Talk:Primer (molecular biology)

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This article was the subject of a Wiki Education Foundation-supported course assignment, between 10 January 2022 and 27 April 2022. Further details are available on the course page. Student editor(s): NMAlbaraiki (article contribs).

Need to create a article for Primer design software

Untitled

I see links in 'External links' to third party and commercial software. Before they become subject to heavy editing, I propose to create a new article listing all such software in a tabular format —Preceding unsigned comment added by 68.49.46.141 (talk) 20:21, 4 January 2011 (UTC)[reply]

Melting temperature versus annealing

I'm not familiar with this process, but from what I know of annealing, I'm not sure that "melting temperature" is the correct equivalent. --Michael Snow 21:48, 12 July 2005 (UTC)[reply]

It's not really about one temperature, but a shifting equilibrium: from annealed to separated and back. So when you lower the temperature, the primer anneals. When you heat it up again it 'melts' (separetes from the dna), but not all at once.

I am a molecular biologist. I modified the optimal length (20bp) and melting temperature (60C) according to my daily experience. I have very good experience with primer3 in picking primers working in experiments later. --Untergasser 14:33, 4 July 2006 (UTC)[reply]

I also use primer3 to help me design primers. Can a link to primer3 be added in addition to the other free (Primerfox) primer designing program? --Lunajurai (talk) 20:06, 18 January 2008 (UTC)[reply]
I think Melting temperature and annealing are similar but not exactly the same thing. Melting temperature refers to breaking apart the hydrogen bonds between two DNA/RNA strands. This depends on the length and makeup of each individual strand, as G-C bonding involves a with triple hydrogen bond, and A-T bonding involves a double hydrogen bonds. So Melting temperature is a temperature at which 50% of multiple copies of the same species of DNA/RNA are breaking apart into single stranded molecules. Annealing is the temperature at which short primers hybridize or bind to their complementary sequence in another DNA/RNA molecule which is not necessarily the same length. This will be at a temperature less than the Melting temperature.
See Polymerase chain reaction for more information --Zven 02:58, 29 August 2006 (UTC)[reply]

Wiki Education Foundation-supported course assignment

This article was the subject of a Wiki Education Foundation-supported course assignment, between 7 January 2019 and 24 April 2019. Further details are available on the course page. Student editor(s): Tcowan1996.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 07:11, 17 January 2022 (UTC)[reply]

Merge proposal

The Polymerase chain reaction article is too big! I propose moving the primer design information here, if it isn't already redundant. I also propose creating a new page PCR optimization and moving all the PCR optimization information there as well. -Madeleine 00:44, 23 March 2007 (UTC)[reply]

Wrong Information

Whoever keeps adding in the bit about Okazaki fragments, correct me if I'm wrong but arent Okazaki fragments the RNA strands produced on the LAGGING strand during DNA replication only, and not the actual primers themselves?

You have a point, Pwnz0r1337 -- I hadn't thought much about how correct the statement was when I undid your edit before. Between your choice of username and the fact you didn't both to leave any sort of comment in the edit summary, your deletion looked like vandalism. I won't apologize for my reversion; in the future, please give the reasoning behind the edits you make in the edit summary.
I'm responsible for the introduction of the statement. I was trying to give an example where readers could read further about naturally occuring primers & extension from them (since this article mostly cares about PCR), but it was a bad one and wrong in its claim of generality. For the introduction of a false statement, I apologize. Madeleine 12:19, 3 May 2007 (UTC)[reply]
No harm done, it could just as easily been me who was at fault. Pwnz0r1377 21:09, 3 May 2007 (UTC)[reply]
Sorry I was defensive in tone, I need to lighten up. I'm actually really glad you caught the mistake, I was just embarrassed. Thanks.  :-) Madeleine 23:17, 3 May 2007 (UTC)[reply]

Introduction

I think the introduction is just fine, can we get rid of the many "warnings" heading this article. Wiki is starting to become very messy with all these so called problems. —Preceding unsigned comment added by 67.162.142.67 (talk) 00:09, 11 November 2007 (UTC)[reply]

Software

I do not think that PrimerFox is the best external link. Primer3 is much more used (according to methods sections of scientific articles), is published, open-source, and has references to the original research it is based on to determine annealing temperatures. 134.160.83.73 (talk) 09:09, 21 May 2009 (UTC) Charles Plessy, molecular biologist.[reply]

I agree. Furthermore, there is the NCBI tool primer-BLAST that combines primer3 and BLAST into one tool. I add these two links since they are useful. --Firefly's luciferase (talk) 15:39, 29 November 2009 (UTC)[reply]

PCR Primer Design

It might be helpful to add in more information about PCR primers. Specifically the three main types used: oligo-dt Priming, Specific Priming, and Random Priming. As well as some general rules for synthesizing primers such as wanting at least a 50% ratio of G-C so that it will anneal strongly and making sure the forward and reverse primers have similiar G-C content and that the 3' end ends with a C or G (this is called the G/C clamp and ensure goods binding of the primer to where synthesis begins. These are interesting and helpful bits of knowledge I have learned in my molecular biology lab class. MicailaSpisak (talk) 07:39, 13 February 2016 (UTC)Micaila[reply]

A Commons file used on this page has been nominated for deletion

The following Wikimedia Commons file used on this page has been nominated for deletion:

Participate in the deletion discussion at the nomination page. —Community Tech bot (talk) 07:55, 14 May 2019 (UTC)[reply]

Primer vs monomer

Because of k-mer and polymer, I wonder if someone may be tempted to think that "primer" somehow means pri-mer. If the connection is helpful, someone might describe the meaning of "primer" as the "initial [poly]mers"). Note, it does not mean "monomer" (or uni-mer, if that were a thing). Intellec7 (talk) 19:59, 15 October 2020 (UTC)[reply]

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