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DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch

Tuan M Pham1, Terrel Miffin2, Hongying Sun3

  • 1Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, United States.

ACS Synthetic Biology
|September 6, 2023
PubMed
Summary

Expanding the DNA base pair alphabet with P-Z pairs improves in silico DNA secondary structure design. This novel approach enhances design accuracy and efficiency, offering a new pipeline for expanded nucleotide inclusion in bioinformatics tools.

Keywords:
DNA folding thermodynamicsDNA secondary structure designexpanded DNA alphabetsynthetic biology

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Area of Science:

  • Synthetic Biology
  • Computational Biology
  • Biochemistry

Background:

  • Current DNA secondary structure design relies on the standard Adenine-Thymine (A-T) and Guanine-Cytosine (G-C) base pairing rules.
  • Limitations exist in accurately predicting and designing complex DNA structures using only the canonical base pairs.
  • Expanding the base pairing alphabet could enhance the precision and capabilities of *in silico* DNA design.

Purpose of the Study:

  • To investigate the impact of incorporating novel base pairs, specifically the P-Z pair, into DNA secondary structure design algorithms.
  • To determine the thermodynamic parameters for P-Z and G-Z wobble pairs and integrate them into existing software.
  • To evaluate the improvement in design accuracy and efficiency using an expanded base pair alphabet.

Main Methods:

  • Conducted 47 optical melting experiments to determine thermodynamic parameters for P-Z and G-Z wobble pairs.
  • Integrated these parameters into the RNAstructure software package for secondary structure prediction and design.
  • Tested the enhanced RNAstructure Design program on 100 design problems from the Eterna challenge, comparing results with and without P-Z pairs.

Main Results:

  • Successfully incorporated P-Z pairs and G-Z wobble pairs (comparable in stability to A-T pairs) into design algorithms.
  • The RNAstructure Design program solved 99 out of 100 design problems when using the expanded alphabet.
  • Designs incorporating P-Z pairs showed significantly reduced normalized ensemble defect (NED) values (0.040 vs. 0.074) and faster convergence.

Conclusions:

  • Extending the DNA base pairing alphabet beyond A-T and G-C to include P-Z pairs substantially improves *in silico* secondary structure design.
  • The inclusion of P-Z pairs enhances design accuracy, reduces off-target structures, and increases computational efficiency.
  • This study presents a viable pipeline for incorporating novel nucleotides into existing bioinformatics prediction and design workflows.