Single-molecule analysis and engineering of DNA motors

S Mohapatra, CT Lin, XA Feng, A Basu, T Ha - Chemical Reviews, 2019 - ACS Publications
Molecular motors are diverse enzymes that transduce chemical energy into mechanical
work and, in doing so, perform critical cellular functions such as DNA replication and …

Acoustic force spectroscopy

G Sitters, D Kamsma, G Thalhammer, M Ritsch-Marte… - Nature …, 2015 - nature.com
Force spectroscopy has become an indispensable tool to unravel the structural and
mechanochemical properties of biomolecules. Here we extend the force spectroscopy …

[HTML][HTML] Characterization of facilitated diffusion of tumor suppressor p53 along DNA using single-molecule fluorescence imaging

K Kamagata, A Murata, Y Itoh, S Takahashi - Journal of Photochemistry and …, 2017 - Elsevier
Sequence-specific DNA-binding proteins can maintain and regulate cellular functions by
accurately and quickly binding to target sequences among large amounts of nontarget DNA …

Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins

RPC Driessen, G Sitters, N Laurens, GF Moolenaar… - Biochemistry, 2014 - ACS Publications
The helical structure of double-stranded DNA is destabilized by increasing temperature.
Above a critical temperature (the melting temperature), the two strands in duplex DNA …

Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A

G Farge, N Laurens, OD Broekmans… - Nature …, 2012 - nature.com
Mitochondria organize their genome in protein–DNA complexes called nucleoids. The
mitochondrial transcription factor A (TFAM), a protein that regulates mitochondrial …

Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices

M Schickinger, M Zacharias, H Dietz - … of the National Academy of Sciences, 2018 - pnas.org
We describe a tethered multifluorophore motion assay based on DNA origami for revealing
bimolecular reaction kinetics on the single-molecule level. Molecular binding partners may …

Gene repression by minimal lac loops in vivo

LM Bond, JP Peters, NA Becker, JD Kahn… - Nucleic acids …, 2010 - academic.oup.com
The inflexibility of double-stranded DNA with respect to bending and twisting is well
established in vitro. Understanding apparent DNA physical properties in vivo is a greater …

A new method for inferring hidden Markov models from noisy time sequences

D Kelly, M Dillingham, A Hudson, K Wiesner - PloS one, 2012 - journals.plos.org
We present a new method for inferring hidden Markov models from noisy time sequences
without the necessity of assuming a model architecture, thus allowing for the detection of …

Enhanced tethered-particle motion analysis reveals viscous effects

S Kumar, C Manzo, C Zurla, S Ucuncuoglu, L Finzi… - Biophysical journal, 2014 - cell.com
Tethered-particle motion experiments do not require expensive or technically complex
hardware, and increasing numbers of researchers are adopting this methodology to …

Visual analysis of concerted cleavage by type IIF restriction enzyme SfiI in subsecond time region

Y Suzuki, JL Gilmore, SH Yoshimura, RM Henderson… - Biophysical journal, 2011 - cell.com
Many DNA regulatory factors require communication between distantly separated DNA sites
for their activity. The type IIF restriction enzyme SfiI is often used as a model system of site …