92 citations · 479 across the 12 of their papers we have counts for
11 papers · 1 filter
Twist-diameter coupling drives DNA twist changes by salt and temperature
Chen Zhang, Fujia Tian, Ying Lu +4
DNA deformations play crucial roles in many biological processes and material applications. During DNA deformation, DNA structural parameters often exhibit non-trivial and counteri…
Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions
Ya-Zhou Shi, Lei Jin, Chen-Jie Feng +2
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological func…
Predicting 3D structure, flexibility and stability of RNA hairpins in monovalent and divalent ion solutions
Ya-Zhou Shi, Lei Jin, Feng-Hua Wang +2
A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility and stability of RNAs. To predict RNA 3D struc…
Flexibility of nucleic acids: from DNA to RNA
Lei Bao, Xi Zhang, Lei Jin +1
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 regulati…
Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA
Yuan-Yan Wu, Zhong-Liang Zhang, Jin-Si Zhang +2
Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds…
Flexibility of short DNA helices with finite-length effect: from base pairs to tens of base pairs
Yuan-Yan Wu, Lei Bao, Xi Zhang +1
Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of t…
A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect
Ya-Zhou Shi, Feng-Hua Wang, Yuan-Yan Wu +1
To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the exist…
RNA structure prediction: progress and perspective
Ya-Zhou Shi, Yuan-Yan Wu, Feng-Hua Wang +1
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 unde…
Calculating potential of mean force between like-charged nanoparticles: a comprehensive study on salt effects
Yuan-Yan Wu, Feng-Hua Wang, Zhi-Jie Tan
Ions are critical to the structure and stability of polyelectrolytes such as nucleic acids. In this work, we systematically calculated the potentials of mean force between two like…
Ion-mediated RNA structural collapse: effect of spatial confinement
Zhi-Jie Tan, Shi-Jie Chen
RNAs are negatively charged molecules residing in macromolecular crowding cellular environments. Macromolecular confinement can influence the ion effects in RNA folding. In this wo…
Salt Contribution to the Flexibility of Single-stranded Nucleic Acid of Finite Length
Feng-Hua Wang, Yuan-Yan Wu, Zhi-Jie Tan
Nucleic acids are negatively charged macromolecules and their structure properties are strongly coupled to metal ions in solutions. In this paper, the salt effects on the flexibili…