Thermodynamic Post-Processing versus GC-Content Pre-Processing for DNA Codes Satisfying the Hamming Distance and Reverse-Complement Constraints

IEEE/ACM Trans Comput Biol Bioinform. Mar-Apr 2014;11(2):441-52. doi: 10.1109/TCBB.2014.2299815.

Abstract

Stochastic, meta-heuristic and linear construction algorithms for the design of DNA strands satisfying Hamming distance and reverse-complement constraints often use a GC-content constraint to pre-process the DNA strands. Since GC-content is a poor predictor of DNA strand hybridization strength the strands can be filtered by post-processing using thermodynamic calculations. An alternative approach is considered here, where the algorithms are modified to remove consideration of GC-content and rely on post-processing alone to obtain large sets of DNA strands with satisfactory melting temperatures. The two approaches (pre-processing GC-content and post-processing melting temperatures) are compared and are shown to be complementary when large DNA sets are desired. In particular, the second approach can give significant improvements when linear constructions are used.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Base Composition
  • Biotechnology / methods*
  • Computational Biology / methods*
  • DNA* / chemical synthesis
  • DNA* / chemistry
  • DNA* / genetics
  • Stochastic Processes
  • Thermodynamics

Substances

  • DNA