Question

Can someone please help clear up some confusion I have regarding transcription?

DNA has two anti-parallel strands. The 5'-3' strand serves as the template strand for RNA synthesis. A promoter region is required for RNA polymerase to bind to the DNA at the correct gene. The promoter is located upstream from the gene of interest (i.e. further up towards the 5' end of the 5'-3' strand. What I don't understand is that, if RNA polymerase, like DNA polymerase, can only read the template strand in the 3'-5' direction, wouldn't the promoter be at the wrong end of the gene to begin transcription

Answer 1

since the promoter has to read the lagging strand from 5' to 3', it needs the help of RNA primer. The new strand is formed by linking Okazaki fragments using enzyme DNA ligase and DNA polymerase removes RNA primers

Answer 2

@ninhi5 .... the promoter doesn't read anything.. It is found on the DNA strand. Actually, promoters are the regions of the DNA that signal initiation of transcription. It is the sigma factor of the RNA polymerase which recognises the promoter regions.

Does RNA polymerase read the DNA strand only in the 3' to 5' direction? I don't think so. However, what is true is that RNA is always synthesised by RNA polymerase in the 5' to 3' direction. Maybe that's why there's no problem in terms of a need for RNA primers during transcription 'cause there's no leading and lagging strand to be taken into consideration..

Answer 3

@norma.. I wanna rectify something.. RNA polymerase does read the DNA strand in the 3' to 5' direction. Just saw that here:
http://wiki.answers.com/Q/In_which_direction_does_RNA_polymerase_read_a_DNA_strand

I think that you should read this:
http://www.physicsforums.com/showthread.php?t=263575

It's interesting..

Answer 4

you made a good point there, i appreciate it

Answer 5

@ninhi5 .. thanks..:)

Answer 6

To add onto what others have already wrote,



You are correct, @Norma, in saying that the template DNA strand is read in a 3' to 5' direction. The promoter, which should and is located upstream of the gene, is indeed located further up towards the 5' end - but of the opposite DNA strand (i.e., the coding strand).

Take a look at the quick sketch to maybe give you a better idea. The boxed in area is the promoter. The arrow indicates where the RNA polymerase will enter and begin transcription, in a 5' to 3' direction of RNA synthesis. You see that the promoter is located to the more 3' area of the /template/ strand, but it's located upstream of the /coding/ (or opposite) strand, which I assume is what is referred to when speaking of the "gene" in this context.