IGEM:Harvard/2006/Brainstorming Papers - Lewis

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  1. Proske D, Blank M, Buhmann R, and Resch A. Aptamers--basic research, drug development, and clinical applications. Appl Microbiol Biotechnol. 2005 Dec;69(4):367-74. DOI:10.1007/s00253-005-0193-5 | PubMed ID:16283295 | HubMed [sb1]
  2. Farokhzad OC, Cheng J, Teply BA, Sherifi I, Jon S, Kantoff PW, Richie JP, and Langer R. Targeted nanoparticle-aptamer bioconjugates for cancer chemotherapy in vivo. Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6315-20. DOI:10.1073/pnas.0601755103 | PubMed ID:16606824 | HubMed [sb2]

All Medline abstracts: PubMed | HubMed

Aptamers--basic research, drug development, and clinical applications

The first of these two papers is a review paper about aptamers. Here are a few of the relevant or interesting details about these things:

First, they are great at binding to things, with dissociation constants in the nano or picomolar range (better than what William said), which rivals and sometimes surpasses the association between known proteins. They also can be potentially be very specific, with better discriminatory power than antibodies, and can bind to either active or allosteric sites of proteins. Because their versatility, I think that proving that we can do something with an aptamer that recognizes one particular substrate will enable us to speculate that we might achieve a similar result with any substrate.

Selection or aptamers to specific proteins can take a few months; automated systems like those from NAsca cell can now do them in a few weeks, but sending a protein to Nascacell and having them do it for you takes 8-10 weeks, so unless there are experts in the area who are willing to devote a lot of time to us (unlikely), we should probably stick to known aptamers (which will be our best bet since these would have the highest binding affinities).

One can use quantitative PCR or ligation of aptamers (two different aptamers bind and different sites on a substrate; if they are close enough it will be possible to ligate them) to figure how much aptamer is binding to a substrate. There are also good assays to test whether or not an aptamer has bound a substrate, in particular the aptamer beacon; essentially, fluorescence is induced in response to binding; real time binding can actually be recorded.

One CRUCIAL detail about these things is that they are often smaller than endogenous DNA molecules, so they do not provoke an immune response. For details about a system which employed aptamers in vivo, see the next article.

Targeted nanoparticle-aptamer bioconjugates for cancer chemotherapy in vivo

In this nifty article, Farokhzad et al. use aptamers to target tumors in mice with prostate cancer. Docetaxyl is a drug used to treat prostate cancer. The group wrapped Docetaxyl in PLGA, a non-immunogenic polymer. To the PLGA, they added PEG chains, which prevent destruction by the immune system. They also added DNA aptamers which were targeted to prostate-specific membrane antigen (PSMA), which are overexpressed in cancer cells. The results were rather startling: by injecting the drug vehicles into tumors of mice, the group achieved a 100% survival rate (after 109 days) and complete reduction of the tumors in 5 of 7 mice, versus 4/7 surviving and complete tumor reduction in 2/7 mice when the vehicle without aptamer was injected.