Works (76)
Updated: April 3rd, 2024 17:39
2023 journal article
Assembly path dependence of telomeric DNA compaction by TRF1, TIN2, and SA1
BIOPHYSICAL JOURNAL, 122(10), 1822–1832.
TL;DR:
It is found that TRF1, TIN2, and SA1 work synergistically to cause a compaction of the DNA substrate, and that maximal compaction occurs if all three proteins are present.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: April 21, 2023
2023 journal article
High-speed AFM imaging reveals DNA capture and loop extrusion dynamics by cohesin-NIPBL
JOURNAL OF BIOLOGICAL CHEMISTRY, 299(11).
TL;DR:
High-speed atomic force microscopy imaging reveals that cohesin-NIPBL captures DNA through arm extension, assisted by feet (shorter protrusions), and followed by transfer of DNA to its lower compartment (SMC heads, RAD21, SA1, and NIPBL).
(via Semantic Scholar)
www.ncbi.nlm.nih.gov (repository)
Sources: Web Of Science, NC State University Libraries
Added: December 11, 2023
2023 article
PARP1 associates with R-loops to promote their resolution and genome stability
Laspata, N., Kaur, P., Mersaoui, S. Y., Muoio, D., Liu, Z. S., Bannister, M. H., … Fouquerel, E. (2023, February 16). NUCLEIC ACIDS RESEARCH, Vol. 2.
MeSH headings : Humans; DNA / chemistry; DNA Repair; Genomic Instability; Poly (ADP-Ribose) Polymerase-1 / genetics; Poly (ADP-Ribose) Polymerase-1 / metabolism; R-Loop Structures; RNA / chemistry
TL;DR:
It is demonstrated that PARP1 binds R-loops in vitro and associates with R-loop formation sites in cells which activates its ADP-ribosylation activity, and highlights thatPARP1 is a suppressor of R- loop-associated genomic instability.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: March 20, 2023
2023 journal article
Single-molecule imaging of genome maintenance proteins encountering specific DNA sequences and structures
DNA REPAIR, 128.
author keywords: Single-molecule imaging; High-speed AFM imaging; Mitochondrial DNA replication; Cohesin; Shelterin; Protein-DNA interactions
TL;DR:
This review highlights how the lab has used SMI techniques over the past decade to study protein-nucleic acid interactions involved in DNA repair, mitochondrial DNA replication, and telomere maintenance, and discusses how DNA substrates containing specific DNA sequences or structures that emulate DNA repair intermediates or telomeres were generated and validated.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 7, 2023
2023 article
Structure-specific roles for PolG2-DNA complexes in maintenance and replication of mitochondrial DNA
Wojtaszek, J. L., Hoff, K. E., Longley, M. J., Kaur, P., Andres, S. N., Wang, H., … Copeland, W. C. (2023, August 18). NUCLEIC ACIDS RESEARCH, Vol. 8.
TL;DR:
Data indicate that PolG2 DNA binding has both PolG-dependent and -independent functions in mitochondrial DNA replication and maintenance, which provide new insight into molecular defects associated with PolG 2 disruption in mitochondrial disease.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 28, 2023
2022 journal article
Densely methylated DNA traps Methyl-CpG-binding domain protein 2 but permits free diffusion by Methyl-CpG-binding domain protein 3
JOURNAL OF BIOLOGICAL CHEMISTRY, 298(10).
MeSH headings : CpG Islands; DNA Methylation; DNA-Binding Proteins / metabolism; Mi-2 Nucleosome Remodeling and Deacetylase Complex / genetics; Mi-2 Nucleosome Remodeling and Deacetylase Complex / metabolism; Nucleosomes; Protein Binding; Transcription Factors / metabolism; Humans; Single Molecule Imaging
TL;DR:
These studies support a model in which MBD2-NuRD strongly localizes to and compacts methylated CpG islands while MBD3-NURD can freely mobilize nucleosomes independent of methylation status.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 29, 2022
2022 article
Structural and dynamic basis of DNA capture and translocation by mitochondrial Twinkle helicase
Li, Z., Kaur, P., Lo, C.-Y., Chopra, N., Smith, J., Wang, H., & Gao, Y. (2022, November 18). NUCLEIC ACIDS RESEARCH, Vol. 11.
MeSH headings : Humans; Mitochondrial Proteins / metabolism; Cryoelectron Microscopy; DNA Helicases / metabolism; Mitochondria / genetics; Mitochondria / metabolism; DNA Replication; DNA, Mitochondrial / genetics
TL;DR:
Cryo-electron microscopy and high-speed atomic force microscope data obtained the atomic-resolution structure of a vertebrate Twinkle homolog with DNA and captured in real-time how Twinkle is self-loaded onto DNA, highlighting the essential role of the non-catalytic N-terminal domain of Twinkle.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: December 5, 2022
2021 journal article
Structure, dynamics, and regulation of TRF1-TIN2-mediated trans- and cis-interactions on telomeric DNA
JOURNAL OF BIOLOGICAL CHEMISTRY, 297(3).
