[HTML][HTML] Structural and molecular kinetic features of activities of DNA polymerases

AA Kuznetsova, OS Fedorova… - International journal of …, 2022 - mdpi.com
DNA polymerases catalyze DNA synthesis during the replication, repair, and recombination
of DNA. Based on phylogenetic analysis and primary protein sequences, DNA polymerases …

The post-PAM interaction of RNA-guided spCas9 with DNA dictates its target binding and dissociation

Q Zhang, F Wen, S Zhang, J Jin, L Bi, Y Lu, M Li… - Science …, 2019 - science.org
Cas9 is an RNA-guided endonuclease that targets complementary DNA for cleavage and
has been repurposed for many biological usages. Cas9 activities are governed by its direct …

Breaking the Concentration Barrier for Single‐Molecule Fluorescence Measurements

S Peng, W Wang, C Chen - Chemistry–A European Journal, 2018 - Wiley Online Library
Fluorescence‐based single‐molecule techniques have become widely used tools to reveal
dynamic processes of biomolecules and elucidate their molecular mechanisms. However …

Dynamics of Staphylococcus aureus Cas9 in DNA target Association and Dissociation

S Zhang, Q Zhang, XM Hou, L Guo, F Wang, L Bi… - EMBO …, 2020 - embopress.org
Abstract Staphylococcus aureus Cas9 (SaCas9) is an RNA‐guided endonuclease that
targets complementary DNA adjacent to a protospacer adjacent motif (PAM) for cleavage. Its …

Joint Efforts of Replicative Helicase and SSB Ensure Inherent Replicative Tolerance of G‐Quadruplex

L Guo, Y Bao, Y Zhao, Z Ren, L Bi, X Zhang… - Advanced …, 2024 - Wiley Online Library
Abstract G‐quadruplex (G4) is a four‐stranded noncanonical DNA structure that has long
been recognized as a potential hindrance to DNA replication. However, how replisomes …

Helicase promotes replication re-initiation from an RNA transcript

B Sun, A Singh, S Sultana, JT Inman, SS Patel… - Nature …, 2018 - nature.com
To ensure accurate DNA replication, a replisome must effectively overcome numerous
obstacles on its DNA substrate. After encountering an obstacle, a progressing replisome …

Efficient DNA interrogation of SpCas9 governed by its electrostatic interaction with DNA beyond the PAM and protospacer

Q Zhang, Z Chen, F Wang, S Zhang… - Nucleic Acids …, 2021 - academic.oup.com
Abstract Streptococcus pyogenes Cas9 (SpCas9), a programmable RNA-guided DNA
endonuclease, has been widely repurposed for biological and medical applications. Critical …

Angular Optical Trapping to Directly Measure DNA Torsional Mechanics

X Gao, JT Inman, MD Wang - Optical Tweezers: Methods and Protocols, 2022 - Springer
Angular optical trapping (AOT) is a powerful technique that permits direct angular
manipulation of a trapped particle with simultaneous measurement of torque and rotation …

Residence time analysis of RNA polymerase transcription dynamics: A Bayesian sticky HMM approach

Z Kilic, I Sgouralis, S Pressé - Biophysical journal, 2021 - cell.com
The time spent by a single RNA polymerase (RNAP) at specific locations along the DNA,
termed" residence time," reports on the initiation, elongation, and termination stages of …

Determining translocation orientations of nucleic acid helicases

HM Perera, MA Trakselis - Methods, 2022 - Elsevier
Helicase enzymes translocate along an RNA or DNA template with a defined polarity to
unwind, separate, or remodel duplex strands for a variety of genome maintenance …