Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells
S Takahashi, N Sugimoto - Chemical Society Reviews, 2020 - pubs.rsc.org
Nucleic acids (DNA and RNA) dynamically fold and unfold to exert their functions in cells.
These folding and unfolding behaviours are also the basis for various technical applications …
These folding and unfolding behaviours are also the basis for various technical applications …
Construction of Branched DNA‐based Nanostructures for Diagnosis, Therapeutics and Protein Engineering
P Hu, Y Dong, C Yao, D Yang - Chemistry–An Asian Journal, 2022 - Wiley Online Library
Branched DNA with multibranch‐like anisotropic topology serves as a promising and
powerful building block in constructing multifunctional‐integrated nanomaterials in a …
powerful building block in constructing multifunctional‐integrated nanomaterials in a …
[HTML][HTML] Novel ssDNA aptamer-based fluorescence sensor for perfluorooctanoic acid detection in water
Per-and polyfluoroalkyl substances (PFAS) are widely detected environmental
contaminants, and there is a great need for development of sensor technologies for rapid …
contaminants, and there is a great need for development of sensor technologies for rapid …
Stem–loop formation drives RNA folding in mechanical unzipping experiments
Accurate knowledge of RNA hybridization is essential for understanding RNA structure and
function. Here we mechanically unzip and rezip a 2-kbp RNA hairpin and derive the 10 …
function. Here we mechanically unzip and rezip a 2-kbp RNA hairpin and derive the 10 …
Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions
S Ghosh, S Takahashi, T Ohyama… - Proceedings of the …, 2020 - National Acad Sciences
The intracellular environment is crowded and heterogeneous. Although the thermodynamic
stability of nucleic acid duplexes is predictable in dilute solutions, methods of predicting …
stability of nucleic acid duplexes is predictable in dilute solutions, methods of predicting …
Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions
S Ghosh, S Takahashi, D Banerjee… - Nucleic Acids …, 2023 - academic.oup.com
RNA performs various spatiotemporal functions in living cells. As the solution environments
significantly affect the stability of RNA duplexes, a stability prediction of the RNA duplexes in …
significantly affect the stability of RNA duplexes, a stability prediction of the RNA duplexes in …
5-Methyl-cytosine stabilizes DNA but hinders DNA hybridization revealed by magnetic tweezers and simulations
XC Zhao, HL Dong, XL Li, HY Yang… - Nucleic acids …, 2022 - academic.oup.com
Methyl-cytosine (5mC) is one of the most important DNA modifications and plays versatile
biological roles. It is well known that 5mC stabilizes DNA duplexes. However, it remains …
biological roles. It is well known that 5mC stabilizes DNA duplexes. However, it remains …
B‐DNA Structure and stability: The role of nucleotide composition and order
We have quantum chemically analyzed the influence of nucleotide composition and
sequence (that is, order) on the stability of double‐stranded B‐DNA triplets in aqueous …
sequence (that is, order) on the stability of double‐stranded B‐DNA triplets in aqueous …
Cooperativity-dependent folding of single-stranded DNA
The folding of biological macromolecules is a fundamental process of which we lack a full
comprehension. Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also …
comprehension. Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also …
Microchemomechanical devices using DNA hybridization
The programmability of DNA oligonucleotides has led to sophisticated DNA nanotechnology
and considerable research on DNA nanomachines powered by DNA hybridization. Here, we …
and considerable research on DNA nanomachines powered by DNA hybridization. Here, we …