MeSH headings : Cell Adhesion Molecules / metabolism; Cell Adhesion Molecules / physiology; DNA / metabolism; DNA-Binding Proteins / metabolism; Humans; Microscopy, Atomic Force / methods; Models, Molecular; Multiprotein Complexes / metabolism; Protein Binding; Protein Isoforms / metabolism; Shelterin Complex / metabolism; Shelterin Complex / physiology; Telomere / metabolism; Telomere-Binding Proteins / metabolism; Telomere-Binding Proteins / physiology; Telomeric Repeat Binding Protein 1 / metabolism; Telomeric Repeat Binding Protein 1 / physiology; Telomeric Repeat Binding Protein 2 / metabolism; Telomeric Repeat Binding Protein 2 / physiology
TL;DR:
Analysis of DNA molecular structures promoted by TRF1-TIN2 interaction supports a molecular model in which protein assemblies at telomeres are heterogeneous with distinct subcomplexes and full shelterin complexes playing distinct roles in telomere protection and elongation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: October 26, 2021
2021 journal article
Structure, dynamics, and regulation of TRF1-TIN2-mediated trans-and cis-interactions on telomeric DNA
Journal of Biological Chemistry, 101080.
Source: ORCID
Added: September 23, 2021
2021 journal article
TIN2 is an architectural protein that facilitates TRF2-mediated trans- and cis-interactions on telomeric DNA
NUCLEIC ACIDS RESEARCH, 49(22), 13000–13018.
MeSH headings : Animals; DNA / chemistry; DNA / genetics; DNA / metabolism; HeLa Cells; Humans; Mice, Inbred C57BL; Microscopy, Atomic Force; Nucleic Acid Conformation; Protein Binding; Shelterin Complex / genetics; Shelterin Complex / metabolism; Telomere / genetics; Telomere / metabolism; Telomere-Binding Proteins / genetics; Telomere-Binding Proteins / metabolism; Telomeric Repeat Binding Protein 2 / genetics; Telomeric Repeat Binding Protein 2 / metabolism
TL;DR:
A molecular model in which TIN2 functions as an architectural protein to promote TRF2-mediated trans and cis higher-order nucleic acid structures at telomeres is proposed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: January 18, 2022
2021 journal article
Using Atomic Force Microscopy to Study the Real Time Dynamics of DNA Unwinding by Mitochondrial Twinkle Helicase
BIO-PROTOCOL, 11(17).
author keywords: Atomic Force Microscope; Twinkle helicase; Mitochondria; Liquid AFM imaging; Mitochondrial replication; Single molecule imaging
TL;DR:
The addition of mitochondrial single-stranded DNA binding protein (mtSSB) facilitates a 5-fold increase in the DNA unwinding rate for the Twinkle helicase, providing new platforms to examine DNA replication and to explore the mechanism driving DNA deletion and human diseases.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: September 20, 2021
2020 journal article
Cohesin SA1 and SA2 are RNA binding proteins that localize to RNA containing regions on DNA
NUCLEIC ACIDS RESEARCH, 48(10), 5639–5655.
MeSH headings : Binding Sites; Cell Cycle Proteins / metabolism; Chromosomal Proteins, Non-Histone / metabolism; DNA / metabolism; R-Loop Structures; RNA / metabolism; RNA-Binding Proteins / metabolism
TL;DR:
It is discovered that both SA1 and SA2 bind to various RNA containing substrates, including ssRNA, dsRNA, RNA:DNA hybrids, and R-loops, and the majority of R-loop-localized SA1and SA2 are also sites where other subunits of the cohesin complex bind.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: October 5, 2020
2020 journal article
Cohesin SA1 and SA2 are RNA binding proteins that localize to RNA containing regions on DNA
Nucleic Acids Research.
Source: ORCID
Added: September 23, 2021
2020 journal article
DNA looping by two 5-methylcytosine-binding proteins quantified using nanofluidic devices
EPIGENETICS & CHROMATIN, 13(1).
author keywords: DNA methylation; MeCP2; MBD2; DNA compaction
MeSH headings : 5-Methylcytosine / chemistry; 5-Methylcytosine / metabolism; Binding Sites; DNA / chemistry; DNA / metabolism; DNA Methylation; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / metabolism; Epigenomics / methods; Humans; Methyl-CpG-Binding Protein 2 / chemistry; Methyl-CpG-Binding Protein 2 / metabolism; Microfluidics / instrumentation; Microfluidics / methods; Microscopy, Atomic Force / methods; Protein Binding
TL;DR:
It is demonstrated that ATTO 565-labeled MBD2 is a good candidate as a staining agent for epigenetic mapping and determined that the mechanism for compaction by MeCP2 is the formation of bridges between distant DNA stretches and theformation of loops.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: April 20, 2020
2020 journal article
Single-molecule level structural dynamics of DNA unwinding by human mitochondrial Twinkle helicase
JOURNAL OF BIOLOGICAL CHEMISTRY, 295(17), 5564–5576.
author keywords: atomic force microscopy (AFM); DNA binding protein; DNA helicase; DNA replication; mitochondrial disease; mitochondrial DNA (mtDNA); single-molecule biophysics; ssDNA-binding protein (SSB); structural dynamics; Twinkle helicase
MeSH headings : DNA / analysis; DNA / metabolism; DNA Helicases / analysis; DNA Helicases / metabolism; Humans; Microscopy, Atomic Force; Mitochondria / metabolism; Mitochondrial Proteins / analysis; Mitochondrial Proteins / metabolism; Nucleic Acid Conformation; Protein Binding; Protein Multimerization; Recombinant Proteins / analysis; Recombinant Proteins / metabolism
TL;DR:
Atomic force microscopy imaging in air and liquids is employed to visualize ring assembly, DNA binding, and unwinding activity of individual Twinkle hexamers at the single-molecule level and finds that the addition of mitochondrial single-stranded DNA–binding protein both influences the ways Twinkle loads onto defined DNA substrates and stabilizes the unwound ssDNA product.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: May 18, 2020
2020 journal article
Single-molecule level structural dynamics of DNA unwinding by human mitochondrial Twinkle helicase
Journal of Biological Chemistry, 295(17), 5564–5576.
