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Related Experiment Videos

Deconvolution of a complex target using DNA aptamers.

Stephen Fitter1, Robert James

  • 1Department of Gastroenterology and Hepatology, Flinders Medical Centre, Adelaide, South Australia 5042.

The Journal of Biological Chemistry
|August 6, 2005
PubMed
Summary
This summary is machine-generated.

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Aptamer selection from complex mixtures like human plasma shows evolving sequence families. A target depletion method was developed to overcome population convergence and isolate diverse aptamers against multiple proteins.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biotechnology

Background:

  • In vitro selection enables isolation of nucleic acid aptamers with high affinity and specificity for single targets.
  • Aptamer libraries possess significant sequence and shape diversity, suggesting potential for complex mixture analysis.
  • Unfractionated human plasma presents a complex biological model for aptamer discovery against multiple proteins.

Purpose of the Study:

  • To investigate aptamer population dynamics during selection from complex biological mixtures.
  • To develop methods for aptamer isolation against numerous proteins in human plasma.
  • To overcome challenges of population convergence during aptamer selection from complex samples.

Main Methods:

  • In vitro selection of single-stranded nucleic acid aptamers from large random libraries using unfractionated human plasma.

Related Experiment Videos

  • Analysis of aptamer sequence representation across increasing selection rounds.
  • Development and application of an aptamer-based target depletion method to mitigate population convergence.

    • Main Results:

    • Aptamer sequence representation dramatically shifted with successive selection rounds.
    • Dominant aptamer families emerged early but were later replaced by other families.
    • The target depletion method successfully reduced the abundance of previously dominant aptamer families and revealed new ones.

    Conclusions:

    • Aptamer selection from complex mixtures is dynamic, with evolving sequence populations.
    • Population convergence is a significant challenge in aptamer selection from complex samples.
    • Aptamer-based target depletion is an effective strategy to enhance aptamer diversity against multiple targets in complex mixtures.