Nucleic acid polymeric properties and electrostatics: Directly comparing theory and simulation with experiment.
Nucleic acids are biopolymers that carry genetic information and are also involved in various gene regulation functions such as gene silencing and protein translation. Because of their negatively charged backbones, nucleic acids are polyelectrolytes. To adequately understand nucleic acid folding and function, we need to properly describe its i) polymer/polyelectrolyte properties and ii) associating ion atmosphere. While various theories and simulation models have been developed to describe nucleic acids and the ions around them, many of these theories/simulations have not been well evaluated due to complexities in comparison with experiment. In this review, I discuss some recent experiments that have been strategically designed for straightforward comparison with theories and simulation models. Such data serve as excellent benchmarks to identify limitations in prevailing theories and simulation parameters.
Bioinformatics Institute (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore 138671. Electronic address: adelenes@bii.a-star.edu.sg.
Adelene Y L
AYL
Sim
D000818:Animals; D003198:Computer Simulation; D006801:Humans; D007477:Ions; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids; D011108:Polymers; D055672:Static Electricity
D007477:Ions; D009696:Nucleic Acids; D011108:Polymers
Benchmarking; Ion atmosphere; Nucleic acids; Poisson–Boltzmann theory; Polyelectrolytes; Polymer theory