Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids

摘要

Nucleic acids are excellent at recognizing complementary sequences through the formation of Watson-Crick base pairs. Since the base pairing enables the highly selective hybridization with a target sequence, synthetic DNA and RNA oligonucleotides are regarded as some of the most promising materials for therapeutic and diagnostic purposes, including human gene regulation,~(1-5) gene expression analysis,~(6-9) and target molecule sensing.~(10-13) In particular, clinical applications have provided many successes in target-specific gene regulations for the treatments of cancers,~(14-16) cardiovascular disease,~(17) and inflammatory diseases.~(18) Quantitative data of nucleic acid interactions are very useful for improving a number of oligonucleotide technologies. The strengths of the interbase hydrogen bonding and base stacking determine the hybridization efficiency and stability of nucleic acid structures; however, considerations of the hydration and counterion condensation are also important because water and cations associate with the polar purine and pyrimidine bases and the negatively charged sugar-phosphate backbone (Figure 1). Since the base pair formation is accompanied by the association or dissociation of ions and water molecules, nucleic acid interaction energies are significantly influenced by the solution composition.~(19-22) The stability of the Watson-Crick base pairing has been extensively studied using aqueous dilute solutions containing salts.~(23-27) These thermodynamic data allow the accurate predictions of the hybridization energy and secondary structures of a given sequence,~(28-30) and the predictions for long RNA sequences can be further improved by combining the chemical modification data.~(31) The energetic aspects are important for the design of oligonucleotide sequences. As an example of the mRNA targeting therapeutics using antisense oligonucleotides, the prediction parameters determined for RNA?DNA hybrid duplexes23,32,33 can be used as a guideline for designing the antisense DNA sequences. Moreover, the thermodynamic properties of the base pair formations of mRNA?DNA and DNA?DNA were found to have a strong correlation with the level of the mRNA transcription in yeast.~(34)