[DIYbio] Re: A better way to share/use DNA?

If people are working in a lab together they most likely are either working on the project together so know the exact sequences that are ordered or are working on completely different projects so as to not compete with each other and so requesting stuff from each other is probably not going to happen except in a few really huge labs. Or will happen so rarely that creating a huge database of everything is not worth it. Have you ever seen 10 years of plasmids and primers? We are talking tens of thousands of tubes in even small-medium size labs and probably hundreds of thousands in big labs. A simple website is not going to fix the organization of this.

Is this just a distributed DNA repository instead of a plasmid repository? The amount of time it takes to run any significant DNA or plasmid sharing repository is hindrance to most labs. It's not that people don't want to share DNA it is that it requires work to do so. Why do you think there is no cheap commercial repository for sharing plasmids? This is why addgene can charge $60 / plasmid. I have thousands of sequences and if someone wants a set of primers I have I am not going to send them to someone I don't know when they cost $20 or less to order on IDT. By the time someone in a lab takes the time to find them aliquot them and mail them you will have definitely received your DNA from IDT. It is fairly obvious that you probably have never asked anyone for a plasmid or DNA before.

Assembly solutions what does that even mean? Assembling DNA from random fragments is not something anyone wants to do and the possibilities and probabilities of being able to do this are extremely small especially if only using popular restriction enzymes. Is your program going to say that the gene is available? Sounds like a basic search function... Sounds like addgene.

The problem with keeping an inventory is not that there is no place to keep an inventory. Excel can keep an inventory of primers and plasmids and there are probably tens of websites out there that also already keep an inventory if people want. Have you ever ordered 50 sets of primers? or 100?  or 1000? Who is going to enter all these into the database and organize them? That is the bottleneck not needing a database.

Most DNA sharing between academic institutions requires the receiver to have a FedEx number to pay for shipping. If people on your website are paying for the DNA and replication and shipping it is easy to see how this method won't be very successful and how most won't take part.

Someone from a lab is not going to trust a 10 year old set of primers(maybe some people but I definitely would not). How do I know if they are contaminated or not? How do I even know what the person was using them for? Did the person purposely or accidentally mix primers in the tube for a primer mix? When it costs less than $20 to order new primers would you bet your experiment and sanity on 5 or 10 year old primers?

Most DNA is not reusable. It is designed for a singular purpose or purposes that are very similar. If I order a gene or primers they can't be reused by someone for a different purpose or it would be extremely difficult for that. Maybe one could perform multiple restriction digests on a gene if they are lucky(but usually restriction sites are avoided inside genes) and then a PCR and then a ligation but this becomes more expensive and much more time consuming than just ordering the DNA you want from IDT or another company. If I have DNA only as a gene that most likely means I have just started working on it. If someone else wanted this gene most people would not send it to them because that is usually direct competition. And I honestly don't know one lab who would ask someone for an uncloned gene. Very bad form in most Science circles. Order it yourself. This seems like a better idea for DIY Bio but ....
Plasmids one can miniprep a bunch of and the plasmid is relatively pure. However, when one orders a gene from IDT how do I send a sufficient quantity of the gene to someone when the company only sends me 200ng? I could PCR it but would you really trust a PCR from someone you never met and know nothing about? So that means I need my own primers and I need to sequence the product they sent me. Most genes are ordered with flanking restriction sites or custom tags which makes direct PCR without mutations or modifications unlikely. In the end the time and effort and money this requires is probably more expensive then ordering the gene for yourself in all but the most extreme cases. Especially with the prices of IDT and others dropping so low recently. You are asking for the sender and receiver to both put in some significant effort to share. Still the reusability of most DNA fragments is so small it is hard to create any sort of significant participation.

Primers that are commonly used(T7 fwd, T7 rev, M13, &c.) which could be the most requested things is like asking someone from another university if you can borrow a ream paper or a box of pipette tips. They would stare at you blankly.

Finally, Scientists are not idiots we don't reorder DNA on accident that we already have as you imply on your website("Eliminates wasted resources by avoiding the synthesis or purchase of existing DNA fragments.") at least not in any lab I have ever been in. And a number of labs I know keep an excel spreadsheet of plasmids or primers that are easily searchable....

In closing, I think the space you are attempting to enter is already full and your idea needs some work because the practicality of it all is very small. But feel free to rebut many of the claims I make. I would be interested to hear your response.



On Monday, June 23, 2014 3:30:09 AM UTC-7, EdwardPerello wrote:

If two people work together in a lab closely, then they will probably have a good idea of each other's DNA sequences/repositories. This information makes it easier for them to borrow and build on each other's work. However, if two people in a lab don't work closely together, they won't be able to do this and any improved productivity from mutual sharing transactions is lost.

My startup company, Desktop Genetics, has built a tool supporting networked DNA repositories for individual scientists/lab groups. Each person or group uploads genbank or fasta files of all the DNA sequences they have in their freezers/boxes, and this is indexed. You can upload a sequence that you have designed and want to build, and the tool will run designs against the index, developing assembly solutions that make use of the most efficient sources of template DNA across the network.

A list of fragment sequences from various "inventory sequences" is generated for any "design sequence", also identifying the smallest "unsourced" fragments you'd need have synthesised. You can request  sourced sequences from the people/groups who own them, and PCR primers are automatically designed to amplify the fragments from sourced sequences. Primers and fragments are designed based on your specific cloning chemistry choice. 

We have been showing the tool to academics and companies and getting a really good response. Its a pretty robust and pretty inventory management system on top of the solution generator, and I'd like to see if this is something the DIYbio community would like to start using. 

I think it would be really cool to have different hackspaces cataloguing their parts and making them all available to one another in this way. Maybe we could start getting some community projects going too.

Is anyone interested in making this happen?