sorsurus Posted February 8, 2006 Share Posted February 8, 2006 hello. I need help in finding a primer for my DNA sample. i need a primer for iron reducing bacteria gene. I've tried to find in over the internet but couldn't find it. Anyone care to help? Link to comment Share on other sites More sharing options...
rhiannon Posted February 8, 2006 Share Posted February 8, 2006 i would, if i understood the question Link to comment Share on other sites More sharing options...
Airmid Posted February 8, 2006 Share Posted February 8, 2006 I'm not quite sure what you're looking for. Check out this article please (Phylogenetic Analysis of Dissimilatory Fe(III)-Reducing Bacteria, and see if it fits your subject. Two primers are mentioned in Materials and Methods, are those what you're looking for? Airmid. Link to comment Share on other sites More sharing options...
prion Posted February 8, 2006 Share Posted February 8, 2006 hello.i need a primer for iron reducing bacteria gene. Can you not design it yourself? I mean design one from the sequence of whatever bit you want and then order it from a company that makes oligonucleotides? Isn't that what most labs do? I take it you're a student - ask where other people get their primers from? Link to comment Share on other sites More sharing options...
sorsurus Posted February 9, 2006 Author Share Posted February 9, 2006 thanx... i am doing PCR and i try to amplify this sequence to prove that the bacteria contain the iron reducing gene. The problem is, i don't know the primer used to amplify the target sequence. I want to use a specific primer, not the 16s rRNA by the way, thanx a lot Link to comment Share on other sites More sharing options...
Airmid Posted February 9, 2006 Share Posted February 9, 2006 I did a bit more reading on the subject (I'm interested in bacterial metabolism anyway) and I've reached the conclusion that there is no such thing as THE gene for iron reducing. The iron-reducing bacteria are a very diverse group and only two organisms, Geobacter and Shewanella, have been studied in detail. Here's two examples of relevant studies of Geobacter: Combining in-situ reverse transcriptase polymerase chain reaction, microscopy and x-ray photoelectron microscopy to investigate mineral surface-associated microbial activities OmcF, a Putative c-Type Monoheme Outer Membrane Cytochrome Required for the Expression of Other Outer Membrane Cytochromes in Geobacter sulfurreducens Studies to find evidence for, and characterisation of, iron-reducing bacteria seems to have been undertaken by 16s rRNS analysis, though some have been using more specific primers than the general bacterial ones. For example, I came across this article, Diversity of Geobacteraceae Species Inhabiting Metal-Polluted Freshwater Lake Sediments Ascertained by 16S rDNA Analyses, which uses a Geobacteraceae-specific primer. Of course, you would be missing out on the other iron-reducing groups this way. I'm afraid this is not really the answer you're looking for. But I hope that you will find a good way to proceed with your work. Airmid. Link to comment Share on other sites More sharing options...
Yggdrasil Posted February 10, 2006 Share Posted February 10, 2006 In order to PCR amplify your putative iron reducing gene, you need to figure out the sequence flanking the gene in the E. coli genome. Using that sequence information, you can design sequences completmentary to the region upstream of the gene on the antisense strand and complementary to the downstream region of the sense strand. In general, PCR primers must be designed by the researcher and are not found by searching on the internet. Link to comment Share on other sites More sharing options...
sorsurus Posted February 10, 2006 Author Share Posted February 10, 2006 thanx for the help. I think, it should be good enough for me to think of something for my work. Really appreciate it. I thought, there is somebody else who already design the primer, so i can find it through the internet, but i couldn't find one. by the way, thanx again. Link to comment Share on other sites More sharing options...
Nashyboyo Posted February 10, 2006 Share Posted February 10, 2006 hello.I need help in finding a primer for my DNA sample. i need a primer for iron reducing bacteria gene. I've tried to find in over the internet but couldn't find it. Anyone care to help? An iron reducing gene? huh? What does that mean? Am I being stupid? Link to comment Share on other sites More sharing options...
sorsurus Posted February 14, 2006 Author Share Posted February 14, 2006 Nashyboyo, my DNA sample contains gene that is able to reduce the iron compound. And, what i am doing rite now is to detect that gene by using the PCR. but the prblem is, i don't have the specific primer to amplify it. So, i thought, maybe, there is someone here could suggest any site or paper that i can use for my study. Thank you. Link to comment Share on other sites More sharing options...
sorsurus Posted February 27, 2006 Author Share Posted February 27, 2006 thanx for all the help... i have another question to ask... does anyone know, what is the unniversal primer for archae? i want to use it to run my PCR Link to comment Share on other sites More sharing options...
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