<?xml version="1.0" encoding="iso-8859-1" ?>
<rss version="2.0">
  <channel>
    <title>Nucleics Forum</title>
    <link>http://www.nucleics.com/forum/index.php</link>
    <description><![CDATA[]]></description>
    <language>EN</language>
    <pubDate>Sat, 17 Jul 2010 20:39:13 -0400</pubDate>
    <lastBuildDate>Sat, 17 Jul 2010 20:39:13 -0400</lastBuildDate>
    <category>Nucleics Forum</category>
    <generator>Phorum 5.1.22</generator>
    <ttl>600</ttl>
    <item>
      <title>[DNA Sequencing Forum] Re: different sequences/same site</title>
      <link>http://www.nucleics.com/forum/read/10/3712/3713.html#msg-3713</link>
      <author>nucleics</author>
      <description><![CDATA[Without seeing the traces it is hard to comment.]]></description>
      <category>DNA Sequencing Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/10/3712/3713.html#msg-3713</guid>
      <pubDate>Sat, 17 Jul 2010 20:39:13 -0400</pubDate>
    </item>
    <item>
      <title>[DNA Sequencing Forum] different sequences/same site</title>
      <link>http://www.nucleics.com/forum/read/10/3712/3712.html#msg-3712</link>
      <author>Tom</author>
      <description><![CDATA[Hi,
I encountered 2 interesting sequencing problems:)

First- In case of one PCR product, forward and reverse primers give me a different nucleotide in certain position. I mean that sequencing with forward primer gives for example A and sequencing with reverse primer gives for example G in the same position. The rest of the sequence is identical. It is not an accident, I repeated PCR and sequencing several times and it was the same all the time. All forwards say A and all reverses say G. The chromatogram looks good, no mixed peaks. 

The second mysterious error is quite similar. 
The sequence from reverse primer looks like that: TTT 
and the sequence from forward looks like that:    -TT 
Peaks surrounding that region are of the good quality  and  they look good and clear in that region too. And again...I repeated PCR and sequencing and the error persisted. How can I know if the true sequence is TTT or just TT? 

Do you have any suggestions? I do not know how to decide about the true sequence in these two cases. Thank you.]]></description>
      <category>DNA Sequencing Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/10/3712/3712.html#msg-3712</guid>
      <pubDate>Sat, 17 Jul 2010 19:48:43 -0400</pubDate>
    </item>
    <item>
      <title>[DNA Sequencing Forum] ABI sequencing</title>
      <link>http://www.nucleics.com/forum/read/10/3520/3520.html#msg-3520</link>
      <author>Jennco</author>
      <description><![CDATA[I am trying to do sequencing for the first time in my lab. We normally only run fragment analysis. We are using the Applied Biosystems 50cm capillary. Does anyone have any experience with them. The manual says 100 runs but when we are doing fragment analysis we can usually get about 400 runs with out sacrificing quality.]]></description>
      <category>DNA Sequencing Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/10/3520/3520.html#msg-3520</guid>
      <pubDate>Tue, 29 Jun 2010 13:35:01 -0400</pubDate>
    </item>
    <item>
      <title>[DNA Sequencing Forum] Re: short sequences problem</title>
      <link>http://www.nucleics.com/forum/read/10/2060/3519.html#msg-3519</link>
      <author>Bernie</author>
      <description><![CDATA[Hi Daniel,
With regard to cleaning capillaries,I would be interested in your protocol for that. We use the 3130xl automated sequencer. After approx 150 runs we buy new capillaries. Does this cleaning protocol extend their life beyond that? 

best wishes
Bernie]]></description>
      <category>DNA Sequencing Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/10/2060/3519.html#msg-3519</guid>
      <pubDate>Tue, 29 Jun 2010 06:35:42 -0400</pubDate>
    </item>
    <item>
      <title>[DNA Sequencing Forum] what are the disadvantages of SR(split read) method in sequencing and how to avoid these disadvantages?</title>
      <link>http://www.nucleics.com/forum/read/10/3455/3455.html#msg-3455</link>
      <author>zengxi</author>
      <description><![CDATA[SR(split read) method is popular now. But SR also will arrive at many wrong results,that is to say, wrong indels such as wrong deletion site or quantity and  wrong insertion site or quantity. I wonder what's the distanvages  of SR and how to avoid these disadvantages.I really appreciate it if anyone help me solve this problem, thank you!]]></description>
      <category>DNA Sequencing Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/10/3455/3455.html#msg-3455</guid>
      <pubDate>Thu, 10 Jun 2010 08:48:33 -0400</pubDate>
    </item>
    <item>
      <title>[DNA Sequencing Forum] GeXP vs ABI 3500</title>
      <link>http://www.nucleics.com/forum/read/10/3454/3454.html#msg-3454</link>
      <author>varvara</author>
      <description><![CDATA[I am interested in the performance and the price of sequencing per sample for both machines.