Source: ORCID
Added: September 23, 2021
2019 journal article
Cohesin SA2 and EWSR1 in R-Loop Regulation
Biophysical Journal, 116(3), 505a.
Sources: Crossref, NC State University Libraries
Added: January 25, 2020
2019 article
Measuring UV Photoproduct Repair in Isolated Telomeres and Bulk Genomic DNA
DNA REPAIR: METHODS AND PROTOCOLS, Vol. 1999, pp. 295–306.
author keywords: UV photoproducts; UV irradiation; Telomeres; Immunospot blot; Telomere isolation; Radiolabeled DNA probes
MeSH headings : Antibodies / immunology; Cell Line; DNA / analysis; DNA / genetics; DNA / radiation effects; DNA Damage / radiation effects; DNA Repair; Genomic Instability; Genomics / methods; Humans; Immunoblotting / methods; Pyrimidine Dimers / analysis; Pyrimidine Dimers / genetics; Pyrimidine Dimers / radiation effects; Telomere / genetics; Telomere / immunology; Telomere / radiation effects; Telomere-Binding Proteins / immunology; Ultraviolet Rays / adverse effects
TL;DR:
A highly sensitive method for quantifying the formation and removal of UV photoproducts in telomeres isolated from UV irradiated cultured human cells is described.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: October 7, 2019
2019 chapter
Measuring UV Photoproduct Repair in Isolated Telomeres and Bulk Genomic DNA
In DNA Repair (pp. 295–306). Springer.
Source: ORCID
Added: September 23, 2021
2019 journal article
Single-Molecule Study of TRF2 Mediated DNA Compaction using Physiologically Relevant Long Telomeric DNA
Biophysical Journal, 116(3), 505a.
Sources: Crossref, NC State University Libraries
Added: January 25, 2020
2019 journal article
TIN2 is an Architectural Protein Stabilizing TRF1 at Telomere
Biophysical Journal, 116(3), 211a–212a.
Sources: Crossref, NC State University Libraries
Added: January 25, 2020
2018 journal article
Cohesin SA2 is a sequence-independent DNA-binding protein that recognizes DNA replication and repair intermediates
JOURNAL OF BIOLOGICAL CHEMISTRY, 293(3), 1054–1069.
MeSH headings : Cell Cycle Proteins / chemistry; Cell Cycle Proteins / metabolism; Chromosomal Proteins, Non-Histone / chemistry; Chromosomal Proteins, Non-Histone / metabolism; DNA Repair / genetics; DNA Repair / physiology; DNA Replication / physiology; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / metabolism; Fluorescence Polarization; Genomic Instability / genetics; Genomic Instability / physiology; Microscopy, Atomic Force; Microscopy, Fluorescence; Protein Binding / genetics; Protein Binding / physiology
TL;DR:
The results suggest that SA2 functions at intermediate DNA structures during DNA transactions in genome maintenance pathways, and has important implications for understanding the function of cohesin in these pathways.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2018 journal article
Single-molecule DREEM imaging reveals DNA wrapping around human mitochondrial single-stranded DNA binding protein
NUCLEIC ACIDS RESEARCH, 46(21), 11287–11302.
MeSH headings : DNA, Mitochondrial / chemistry; DNA, Mitochondrial / metabolism; DNA, Single-Stranded / chemistry; DNA, Single-Stranded / metabolism; DNA-Binding Proteins / analysis; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / metabolism; Fluorescence Polarization; Humans; Microscopy, Atomic Force / methods; Mitochondrial Proteins / analysis; Mitochondrial Proteins / chemistry; Mitochondrial Proteins / metabolism; Protein Conformation; Protein Stability; Recombinant Proteins / genetics; Single Molecule Imaging / methods; Static Electricity
TL;DR:
Single-molecule imaging suggests mtSSB may not saturate or fully protect single-stranded replication intermediates during mtDNA synthesis, leaving the mitochondrial genome vulnerable to chemical mutagenesis, deletions driven by primer relocation or other actions consistent with clinically observed deletion biases.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: February 11, 2019
2017 journal article
Cohesin SA2 is a sequence independent DNA binding protein that recognizes DNA replication and repair intermediates
Journal of Biological Chemistry, jbc-M117.
Source: ORCID
Added: September 23, 2021
2017 journal article
CpG and methylation-dependent DNA binding and dynamics of the methylcytosine binding domain 2 protein at the single-molecule level
NUCLEIC ACIDS RESEARCH, 45(15), 9164–9177.
MeSH headings : 5-Methylcytosine / chemistry; 5-Methylcytosine / metabolism; Animals; Binding Sites; Chickens; Cloning, Molecular; CpG Islands; DNA / chemistry; DNA / metabolism; DNA Methylation; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / genetics; DNA-Binding Proteins / metabolism; Escherichia coli / genetics; Escherichia coli / metabolism; Fluorescence Polarization; Gene Expression; Humans; Magnetic Resonance Spectroscopy; Mi-2 Nucleosome Remodeling and Deacetylase Complex / metabolism; Mi-2 Nucleosome Remodeling and Deacetylase Complex / ultrastructure; Nucleic Acid Conformation; Nucleosomes / metabolism; Nucleosomes / ultrastructure; Protein Binding; Protein Isoforms / chemistry; Protein Isoforms / genetics; Protein Isoforms / metabolism; Recombinant Proteins / chemistry; Recombinant Proteins / genetics; Recombinant Proteins / metabolism; Single Molecule Imaging
TL;DR:
The results suggest that MBD2 targets NuRD to unmethylated or methylated CpG islands where its distinct dynamic binding modes help maintain open or closed chromatin, respectively.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2017 journal article
Nucleosome-like, Single-stranded DNA (ssDNA)-Histone Octamer Complexes and the Implication for DNA Double Strand Break Repair
Journal of Biological Chemistry, 292(13), 5271–5281.
