During transcription: Direction

Just like roads have lanes that operate in different directions, DNA and RNA have direction! Let’s get oriented on how directions work in nucleic acids. Recall that DNA and RNA nucleotides have a ribose sugar that is bound to an OH group at carbon C3 and a phosphate group that is bound to carbon C5 (Figure 4-19).

Figure 4-19. Comparing the nucleotide of DNA (left) and RNA (right), you’ll notice only a very minor difference in the structure

It is common language to say that the phosphate attached at the C5 carbon position of the ribose sugar is the “5’ phosphate” (‘flve-prime-phos- phate’). The OH group on carbon C3 is referred to as the “3’ OH” (‘three-prime-o-H’). The apostrophe is pronounced as “prime”.

These two positions of the ribose are what become connected to form a chain of nucleotides. If you look again at Figure 1-17, you will see that at the beginning of the strands there is a 5’ phosphate group that is not attached to anything. Also, you’ll see at the other end a 3’ OH that is not connected to anything. These two end groups are how we understand the position and directionality of DNA.

In the world of nucleic acids, the 5’ phosphate of a DNA (Figure 1-17) or RNA (Figure 4-20) strand is always considered the ‘beginning’. The 3’ OH of the DNA or RNA is considered the ‘end’ and cellular machines such as RNA polymerase, travel from the 5’ P toward the 3’ OH (Figure 4-20). A very common way in which scientists describe the location in a DNA sequence is using ‘upstream’ and ‘downstream’. The 5’ phosphate is upstream of the 3’ OH (Figure 4-24).

Figure 4-24. When using “upstream of” and “downstream from” terminology, you refer to whether something is closer to the 5’ phosphate (upstream) or the 3’OH (downstream) of a specific strand. Be careful! You also have to know what strand you’re referring to. Here, we are referring to the pink DNA strand

Genetic Engineering Heroes often use upstream and downstream to describe a location or direction on a strand of nucleic acid. For example, you can say “the promoter is just upstream of the coding region”, or “I get it, the coding sequence is just downstream of the promoter!” (Figure 4-24).

But DNA has two strands. What happens when they come together? There are two directions, and each depends on which strand you are referring to. When two DNA strands zip together to form the DNA double helix, the strands bind in an “antiparallel fashion”, meaning that the 5’ phosphate ends of each strand are at the opposite ends (Figure 4-25).

Figure 4-25. Strands of nucleic acids have directionality, meaning one end is different from the other. When two strands of DNA bind together, they bind in an anti-parallel manner so that the 5’ end of one strand is at the 3’ end of the other

Look back to Figure 1-17 and notice where the 5’ phosphate and 3’ OH are located on the two strands. This means that the ‘upstream’ and ‘downstream’ terminology depends on which strand you’re referring to.