Many thanks]]></description>
      <category>DNA Sequencing Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/10/3454/3454.html#msg-3454</guid>
      <pubDate>Wed, 09 Jun 2010 16:02:31 -0400</pubDate>
    </item>
    <item>
      <title>[PCR Forum] Platinum Pfx Polymerase by Invitrogen</title>
      <link>http://www.nucleics.com/forum/read/12/3447/3447.html#msg-3447</link>
      <author>desireeazanes</author>
      <description><![CDATA[I am doing some cloning work so I used Platinum Pfx Polymerase for my PCR.  I also used two sets of primers.  The results were great for the second primer set but not with the first primer set. I tried including varying amounts of PCR enhancer that comes with the kit but again, no product.  

Has anyone used this product before?

Please suggest what I can do to optimize the conditions.

Thanks!]]></description>
      <category>PCR Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/12/3447/3447.html#msg-3447</guid>
      <pubDate>Wed, 12 May 2010 23:46:24 -0400</pubDate>
    </item>
    <item>
      <title>[PCR Forum] Re: PCR product storage</title>
      <link>http://www.nucleics.com/forum/read/12/409/3076.html#msg-3076</link>
      <author>Mark Flinn</author>
      <description><![CDATA[After having mixed together the master mix along with primers, templates, et cetera, how long (and how) can I store the tubes BEFORE running PCR?]]></description>
      <category>PCR Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/12/409/3076.html#msg-3076</guid>
      <pubDate>Mon, 19 Apr 2010 22:17:46 -0400</pubDate>
    </item>
    <item>
      <title>[DNA Isolation Forum] Air drying</title>
      <link>http://www.nucleics.com/forum/read/13/3069/3069.html#msg-3069</link>
      <author>sarah</author>
      <description><![CDATA[Once air dried, what is the best emthod for re-suspending DNA prior to PCR assays?]]></description>
      <category>DNA Isolation Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/13/3069/3069.html#msg-3069</guid>
      <pubDate>Mon, 12 Apr 2010 04:57:00 -0400</pubDate>
    </item>
    <item>
      <title>[PCR Forum] SSP=PCR</title>
      <link>http://www.nucleics.com/forum/read/12/3062/3062.html#msg-3062</link>
      <author>cyang</author>
      <description><![CDATA[What is sequence specific primer and single specific primer?
I would like to know what do the sequence specific primer and the  single specific primer same ?]]></description>
      <category>PCR Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/12/3062/3062.html#msg-3062</guid>
      <pubDate>Tue, 30 Mar 2010 22:24:39 -0400</pubDate>
    </item>
    <item>
      <title>[DNA Sequencing Forum] Re: Strange looking chromatogram</title>
      <link>http://www.nucleics.com/forum/read/10/2950/2952.html#msg-2952</link>
      <author>nucleics</author>
      <description><![CDATA[Send me the trace file and I will take a look at it.]]></description>
      <category>DNA Sequencing Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/10/2950/2952.html#msg-2952</guid>
      <pubDate>Fri, 05 Mar 2010 05:13:36 -0500</pubDate>
    </item>
    <item>
      <title>[DNA Sequencing Forum] Strange looking chromatogram</title>
      <link>http://www.nucleics.com/forum/read/10/2950/2950.html#msg-2950</link>
      <author>Amy Chin</author>
      <description><![CDATA[Hi again,

In our recent sequencing runs, we noticed that the chromatograms of a few samples had peaks that overlap a little, which could be an indication that the capillary is going bad. It's not all the samples, and the incidence seems pretty random. 

We're not sure what the real problem is, so if anyone can help, I can send the chromatogram over. Thanks!]]></description>
      <category>DNA Sequencing Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/10/2950/2950.html#msg-2950</guid>
      <pubDate>Fri, 05 Mar 2010 02:11:20 -0500</pubDate>
    </item>
    <item>
      <title>[DNA Sequencing Forum] Re: Mixed signal in the middle of sequencing trace</title>
      <link>http://www.nucleics.com/forum/read/10/2790/2949.html#msg-2949</link>
      <author>Amy Chin</author>
      <description><![CDATA[nucleics Wrote:
-------------------------------------------------------
&gt; This sound like an indel. Are you sequencing PCR
&gt; products from a heterozygous individual?