Source: ORCID
Added: September 23, 2021
2017 journal article
Single Molecule Fluorescence and Atomic Force Microscopy Studies of DNA Repair
Biophysical Journal, 112(3), 7a.
TL;DR:
How AFM, DREEM, and single-molecule fluorescence can be powerful tools to study the stoichiometries, conformations, and dynamic assembly of multi-component complexes is discussed.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: February 5, 2020
2017 journal article
Using Atomic Force Microscopy to Characterize the Conformational Properties of Proteins and Protein--DNA Complexes That Carry Out DNA Repair
Methods in Enzymology, 592, 187–212.
Sources: NC State University Libraries, ORCID
Added: August 6, 2018
2017 journal article
Walking the DNA Methylation Tightrope: The Involvement of Intrinsically Disordered Regions of Transcription Factors
Biophysical Journal, 112(3), 207a.
TL;DR:
Data reveals how MBD2 dynamically achieves DNA binding specificity for methylated DNA and supports that the IDR ofMBD2 modulates MBD 2-binding dynamics, and is important for further deciphering the molecular mechanisms of MBD and mCpG epigenetic regulation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: Crossref, NC State University Libraries
Added: February 24, 2020
2016 journal article
Enhanced electrostatic force microscopy reveals higher-order DNA looping mediated by the telomeric protein TRF2
Scientific Reports, 6(1).
MeSH headings : DNA / chemistry; DNA / metabolism; HeLa Cells; Humans; Microscopy; Multiprotein Complexes / chemistry; Multiprotein Complexes / metabolism; Nucleic Acid Conformation; Static Electricity; Telomeric Repeat Binding Protein 2 / chemistry; Telomeric Repeat Binding Protein 2 / metabolism
TL;DR:
Supporting coarse-grained molecular dynamics simulations uncover the structural requirement and sequential steps during TRF2-mediated DNA compaction and result in folded DNA structures with protruding DNA loops as seen in DREEM imaging.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Crossref, NC State University Libraries, NC State University Libraries, ORCID
Added: August 6, 2018
2016 journal article
Functional interplay between SA1 and TRF1 in telomeric DNA binding and DNA--DNA pairing
Nucleic Acids Research, gkw518.
Source: ORCID
Added: September 23, 2021
2016 journal article
Functional interplay between SA1 and TRF1 in telomeric DNA binding and DNA-DNA pairing
NUCLEIC ACIDS RESEARCH, 44(13), 6363–6376.
MeSH headings : AT-Hook Motifs / genetics; Chromatids / genetics; Chromatids / ultrastructure; Chromosome Segregation / genetics; DNA-Binding Proteins / genetics; Humans; Microscopy, Atomic Force; Mitosis / genetics; Nuclear Proteins / genetics; Nuclear Proteins / metabolism; Telomere / genetics; Telomere / ultrastructure; Telomere-Binding Proteins / genetics; Telomere-Binding Proteins / metabolism; Telomeric Repeat Binding Protein 1 / genetics; Telomeric Repeat Binding Protein 1 / metabolism
TL;DR:
The results suggest that at telomeres cohesion relies on the molecular interplay between TRF1 and SA1 to promote DNA–DNA pairing, while along chromosomal arms the core cohesin assembly might also depend on SA1 1D diffusion on DNA and sequence-specific DNA binding.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2016 journal article
TRF2-Mediated Control of Telomere DNA Topology as a Mechanism for Chromosome-End Protection
Molecular Cell.
Source: ORCID
Added: September 23, 2021
2016 journal article
TRF2-mediated control of telomere DNA topology as a mechanism for chromosome-end protection
Molecular Cell, 61(2), 274–286.
Source: NC State University Libraries
Added: August 6, 2018
2016 journal article
Visualizing the Path of DNA through Proteins Using DREEM Imaging
MOLECULAR CELL, 61(2), 315–323.
MeSH headings : DNA / chemistry; DNA Mismatch Repair; Imaging, Three-Dimensional; Microscopy, Atomic Force; Nucleosomes / metabolism; Proteins / metabolism; Static Electricity
TL;DR:
This work combines AFM with an electrostatic force microscopy (EFM) method to develop an exquisitely sensitive dual-resonance-frequency-enhanced EFM (DREEM) capable of resolving DNA within protein-DNA complexes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2015 journal article
Determining the DNA Diffusion Behavior of SA2 on Various DNA Substrates
Biophysical Journal, 108(2), 397a.
