IGEM:Harvard/2006/Adaptamers/Literature

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=Aptamers and Adaptamers=
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<biblio>
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#apt1 pmid=15541352
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#apt2 pmid=11808691
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#apt3 pmid=12000850
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#apt4 pmid=16199086
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#apt5 pmid=10744017
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#apt6 pmid=1741036
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#apt7 pmid=12219078
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</biblio>
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'''Quantum dots conjugated to aptamers (apt1) 15541352'''
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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...
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'''Adaptamers (apt3) 12000850'''
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This paper is also listed in the streptavidin section. See "Notes" under "Demonstrate Control.." project for a description.
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'''CopA/CopT (apt4) 16199086'''
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This recent review paper has a description of the CopA/CopT interaction which is utilized in apt3.
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'''CopA/CopT (apt5) 10744017'''
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This paper reveals the extremely intricate "deep-kissing" structure formed between CopA and CopT.
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'''Thrombin (apt6) 1741036'''
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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).
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'''DNA aptamer to streptavidin (apt7)'''
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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).

Current revision


Aptamers and Adaptamers

  1. Dwarakanath S, Bruno JG, Shastry A, Phillips T, John AA, Kumar A, and Stephenson LD. . pmid:15541352. PubMed HubMed [apt1]
  2. Bruno JG and Kiel JL. . pmid:11808691. PubMed HubMed [apt2]
  3. Tahiri-Alaoui A, Frigotto L, Manville N, Ibrahim J, Romby P, and James W. . pmid:12000850. PubMed HubMed [apt3]
  4. Nordström K. . pmid:16199086. PubMed HubMed [apt4]
  5. Kolb FA, Malmgren C, Westhof E, Ehresmann C, Ehresmann B, Wagner EG, and Romby P. . pmid:10744017. PubMed HubMed [apt5]
  6. Bock LC, Griffin LC, Latham JA, Vermaas EH, and Toole JJ. . pmid:1741036. PubMed HubMed [apt6]
  7. Bittker JA, Le BV, and Liu DR. . pmid:12219078. PubMed 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).
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