Molecular Modeling of ssDNA—Salt Interactions via Mean Field Theory and Molecular Dynamics Simulations

摘要

1. Many kinds of biotechnology frequently incorporate the phenomena of DNA binding to various ligands. To this end, single-stranded DNA (ssDNA) is frequently used in biosensors and microarrays. 2. ssDNA biosensors have been predicted to become an important new feature of medical diagnostics as they allow investigators to detect abnormalities in genetic sequences and to assess how DNA sequences interact with surrounding molecules. 3. These devices immobilize one end of the aptamers (short strands of naturally occurring nucleotides) to a surface, allowing the rest of the strand to interact with target molecules. 4. These systems are immersed in ionic solutions to mimic the complex salt environments of cells. 5. XPS studies and earlier mean field studies showed a tradeoff between the protonation fraction and ion incorporation into ssDNA structure.