TL;DR:
It is proposed that 1-D sliding and sequence dependent pausing by SA1 provides binding specificity and stability during the cohesion process at telomeres, while SA2 alone, lacking the AT hook domain, uses different DNA binding mechanisms.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: February 24, 2020
2015 journal article
Interference of ATP with the fluorescent probes YOYO-1 and YOYO-3 modifies the mechanical properties of intercalator-stained DNA confined in nanochannels
Microchimica Acta, 182(7-8), 1561–1565.
author keywords: DNA; ATP; Intercalating dye; YOYO-1; DAPI; Nanofluidics
TL;DR:
Investigation of the mechanical properties of DNA stained with the fluorescent intercalating dyes YOYO-1 and YoyO-3 as a function of ATP concentrations by stretching single molecules in nanofluidic channels finds negligible effects if DNA is visualized with the minor groove-binding probe 4′,6-diamidino-2-phenylindole.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Crossref, Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 journal article
Revealing Structure and Dynamics of Telomere Maintenance Proteins on DNA: One Molecule at a Time
Biophysical Journal, 108(2), 7a.
TL;DR:
Three complementary single-molecule imaging platforms are established: a newly developed Dual-Resonance-frequency-Enhanced Electrostatic force Microscopy technique capable of revealing DNA paths in protein-DNA complexes, fluorescence imaging of quantum dot-labeled proteins for tracking dynamics of proteins on DNA tightropes, and a nanochannel based imaging platform for studying protein-mediated DNA-DNA pairing/looping in real time.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: February 24, 2020
2015 journal article
Single-Molecule Imaging Reveals Dynamics of SA1-TRF1 Interactions on Telomeric DNA
Biophysical Journal, 108(2), 206a.
TL;DR:
The cohesin complex plays a crucial role in accurate chromosome segregation, organization of interphase chromatin, DNA replication, and post replicative DNA repair in part by promoting DNA-DNA pairing.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: February 24, 2020
2015 journal article
Telomeres are partly shielded from ultraviolet-induced damage and proficient for nucleotide excision repair of photoproducts
NATURE COMMUNICATIONS, 6.
MeSH headings : Cell Line; Cell Proliferation; Cell Survival; DNA Damage / radiation effects; DNA Repair / physiology; Fibroblasts / cytology; Fibroblasts / radiation effects; Humans; Telomere / radiation effects; Ultraviolet Rays
TL;DR:
Examination of the efficiency of photoproduct formation and removal at telomeres purified from UVC irradiated cells at various recovery times provides new evidence that telomes are partially protected from ultraviolet irradiation and that NER preserves telomere integrity.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2014 journal article
Probing transient protein-mediated DNA linkages using nanoconfinement
Biomicrofluidics, 8(3), 034113.
Contributors: M. Roushan n, P. Kaur n, A. Karpusenko n, P. Countryman n, C. Ortiz n, S. Lim n , n , R. Riehn n
TL;DR:
The study of the interaction between T4 DNA ligase and DNA concludes that ligase can transiently stabilize folded DNA configurations by coordinating genetically distant DNA stretches.
(via Semantic Scholar)
Sources: Crossref, ORCID, NC State University Libraries, NC State University Libraries
Added: August 6, 2018
2014 journal article
Single-molecule analysis reveals human UV-damaged DNA-binding protein (UV-DDB) dimerizes on DNA via multiple kinetic intermediates
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111(18), E1862–E1871.
author keywords: DNA damage recognition; single-molecule tracking; DNA tightrope; human nucleotide excision repair
MeSH headings : Amino Acid Substitution; DNA / chemistry; DNA / metabolism; DNA / radiation effects; DNA Damage; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / genetics; DNA-Binding Proteins / metabolism; Humans; Kinetics; Microscopy, Fluorescence; Models, Molecular; Mutagenesis, Site-Directed; Nucleic Acid Conformation; Osmolar Concentration; Protein Conformation; Protein Multimerization; Pyrimidine Dimers / metabolism; Pyrimidine Dimers / radiation effects; Quantum Dots; Ultraviolet Rays / adverse effects; Xeroderma Pigmentosum / genetics; Xeroderma Pigmentosum / metabolism
TL;DR:
This study performed single-molecule experiments, which revealed that the human UV-damaged DNA-binding protein (UV-DDB) performs a 3D search mechanism and displays a remarkable heterogeneity in the kinetics of damage recognition.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2014 conference paper
Single-molecule imaging reveals DNA-binding properties of cohesin proteins SA1 and SA2.
Environmental and Molecular Mutagenesis, 55, S29–29.
Source: NC State University Libraries
Added: August 6, 2018
2014 journal article
TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres
NUCLEIC ACIDS RESEARCH, 42(4), 2493–2504.
MeSH headings : DNA / chemistry; DNA / metabolism; Diffusion; Protein Binding; Protein Structure, Tertiary; Repetitive Sequences, Nucleic Acid; Telomere / chemistry; Telomere / metabolism; Telomeric Repeat Binding Protein 1 / metabolism; Telomeric Repeat Binding Protein 2 / chemistry; Telomeric Repeat Binding Protein 2 / metabolism
TL;DR:
It is proposed that the TRF proteins use 1D sliding to find protein partners and assemble the shelterin complex, which in turn stabilizes the interaction with specific telomeric DNA.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2014 journal article
TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres
Nucleic Acids Research, 42(4), 2493–2504.
Source: ORCID
Added: September 23, 2021
2014 journal article
Unraveling secrets of telomeres: One molecule at a time
DNA REPAIR, 20, 142–153.
author keywords: Telomeres; Single-molecule imaging; Atomic force microscopy; Fluorescence microscopy; FRET; Laser tweezers; Magnetic tweezers; Protein DNA interactions
MeSH headings : Animals; Fluorescence Resonance Energy Transfer / methods; Humans; Microscopy, Atomic Force / methods; Microscopy, Fluorescence / methods; Optical Tweezers; Telomere / chemistry; Telomere / metabolism; Telomere-Binding Proteins / chemistry; Telomere-Binding Proteins / metabolism
TL;DR:
This review presents a brief overview of the principles of single-molecule imaging and manipulation techniques and highlights results obtained from applying these single- molecule techniques for studying structure, dynamics and functions of G-quadruplexes, telomerase, and shelterin proteins.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2013 journal article
DNA polymerase delta stalls on telomeric lagging strand templates independently from G-quadruplex formation
NUCLEIC ACIDS RESEARCH, 41(22), 10323–10333.
