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Side chain determinants of biopolymer function during selection and replication.

Phillip A Lichtor1,2, Zhen Chen1,2, Nadine H Elowe2

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Artificial biopolymers with nonpolar side chains show enhanced binding capabilities, suggesting these groups are key for molecular recognition and may explain protein evolution over nucleic acids.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Synthetic Biology

Background:

  • Biopolymer properties and functions are dictated by their chemical functionalities, particularly side chains.
  • Studying the link between side chain diversity and polymer function is experimentally challenging.
  • Natural nucleic acids lack the nonpolar side chain functionalities found in proteins.

Purpose of the Study:

  • To investigate the impact of diverse side chains on the binding activity of artificial biopolymers.
  • To determine if nonpolar side chains enhance molecular recognition capabilities.
  • To explore the evolutionary implications of side chain composition in biopolymers.

Main Methods:

  • Utilized artificial translation to create nucleic acid polymer libraries with varied charged, polar, and nonpolar side chains.
  • Employed in vitro selection to isolate polymers with binding affinity for target proteins (PCSK9 and IL-6).
  • Performed sequence convergence analysis, bulk binding assays, individual polymer affinity measurements, and competitive binding experiments.

Main Results:

  • Libraries incorporating nonpolar side chains demonstrated superior binding performance compared to those without.
  • Sequence convergence indicated selection for specific polymer structures.
  • Individual polymer affinities and competitive binding confirmed the enhanced activity of nonpolar-containing polymers.

Conclusions:

  • Nonpolar side chains significantly enhance the molecular binding activity of artificial biopolymers.
  • The presence of nonpolar groups, analogous to those in proteins, is a critical determinant of binding.
  • This finding supports the hypothesis that nonpolar functionalities contributed to the evolutionary advantage of proteins for molecular recognition.