Yes. We finally understood why we got these results are you're right indeed. It was a heterozygous individual. Thanks!]]></description>
      <category>DNA Sequencing Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/10/2790/2949.html#msg-2949</guid>
      <pubDate>Fri, 05 Mar 2010 02:05:06 -0500</pubDate>
    </item>
    <item>
      <title>[PCR Forum] Failure to sequence DNA from amniotic fluid</title>
      <link>http://www.nucleics.com/forum/read/12/2947/2947.html#msg-2947</link>
      <author>Nethra</author>
      <description><![CDATA[Hi im a molecular biologist working at a genetic diagnostic laboratory and am currently facing a problem with sequencing DNA from amniotic fluid samples for diagnosis of ß-thalassemia. We use and ABI 3130 sequencing machine and have the usual protocol of PCR, purification and cycle sequencing. Since of late we are unable to get any product from DNA extracted from amniotic fluid. We have ruled out possibility of Primer and PCR cycle problems and DNA from blood gives a clear cut result. I value any suggestions or advice anyone has to offer and asap please. If a similar work is going on I would also appreciate any references that will help. Thanks]]></description>
      <category>PCR Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/12/2947/2947.html#msg-2947</guid>
      <pubDate>Tue, 02 Mar 2010 11:57:17 -0500</pubDate>
    </item>
    <item>
      <title>[DNA Sequencing Forum] Re: AppliedBiosystems vs Beckman-Coulter</title>
      <link>http://www.nucleics.com/forum/read/10/2839/2935.html#msg-2935</link>
      <author>Bill</author>
      <description><![CDATA[Hi there.

Can I suggest a third option?
Did you ever considered buying a refurbished instrument? Maybe a 3130 or even a 3730.

Cheers 

Bill]]></description>
      <category>DNA Sequencing Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/10/2839/2935.html#msg-2935</guid>
      <pubDate>Sat, 20 Feb 2010 09:05:07 -0500</pubDate>
    </item>
    <item>
      <title>[PCR Forum] weird pcr product  ask for help!</title>
      <link>http://www.nucleics.com/forum/read/12/2871/2871.html#msg-2871</link>
      <author>nccutudou</author>
      <description><![CDATA[I did three batches of pcr last Monday and Tuesday. Got bands every time. Weird things happened when I tried a large batch of samples last Thursday. Target bands did not show in gel. But you could see that pcr products showed near gel wells. I tried new tubes of buffers,dntps,primers and taq for three times and it didn't work. I even tried the exactly same templates which got bands before. The result were still same. No bands at all. What could be the reason? Thanks
I'm new here. I don't know how to post picture here? I think the picutres of gel may help to know the problems better.]]></description>
      <category>PCR Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/12/2871/2871.html#msg-2871</guid>
      <pubDate>Sun, 17 Jan 2010 12:47:26 -0500</pubDate>
    </item>
    <item>
      <title>[PCR Forum] Re: PCR product storage</title>
      <link>http://www.nucleics.com/forum/read/12/409/2865.html#msg-2865</link>
      <author>suranjana</author>
      <description><![CDATA[Jinous Wrote:
-------------------------------------------------------
&gt; How long we can keep our PCR products(if they are
&gt; in water) in the fridge before purificatin
&gt; procedue and how long before cloning? Don't
&gt; freezing and thawing influence our tests? Do you
&gt; recommend us to freeze all of our samples in water
&gt; after PCR,if we don't have time to continue the
&gt; procedure immediately?
My refrigerator (-20 c) was switched off for overnight and my PCR products were there. Is it o.k ?]]></description>
      <category>PCR Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/12/409/2865.html#msg-2865</guid>
      <pubDate>Mon, 11 Jan 2010 03:36:40 -0500</pubDate>
    </item>
    <item>
      <title>[PCR Forum] Rapid Amplification of cDNA Ends question</title>
      <link>http://www.nucleics.com/forum/read/12/2853/2853.html#msg-2853</link>
      <author>hianghao</author>
      <description><![CDATA[Hi, i am new in molecular biology and i need some help in RACE...
In 5' RACE, after the production of 1st strand cDNA using gene-specific-primer 1 and addition of polyT tail, another gsp 2 is used together with anchor primer to amplify that cDNA. My question is, why don't we use gsp1 for amplification instead of gsp2?
2nd is, if gsp1 &amp; 2 are parts of known sequence (designated as X) which i obtain from 3'RACE, will X have overlapping sequence with cDNA obtain from 5'RACE? If yes, can i assume that the overlapping sequence is the sequence of gsp2+a few nucleotide, since i get gsp1 from X?
3rd, can i directly use cDNA generated from 3'RACE as primer for 5'RACE, instead of using some part of it to design gsp1? If not, y?]]></description>
      <category>PCR Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/12/2853/2853.html#msg-2853</guid>
      <pubDate>Mon, 04 Jan 2010 19:33:47 -0500</pubDate>
    </item>
    <item>
      <title>[PCR Forum] PCR primer concentration- pls read this n pls reply!!</title>
      <link>http://www.nucleics.com/forum/read/12/2841/2841.html#msg-2841</link>
      <author>DK</author>
      <description><![CDATA[I'm working with DNA aptamers and i cannot figure out how to set up my PCR. My oligos are around 100 bases in length and i need to perform a PCR after each Selex round.. the general PCR setup suggests a primer concentration of 1uM..that wud be around 100pmoles of primer in a 100ul reaction rite??So if i wanted to amplify my oligos..for say 10 rounds.. how do i calculate the amount of template i start with? The way i figure...with a lot of calculation.. is that i cannot even amplify..say 1 pmol of my oligos?? Is there an easier way to calculate the template vs primer ratio? Keeping in mind the size of my oligos?]]></description>
      <category>PCR Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/12/2841/2841.html#msg-2841</guid>
      <pubDate>Wed, 23 Dec 2009 22:30:00 -0500</pubDate>
    </item>
    <item>
      <title>[DNA Sequencing Forum] AppliedBiosystems vs Beckman-Coulter</title>
      <link>http://www.nucleics.com/forum/read/10/2839/2839.html#msg-2839</link>
      <author>genomer</author>
      <description><![CDATA[Hi people!