MeSH headings : DNA / biosynthesis; DNA / chemistry; DNA Polymerase III / metabolism; G-Quadruplexes; Humans; Repetitive Sequences, Nucleic Acid; Telomere / metabolism; Templates, Genetic
TL;DR:
It is suggested that an alternative mechanism, in addition to stable G4s, contributes to replication stalling at telomeres and is provided evidence that G4 folding is less stable on single-stranded circular TTAGGG templates where ends are constrained, compared with linear oligonucleotides.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2013 review
Investigating bioconjugation by atomic force microscopy
[Review of ]. Journal of Anobiotechnology, 11.
Source: NC State University Libraries
Added: August 6, 2018
2013 journal article
Investigating bioconjugation by atomic force microscopy
J. Nanobiotechnol, 11, 25.
Source: ORCID
Added: September 23, 2021
2013 journal article
Real-time single-molecule imaging reveals a direct interaction between UvrC and UvrB on DNA tightropes
Nucleic Acids Research, gkt177.
Source: ORCID
Added: September 23, 2021
2013 journal article
WT UV-DDB Performs a 3D Search on DNA whereas the XP-E Mutant (K244E DDB2) Mutant Slides
Biophysical Journal, 104(2), 77a.
TL;DR:
The results reveal the stoichiometry and search mechanism of UV-DDB in damage surveillance and are consistent with several salt-bridges observed in the co-crystal structure, which found that the mobility ofUV-D DB on DNA is salt dependent.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: Crossref, NC State University Libraries
Added: December 12, 2021
2012 journal article
A New Role for UvrB in NER? Single Molecule Imaging of the NER Complex UvrBC-DNA
Biophysical Journal, 102(3), 485a.
TL;DR:
A new chaperoning role for UvrB is proposed in NER, where it protects the genome from unwanted UvrC nuclease activity but facilitates UVRC's location of pre-incision UVRB complexes.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: December 12, 2021
2012 journal article
Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair
Proceedings of the National Academy of Sciences, 109(41), E2737–E2746.
author keywords: UV damage; ubiquitin-proteosome system; X-ray crystallography
MeSH headings : Chromatin / chemistry; Chromatin / genetics; Chromatin / metabolism; Crystallography, X-Ray; Cullin Proteins / chemistry; Cullin Proteins / metabolism; DNA / chemistry; DNA / genetics; DNA / metabolism; DNA Damage; DNA Repair; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / metabolism; Humans; Microscopy, Atomic Force; Microscopy, Electron; Models, Molecular; Multiprotein Complexes / chemistry; Multiprotein Complexes / metabolism; Multiprotein Complexes / ultrastructure; Nucleic Acid Conformation; Protein Binding; Protein Folding; Protein Multimerization; Protein Structure, Secondary; Protein Structure, Tertiary
TL;DR:
It is proposed that the binding of UV-damaged DNA results in conformational changes in the N-terminal domain of DDB2, inducing helical folding in the context of the bound DNA and inducing dimerization as a function of nucleotide binding.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: September 23, 2021
2012 journal article
Werner syndrome protein suppresses the formation of large deletions during the replication of human telomeric sequences
Cell Cycle, 11(16), 3036–3044.
Source: ORCID
Added: September 23, 2021
2011 journal article
High accuracy FIONA–AFM hybrid imaging
Ultramicroscopy, 111(5), 350–355.
author keywords: Atomic force microscopy (AFM); Fluorescence imaging with one nanometer accuracy (FIONA); Single molecule; Multi-protein complexes; Image registration
MeSH headings : Bacillus / chemistry; Bacterial Proteins / chemistry; Microscopy, Atomic Force / methods; Microscopy, Fluorescence / methods; Quantum Dots
TL;DR:
A combination of the two orthogonal techniques (FIONA and AFM) opens a wide spectrum of possible applications to the study of protein interactions, because AFM can yield high resolution information about the conformational properties of multi-protein complexes and the fluorescence can indicate spatial relationships of the proteins in the complexes.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: September 23, 2021
2011 journal article
Investigating Nucleotide Excision DNA Repair by Single-Molecule Imaging of Quantum Dot Labeled Proteins Reveals Unique Scanning Mechanisms
Biophysical Journal, 100(3), 240a.
TL;DR:
The next enzyme in the pathway is introduced, UvrC, which nicks the DNA backbone 5’ and 3’ to the pre-incision complex formed after UvrAB finds the lesion, providing a substrate for DNA helicase II which subsequently removes the damage-containing oligonucleotide.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: December 12, 2021
2011 chapter
Nucleotide excision repair from bacteria to humans: Structure--function studies
In Chemical Carcinogenesis (pp. 267–296). Springer.
Source: ORCID
Added: September 23, 2021
2011 journal article
Single Molecule Studies of Physiologically Relevant Telomeric Tails Reveal POT1 Mechanism for Promoting G-quadruplex Unfolding
Journal of Biological Chemistry, 286(9), 7479–7489.
