1

An open reading frame is that sequence of DNA or RNA which codes for protein. It is a continuous stretch of codons. If a DNA sequence is

5' CAA TGG CTA GGT ACT ATG TAT GAG 3'

3' GTT ACC GAT CCA TGA TAC ATA CTC 5'

Now, these sequences can be read in three ways - It can start from the first letter or the second letter or the third letter.

If the top strand acts as the template strand, then the reading frame can be

3' GAG TAT GTA TCA TGG ATC GGT AAC 5'

Or, 3' G AGT ATG TAT CAT GGA TCG GTA AC 5'

Or, 3' GA GTA TGT ATC ATG GAT CGG TAA C 5'

If the bottom strand acts as the template strand, then also three reading frames are possible in 3'-5' direction in the same manner. That is why six reading frames are possible in double stranded DNA strand, whereas RNA has three reading frames as it is single stranded.

ORF is used for searching genes. If it is part of a gene, rather than a complete gene, then the given sequence may be a segment of the original whose transcription has already started. The first nucleotide or the second nucleotide of the given sequence may be part of the previous codon. That is why, the first nucleotide itself or the first and second nucleotide together is taken out forming two different reading frames. As the codon is read in triplets, if one base is left out, then the reading frame will be different. If two bases are left out, then also the reading frame will change. But, if three bases are taken , then no change, means it will be like the original codon. That is why, for each strand, only, three combinations are possible.

cDNA is that DNA which is produced from a single stranded RNA. Because, RNA translates into protein, so, the DNA sequence obtained from RNA --->DNA conversion is the correct reading frame.