Will somebody help me to make right choice?
The problem is like that: I'm going to get sequencer for my genotyping laboratory and I've got 2 options to choose between - ABI 3500 and GenomeLab (from Beckman).

So which one would you recommend to obtain?

Some people say that GenomeLab uses the chemistry that is too fastidious in terms of PCR product purity - due to (probably) poor ability of Beckman proprietary Taq polymerase to incorporate ddNTPs.
That is in contrast to nearly completely &quot;adjusted&quot; Taq polymerase produced by Applied Biosystems.
Again, these are only rumours.

So, does anybody know anything more precise about all this stuff?

Thank you in advance!]]></description>
      <category>DNA Sequencing Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/10/2839/2839.html#msg-2839</guid>
      <pubDate>Wed, 23 Dec 2009 13:44:45 -0500</pubDate>
    </item>
    <item>
      <title>[PCR Forum] Thermal Detector for PCR machines</title>
      <link>http://www.nucleics.com/forum/read/12/2828/2828.html#msg-2828</link>
      <author>MMM</author>
      <description><![CDATA[Does anybody know anything that can be used for measuring the temperatures in the wells of PCR machines during thermal cycles?

Thanks in advance!]]></description>
      <category>PCR Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/12/2828/2828.html#msg-2828</guid>
      <pubDate>Wed, 16 Dec 2009 17:49:45 -0500</pubDate>
    </item>
    <item>
      <title>[PCR Forum] Re: RE failure</title>
      <link>http://www.nucleics.com/forum/read/12/2734/2822.html#msg-2822</link>
      <author>nucleics</author>
      <description><![CDATA[Yes it might be methylation that is the cause. Unless there is another enzyme that is not affected by methylation that you can use you won't be much you can do about this. Might be worth trying another enzyme site.]]></description>
      <category>PCR Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/12/2734/2822.html#msg-2822</guid>
      <pubDate>Mon, 14 Dec 2009 17:26:01 -0500</pubDate>
    </item>
    <item>
      <title>[PCR Forum] Re: PCR product storage</title>
      <link>http://www.nucleics.com/forum/read/12/409/2821.html#msg-2821</link>
      <author>nucleics</author>
      <description><![CDATA[The problem with storing PCR products in water is if you have any nucleases around. It is better to store them in 10/0.1 TE. This way the pH won't drop from absorbance of CO2 and the EDTA will keep the nucleases from chewing up the DNA.]]></description>
      <category>PCR Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/12/409/2821.html#msg-2821</guid>
      <pubDate>Mon, 14 Dec 2009 17:23:51 -0500</pubDate>
    </item>
    <item>
      <title>[PCR Forum] Re: Primers out overnight</title>
      <link>http://www.nucleics.com/forum/read/12/2738/2820.html#msg-2820</link>
      <author>nucleics</author>
      <description><![CDATA[Most likely yes, especially if you store them in 10/0.1 TE.]]></description>
      <category>PCR Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/12/2738/2820.html#msg-2820</guid>
      <pubDate>Mon, 14 Dec 2009 17:21:53 -0500</pubDate>
    </item>
    <item>
      <title>[General Questions] Re: ABI 310 - Discussion/ troubleshooting/ community....</title>
      <link>http://www.nucleics.com/forum/read/11/2791/2817.html#msg-2817</link>
      <author>j</author>
      <description><![CDATA[I hear the same thing...hopefully not a big deal?  I got some arcing when I had extra buffer around the septas holder in position one.  Blue light and sparks were coming out and every time I hear that clicking sound I think it's happening again...but I look and I don't see anything.]]></description>
      <category>General Questions</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/11/2791/2817.html#msg-2817</guid>
      <pubDate>Mon, 14 Dec 2009 11:33:06 -0500</pubDate>
    </item>
    <item>
      <title>[DNA Sequencing Forum] genomic DNA sequence</title>
      <link>http://www.nucleics.com/forum/read/10/2808/2808.html#msg-2808</link>