MeSH headings : Animals; Cell Line; Combinatorial Chemistry Techniques; DNA, Single-Stranded / chemistry; G-Quadruplexes; Humans; Insecta; Microscopy, Atomic Force; Models, Chemical; Oligonucleotides, Antisense; Protein Binding; Shelterin Complex; Telomere / chemistry; Telomere / genetics; Telomere / metabolism; Telomere-Binding Proteins / chemistry; Telomere-Binding Proteins / genetics; Telomere-Binding Proteins / metabolism
TL;DR:
It is observed that the majority of the telomeric tails of 16 repeats formed two quadruplexes even though four were possible, indicating a novel POT1 activity beyond simply preventing quadruplex folding.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: September 23, 2021
2010 journal article
Collaborative Dynamic DNA Scanning by Nucleotide Excision Repair Proteins Investigated by Single- Molecule Imaging of Quantum-Dot-Labeled Proteins
Molecular Cell, 37(5), 702–713.
MeSH headings : Adenosine Triphosphatases / chemistry; Adenosine Triphosphatases / genetics; Adenosine Triphosphatases / metabolism; Adenosine Triphosphate / metabolism; Binding Sites; DNA / chemistry; DNA / metabolism; DNA Helicases / chemistry; DNA Helicases / genetics; DNA Helicases / metabolism; DNA Repair; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / genetics; DNA-Binding Proteins / metabolism; Electrophoretic Mobility Shift Assay; Escherichia coli Proteins / chemistry; Escherichia coli Proteins / genetics; Escherichia coli Proteins / metabolism; Kinetics; Microscopy, Atomic Force; Microscopy, Fluorescence; Models, Molecular; Nucleic Acid Conformation; Protein Binding; Protein Conformation; Protein Multimerization; Quantum Dots
TL;DR:
This work uniquely labeled bacterial UvrA and UvrB with differently colored quantum dots and visualized how they interacted with DNA individually or together using oblique-angle fluorescence microscopy, allowing more rapid and efficient scanning of the genome for damage.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: September 23, 2021
2009 journal article
Replication Protein A Stimulates the Werner Syndrome Protein Branch Migration Activity
Journal of Biological Chemistry, 284(50), 34682–34691.
MeSH headings : Animals; DNA Replication; DNA, Single-Stranded / chemistry; DNA, Single-Stranded / genetics; DNA, Single-Stranded / metabolism; Exodeoxyribonucleases / genetics; Exodeoxyribonucleases / metabolism; Humans; Nucleic Acid Conformation; RecQ Helicases / genetics; RecQ Helicases / metabolism; Recombination, Genetic; Replication Protein A / genetics; Replication Protein A / metabolism; Shelterin Complex; Telomere / metabolism; Telomere-Binding Proteins / genetics; Telomere-Binding Proteins / metabolism; Werner Syndrome / genetics; Werner Syndrome / metabolism; Werner Syndrome Helicase
TL;DR:
The results are consistent with cellular data that support RPA enhancement of branch migration during HR repair and POT1 limitation of inappropriate recombination and branch migration at telomeric ends and are, to the authors' knowledge, the first evidence that RPA can stimulate branch migration activity.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: September 23, 2021
2009 journal article
The Werner syndrome helicase/exonuclease processes mobile D-loops through branch migration and degradation
PLoS One, 4(3), e4825.
Source: ORCID
Added: September 23, 2021
2008 journal article
Efficient processing of TFO-directed psoralen DNA interstrand crosslinks by the UvrABC nuclease
Nucleic Acids Research, 36(22), 7136–7145.
Source: ORCID
Added: September 23, 2021
2008 journal article
Functional Characterization and Atomic Force Microscopy of a DNA Repair Protein Conjugated to a Quantum Dot
Nano Letters, 8(6), 1631–1637.
MeSH headings : Binding Sites; DNA Repair Enzymes / chemistry; DNA Repair Enzymes / ultrastructure; Microscopy, Atomic Force / methods; Protein Binding; Protein Interaction Mapping / methods; Quantum Dots
TL;DR:
It is demonstrated that quantum dots can serve as a molecular marker to unambiguously identify the presence of a labeled protein in AFM images and be used to evaluate the DNA binding function of UvrB-QD conjugates.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: September 23, 2021
2007 chapter
Characterization of protein--protein interactions using atomic force microscopy
In Protein Interactions (pp. 39–77). Springer.
Source: ORCID
Added: September 23, 2021
2006 journal article
Structural basis for DNA recognition and processing by UvrB
Nature Structural & Molecular Biology, 13(4), 360–364.
MeSH headings : Bacillus / genetics; Bacillus / metabolism; Bacterial Proteins / chemistry; Bacterial Proteins / metabolism; Base Sequence; Crystallography, X-Ray; DNA Damage; DNA Repair; DNA, Bacterial / chemistry; DNA, Bacterial / genetics; DNA, Bacterial / metabolism; Macromolecular Substances; Models, Molecular; Static Electricity
TL;DR:
The first structure of a UvrB–double-stranded DNA complex is reported, providing insights into the mechanism by which Uvr B binds DNA, leading to formation of the preincision complex.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: September 23, 2021
2006 journal article
The C-terminal Zinc Finger of UvrA Does Not Bind DNA Directly but Regulates Damage-specific DNA Binding
Journal of Biological Chemistry, 281(36), 26370–26381.
