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Aptamers and Adaptamers

  1. Dwarakanath S, Bruno JG, Shastry A, Phillips T, John AA, Kumar A, and Stephenson LD. Quantum dot-antibody and aptamer conjugates shift fluorescence upon binding bacteria. Biochem Biophys Res Commun. 2004 Dec 17;325(3):739-43. DOI:10.1016/j.bbrc.2004.10.099 | PubMed ID:15541352 | HubMed [apt1]
  2. Bruno JG and Kiel JL. Use of magnetic beads in selection and detection of biotoxin aptamers by electrochemiluminescence and enzymatic methods. Biotechniques. 2002 Jan;32(1):178-80, 182-3. DOI:10.2144/02321dd04 | PubMed ID:11808691 | HubMed [apt2]
  3. Tahiri-Alaoui A, Frigotto L, Manville N, Ibrahim J, Romby P, and James W. High affinity nucleic acid aptamers for streptavidin incorporated into bi-specific capture ligands. Nucleic Acids Res. 2002 May 15;30(10):e45. PubMed ID:12000850 | HubMed [apt3]
  4. Nordström K. Plasmid R1--replication and its control. Plasmid. 2006 Jan;55(1):1-26. DOI:10.1016/j.plasmid.2005.07.002 | PubMed ID:16199086 | HubMed [apt4]
  5. Kolb FA, Malmgren C, Westhof E, Ehresmann C, Ehresmann B, Wagner EG, and Romby P. An unusual structure formed by antisense-target RNA binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment. RNA. 2000 Mar;6(3):311-24. PubMed ID:10744017 | HubMed [apt5]
  6. Bock LC, Griffin LC, Latham JA, Vermaas EH, and Toole JJ. Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature. 1992 Feb 6;355(6360):564-6. DOI:10.1038/355564a0 | PubMed ID:1741036 | HubMed [apt6]
  7. Bittker JA, Le BV, and Liu DR. Nucleic acid evolution and minimization by nonhomologous random recombination. Nat Biotechnol. 2002 Oct;20(10):1024-9. DOI:10.1038/nbt736 | PubMed ID:12219078 | HubMed [apt7]
All Medline abstracts: PubMed | HubMed

Quantum dots conjugated to aptamers (apt1) 15541352 This was a neat study in which quantum dots were conjugated to antibodies or aptamers that target E. coli cell surfaces. The point of the article is that the emissions from the quantum dots changed following binding, but what's relevant to us is the aptamer they used. They evolved it on their own using the method of apt2 (probably out of convenience: both were Austin-based companies). The aptamer recognizes lipopolysaccharide (LPS O111:B4). I am currently emailing to find out why they chose LPS. At least we know of one aptamer that binds the E. coli cell surface...

Adaptamers (apt3) 12000850 This paper is also listed in the streptavidin section. See "Notes" under "Demonstrate Control.." project for a description.

CopA/CopT (apt4) 16199086 This recent review paper has a description of the CopA/CopT interaction which is utilized in apt3.

CopA/CopT (apt5) 10744017 This paper reveals the extremely intricate "deep-kissing" structure formed between CopA and CopT.

Thrombin (apt6) 1741036 Paper talking about selection for a DNA aptamer that binds thrombin. Seems like no one's evolved a better version yet: even recent papers talk about the same motif (16616893).

DNA aptamer to streptavidin (apt7) David Liu's paper about selecting for a DNA aptamer that binds streptavidin. The point here was using the nonhomolous random recombination instead of error-prone PCR to select for aptamers. The point for us is that it gives a DNA aptamer that binds streptavidin pretty well (40 bp motif kD ~100 nM).