      <author>Kalpataru Halder</author>
      <description><![CDATA[I have faced the problem about genomic DNA sequence. When I have used the genomic DNA as template, no signal was obtained. How much template should I use for successful reaction?]]></description>
      <category>DNA Sequencing Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/10/2808/2808.html#msg-2808</guid>
      <pubDate>Fri, 04 Dec 2009 11:38:21 -0500</pubDate>
    </item>
    <item>
      <title>[PCR Forum] Re: one day pcr works, the next it doesn't</title>
      <link>http://www.nucleics.com/forum/read/12/2782/2806.html#msg-2806</link>
      <author>nucleics</author>
      <description><![CDATA[This sounds like primer poisoning. What happens is you end up contaminating your work area with primer dimers and small fragments from your PCR and they kill the later PCR reactions. This is arely problem with long PCR. The solution is to make all new solutions and use different pippetors (go to a different lab to set up the reaction).]]></description>
      <category>PCR Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/12/2782/2806.html#msg-2806</guid>
      <pubDate>Thu, 03 Dec 2009 00:53:31 -0500</pubDate>
    </item>
    <item>
      <title>[DNA Sequencing Forum] Re: Mixed signal in the middle of sequencing trace</title>
      <link>http://www.nucleics.com/forum/read/10/2790/2805.html#msg-2805</link>
      <author>nucleics</author>
      <description><![CDATA[This sound like an indel. Are you sequencing PCR products from a heterozygous individual?]]></description>
      <category>DNA Sequencing Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/10/2790/2805.html#msg-2805</guid>
      <pubDate>Thu, 03 Dec 2009 00:50:07 -0500</pubDate>
    </item>
    <item>
      <title>[PCR Forum] ETS amplification problem</title>
      <link>http://www.nucleics.com/forum/read/12/2804/2804.html#msg-2804</link>
      <author>Simon Uribe</author>
      <description><![CDATA[Hi all, 
I've been having problems amplifying ETS from plant samples. I've been getting a band in my negatives and this band has been around in my lab for some time now. Some people have sequenced it without getting any results (i.e. nothing, being a dye blob or something) but then i sequenced it and I got a full 400bp sequence! 
Now everybody is freaking out and we can't get rid off it. I've tried UVing the stock primer, change set of primers (ETS B - 18sIGS  to ETS B - 18sE) reduce amount of primer in master mix to half, amplifying without BSA, and changing annealing temperature. I was wondering if anyone has had this problem too. 
Thanks a lot 

Simon]]></description>
      <category>PCR Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/12/2804/2804.html#msg-2804</guid>
      <pubDate>Thu, 03 Dec 2009 00:47:44 -0500</pubDate>
    </item>
    <item>
      <title>[General Questions] ABI 310 - Discussion/ troubleshooting/ community....</title>
      <link>http://www.nucleics.com/forum/read/11/2791/2791.html#msg-2791</link>
      <author>Mike</author>
      <description><![CDATA[Not sure if this is an appropriate forum but here goes anyway....

I'm using an old ABI 310 sequencer - which it seems is so dated that there are no discussion groups/forums around.  Now I'm sure I'm not the only one still using one of these-  any want to point me in the direction of a forum?  Or can we start one? Is anyone there?

I have hit a few problems with the intstrument which I've overcome, a few which I haven't -  lets try and find some more users.

Right now everything seems to be working fine however I've noticed a new clicking type sound when the electrophoresis is running-  sounds almost like electrical shorting/arching - not that I can find any apparent cause....  Any thoughts?]]></description>
      <category>General Questions</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/11/2791/2791.html#msg-2791</guid>
      <pubDate>Thu, 12 Nov 2009 12:10:03 -0500</pubDate>
    </item>
  </channel>
</rss>
