DNA Directionality: 3' to 5' & Bacterial DNA Explained

[at2341]

Hi,

To my understanding, the directionality of DNA (3' to 5') (5' to 3') is based on where the free(unattached) end of the ribose is.

With this idea, how can bacterial DNA (where the ends are joined together) have directionality?

 

[matteo83]

Cut it!

 

[BoomBoom]

Circular DNA is still DNA. One strand will be 3'-5' and the other 5'-3'. Bases may only be added to the 3' end of any DNA strand, so that it is unidirectional.

To clarify: the 5' end is a phosphate grp and the 3' is a hydroxyl grp

 

[at2341]

I appreciate your replies,

Once the 3' end joins the 5' end to make a circle, you really can't tell where the 3' and 5' ends start. Is this correct? thanks

 

[BoomBoom]

Once the 3' end joins the 5' end to make a circle, you really can't tell where the 3' and 5' ends start. Is this correct? thanks

There is no start or end really, just direction. One strand will be in one direction, and the other complimentary strand in the other. As Matteo said...cut it! :)

 

[at2341]

1) Without cutting the DNA, there is no way to tell which strand is going in which direction? Is this correct?

2) If we can't tell which strand is which, how can the polymerase differentiate?

Thanks

 

[NoTime]

I think what you may be asking about is which is the sense and anti sense strand.
If so then several steps are required for translation of a segment.
Unfolding, attachment of one or more promoters, and an available start codon.
AFAIK both sides of the DNA molecule can satisfy these conditions.
So the sense strand is the one that satisfies the requirements.

 

[BoomBoom]

1) Without cutting the DNA, there is no way to tell which strand is going in which direction? Is this correct?

2) If we can't tell which strand is which, how can the polymerase differentiate?

It depends on whether you are talking about replication (DNA polymerase) or transcription (RNA polymerase).

In replication, I believe there is an enzyme that "nicks" the DNA strand at a certain location (based on sequence) making a 3' and a 5' end. In transcription, the RNA polymerase binds to a promoter sequence which is aligned in a certain direction. Polymerase reads from 3' to 5' direction so that the new DNA or RNA it makes is building in the 5' to 3' direction.

 

[at2341]

thank you guys for replying.

BoomBoom, that's exactly what I wanted to know... how do the enzymes differentiate which way to go. thanks

 

[JonMoulton]

Consider a strand of DNA from the perspective of the middle of the ribose ring. The 3' direction is toward where the oxygen of a phosphate group hooks directly to the ring. The 5' direction is toward the extracyclic methylene which is bound to another phosphate. You don't need to cut the strand to see this directionality. Let's arbitrarily call one end of an enzyme's binding site the front; the enzyme would encounter a very different shape of substrate surface if it binds a strand of DNA with its front in the 3' direction as opposed to binding with its front in the 5' direction. No nick of the strand is needed, the shape of the ribose ring is enough to determine directions on the strand.

 

[BoomBoom]

No nick of the strand is needed, the shape of the ribose ring is enough to determine directions on the strand.

Good point...I didn't think of that. Thanks Jon!