199 citations · 2.1k across the 42 of their papers we have counts for
42 papers
Weak tension accelerates hybridization and dehybridization of short oligonucleotides
Derek J. Hart, Jiyoun Jeong, James C. Gumbart +1
The hybridization and dehybridization of DNA subject to tension is relevant to fundamental genetic processes and to the design of DNA-based mechanobiology assays. While strong tens…
First passage time study of DNA strand displacement
D. W. Bo Broadwater, Alexander W. Cook, Harold D. Kim
DNA strand displacement, where a single-stranded nucleic acid invades a DNA duplex, is pervasive in genomic processes and DNA engineering applications. The kinetics of strand displ…
Base-pair mismatch can destabilize small DNA loops through cooperative kinking
Jiyoun Jeong, Harold D. Kim
Base pair mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule Fluorescence Reson…
Determinants of cyclization-decyclization kinetics of short DNA with sticky ends
Jiyoun Jeong, Harold D. Kim
Cyclization of DNA with sticky ends is commonly used to construct DNA minicircles and to measure DNA bendability. The cyclization probability of short DNA (< 150 bp) has a strong l…
Force distribution in a semiflexible loop
James T. Waters, Harold D. Kim
Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category…
The effect of base pair mismatch on DNA strand displacement
Bo Broadwater, Harold Kim
DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its…