The structural flexibility of nucleic acids plays a key role in many fundamental life processes, such as gene replication and expression, DNA-protein recognition, and gene regulation. To obtain a thorough understanding of nucleic acid flexibil- ity, extensive studies have been performed using various experimental methods and theoretical models. In this review, we will introduce the progress that has been made in understanding the flexibility of nucleic acids including DNAs and RNAs, and will emphasize the experimental findings and the effects of salt, temperature, and sequence. Finally, we will discuss the maior unanswered questions in understanding the flexibility of nucleic acids.
Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some structure prediction models have been developed in recent years. In this review, the progress in computational models for RNA structure prediction is introduced and the distinguishing features of many outstanding algorithms are discussed, emphasizing three- dimensional （3D） structure prediction. A promising coarse-grained model for predicting RNA 3D structure, stability and salt effect is also introduced briefly. Finally, we discuss the major challenges in the RNA 3D structure modeling.
Nucleic acids are negatively charged biomolecules, and metal ions in solutions are important to their folding structures and thermodynamics, especially multivalent ions. However, it has been suggested that the binding of multivalent ions to nucleic acids cannot be quantitatively described by the well-established Poisson-Boltzmann （PB） theory. In this work, we made extensive calculations of ion distributions around various RNA-like macroions in divalent and trivalent salt solutions by PB theory and Monte Carlo （MC） simulations. Our calculations show that PB theory appears to underestimate multi- valent ion distributions around RNA-like macroions while can reliably predict monovalent ion distributions. Our extensive comparisons between PB theory and MC simulations indicate that when an RNA-like macroion gets ion neutralization be- yond a ＂critical＂ value, the multivalent ion distribution around that macroion can be approximately described by PB theory. Furthermore, an empirical formula was obtained to approximately quantify the critical ion neutralization for various RNA- like macroions in multivalent salt solutions, and this empirical formula was shown to work well for various real nucleic acids including RNAs and DNAs.
