Which one is the correct answer?

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

Moderators: honeev, Leonid, amiradm, BioTeam

User avatar
kanak33
Garter
Garter
Posts: 25
Joined: Sun Jun 10, 2007 9:57 am
Location: Paris and Laval - France
Contact:

Post by kanak33 » Mon Jun 11, 2007 1:33 pm

humm..Im sorry, Im trying to understand.
In your first answer you have wrote: "the first primer (5'-TAGCA-3' ) is the bottom strand" I didnt understand because (first Im not good in biological english vocabulary) the primer has the same letters (dont know the words for that molecules) than the bottom strand in the 5'-3' way. I mean there was no complementarity.

Then you just wrote:
The first primer in c) is complemtary to the upper strand and will extend (5'-->3') making a copy of the bottom strand

I agree with that...my problem was just the first answer...
Kanak
=>Is looking for some people to talk with to learn the biological english vocabulary in view of doing an internship in the US
Email or IM me!
Thank you!

blcr11
Viper
Viper
Posts: 672
Joined: Fri Mar 30, 2007 4:23 am

Post by blcr11 » Mon Jun 11, 2007 2:23 pm

Maybe what I should have said the first time was that the first primer is for making a copy of the bottom strand. It is complementary to the top strand. I was concentrating on keeping the 5'-3' directions straight because it is often confusing especially when designing the 3' primer. It's easy to order the wrong oligo by inadvertantly reversing the order of the bases. My original point was that the 5'-to-3' direction on the bottom strand reads from right to left--which is opposite the direction for the top strand.

I dunno, am I making this worse? Try writing (roughly) how the primers in c) might be bound to the DNA molecule. What you should see is that the first primer will displace a little piece of the bottom strand, with the 3' end of the primer pointing towards the rest of the bolded bases, while the second primer will displace a piece of the top strand with the 3' end of the primer also pointing toward the rest of the bolded bases.

If I ask you to design 5-base primers to amplify the bolded sequence, what would you design?

User avatar
kanak33
Garter
Garter
Posts: 25
Joined: Sun Jun 10, 2007 9:57 am
Location: Paris and Laval - France
Contact:

Post by kanak33 » Tue Jun 12, 2007 8:28 am

What do you mean by "the first primer will displace a little piece of the bottom strand, with the 3' end of the primer pointing towards the rest of the bolded bases" and same question for the top strand? Well this is everything that I didnt understand (if you could explain both in french and english..)

And I wonder something...Why the B answer wont be correct?
The first primer bound to the top strand in the 5'-3' way, and the second primer bound to the bottom strand in the same sense but reverse (right to left)...

I think that would be hard to explain..
Kanak
=>Is looking for some people to talk with to learn the biological english vocabulary in view of doing an internship in the US
Email or IM me!
Thank you!

blcr11
Viper
Viper
Posts: 672
Joined: Fri Mar 30, 2007 4:23 am

Post by blcr11 » Tue Jun 12, 2007 4:42 pm

Sorry. I only speak English—not necessarily well, but English. The primer binds to its complementary sequence. If the primer sequence is 5’-TAGCA-3’ on the bottom strand—if you prefer: it will read from left to right, 3’-ACGAT-5’—it will displace this part of the sequence of the bottom strand. The primer will then be positioned with its 3’ end pointing to the left. As the primer is extended, it displaces more of the bottom strand, using the top strand as a template to make a copy of the bottom strand. The same thing happens for the other primer, except that it is the top strand being displaced and the extension runs to the right. I’m sorry. I don’t know how to make it any clearer than that.

Hmm. I hadn't realized there was an upstream 5'-CTAGC-3' in the top strand, so actually b) will amplify the sequence in bold, but it amplifies some extra sequence as well. I think that was an unnecessary bit of confusion on the part of the teacher and you can make a case for either b) or c), though the strictest interpretation of the question asked means that c) is more correct - in my opinion anyway.

User avatar
kanak33
Garter
Garter
Posts: 25
Joined: Sun Jun 10, 2007 9:57 am
Location: Paris and Laval - France
Contact:

Post by kanak33 » Wed Jun 13, 2007 11:55 am

Hey, Its ok...

I just wrote the strand and primers on a paper and that match..I just needed to do that...
So yes, I agree, its the C answer which is correct.
Kanak
=>Is looking for some people to talk with to learn the biological english vocabulary in view of doing an internship in the US
Email or IM me!
Thank you!

hajimemasho
Garter
Garter
Posts: 3
Joined: Sun Jul 08, 2007 10:26 pm

Re: Which one is the correct answer?

Post by hajimemasho » Mon Jul 09, 2007 11:37 am

[quote="and also the sequence is reverse... "]

Don't forget primers are synthesised in reverse 3' - 5' direction because these disables , if you will the free hydroxyl groups on the 5' and 3'...

hajimemasho
Garter
Garter
Posts: 3
Joined: Sun Jul 08, 2007 10:26 pm

Post by hajimemasho » Tue Jul 10, 2007 8:58 am

Actually I was wrong..synthesis is always 5`-3`what I meant was..the addition of the nucleotide is from the 3`end...doh`!!

Post Reply

Who is online

Users browsing this forum: No registered users and 3 guests