MeSH headings : Adenosine Triphosphatases / chemistry; Adenosine Triphosphatases / genetics; Adenosine Triphosphatases / metabolism; Adenosine Triphosphate / metabolism; Amino Acid Sequence; DNA / metabolism; DNA Damage; DNA Helicases / genetics; DNA Helicases / metabolism; DNA Repair; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / genetics; DNA-Binding Proteins / metabolism; Dimerization; Escherichia coli / genetics; Escherichia coli / metabolism; Escherichia coli Proteins / chemistry; Escherichia coli Proteins / genetics; Escherichia coli Proteins / metabolism; Magnesium / metabolism; Models, Molecular; Molecular Sequence Data; Mutation; Protein Binding; Protein Structure, Quaternary; Protein Structure, Secondary; Recombinant Fusion Proteins / genetics; Recombinant Fusion Proteins / metabolism; Sequence Alignment; Ultraviolet Rays; Zinc Fingers
TL;DR:
Data demonstrate that the C-terminal zinc finger of UvrA is required for regulation of damage-specific DNA binding.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: September 23, 2021
2006 journal article
UvrB Domain 4, an Autoinhibitory Gate for Regulation of DNA Binding and ATPase Activity
Journal of Biological Chemistry, 281(22), 15227–15237.
MeSH headings : Adenosine Triphosphatases / genetics; Adenosine Triphosphatases / metabolism; Amino Acid Sequence; Bacillus / genetics; Bacillus / metabolism; Bacterial Proteins / chemistry; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Base Sequence; DNA Damage; DNA Repair; DNA, Bacterial / genetics; DNA, Bacterial / metabolism; Dimerization; Kinetics; Models, Biological; Molecular Sequence Data; Protein Structure, Quaternary; Protein Structure, Tertiary; Sequence Homology, Amino Acid
TL;DR:
Using atomic force microscopy and biochemical assays, it is found that truncation of domain 4 of Bacillus caldotenax UvrB (UvrBΔ4) leads to multiple changes in protein function and is proposed that other than its previously discovered role in regulating protein-protein interactions, domain 4 is an autoinhibitory domain regulating the DNA binding and ATPase activities of Uvr B.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: September 23, 2021
2005 journal article
Structural insights into the first incision reaction during nucleotide excision repair
The EMBO Journal, 24(5), 885–894.
author keywords: crystallography; DNA damage; DNA repair; nucleotide excision repair; UvrC
MeSH headings : Amino Acid Sequence; Bacillus / enzymology; Bacillus / genetics; Catalytic Domain / genetics; Cations, Divalent / metabolism; Conserved Sequence; Crystallography, X-Ray; DNA Repair / physiology; DNA, Bacterial / chemistry; DNA, Bacterial / metabolism; Endodeoxyribonucleases / chemistry; Endodeoxyribonucleases / genetics; Endodeoxyribonucleases / metabolism; Escherichia coli Proteins; Models, Molecular; Molecular Sequence Data; Mutagenesis, Site-Directed; Protein Structure, Tertiary; Recombinant Proteins / chemistry; Recombinant Proteins / genetics; Recombinant Proteins / metabolism; Sequence Homology, Amino Acid; Static Electricity
TL;DR:
The crystal structure of the N‐terminal catalytic domain of UvrC is reported at 1.5 Å resolution, which catalyzes the 3′ incision reaction and shares homology with the catalyticdomain of the GIY‐YIG family of intron‐encoded homing endonucleases.
(via Semantic Scholar)
Source: Crossref
Added: December 12, 2021
2005 journal article
Structural insights into the first incision reaction during nucleotide excision repair
The EMBO Journal, 24(5), 885–894.
Source: ORCID
Added: September 23, 2021
2005 journal article
‘Close-fitting sleeves’: DNA damage recognition by the UvrABC nuclease system
Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 577(1-2), 92–117.
author keywords: protein-DNA interaction; bacterial nucleotide excision repair; DNA damage recognition
MeSH headings : DNA Damage; Endodeoxyribonucleases / chemistry; Endodeoxyribonucleases / genetics; Endodeoxyribonucleases / metabolism; Escherichia coli Proteins / chemistry; Escherichia coli Proteins / genetics; Escherichia coli Proteins / metabolism; Models, Molecular; Substrate Specificity
TL;DR:
The current knowledge of how damage recognition is achieved in bacterial nucleotide excision repair through the concerted action of the UvrA, UvrB, and UvrC proteins is reviewed.
(via Semantic Scholar)
Sources: Crossref, ORCID
Added: September 23, 2021
2003 journal article
DNA bending and unbending by MutS govern mismatch recognition and specificity
Proceedings of the National Academy of Sciences, 100(25), 14822–14827.
Source: ORCID
Added: September 23, 2021
2003 journal article
Functional oligomeric state of avian sarcoma virus integrase
Journal of Biological Chemistry, 278(2), 1323–1327.
Source: ORCID
Added: September 23, 2021
2003 journal article
Quantitative characterization of biomolecular assemblies and interactions using atomic force microscopy
Methods, 29(2), 175–187.
Source: ORCID
Added: September 23, 2021
2002 journal article
A minimal exonuclease domain of WRN forms a hexamer on DNA and possesses both 3'-5'exonuclease and 5'-protruding strand endonuclease activities
Biochemistry, 41(9), 2901–2912.
Source: ORCID
Added: September 23, 2021
2002 journal article
DNA binding properties of the yeast Msh2-Msh6 and Mlh1-Pms1 heterodimers
Biological Chemistry, 383(6), 969–975.
Source: ORCID
Added: September 23, 2021
2001 journal article
High affinity cooperative DNA binding by the yeast Mlh1-Pms1 heterodimer
Journal of Molecular Biology, 312(4), 637–647.
Source: ORCID
Added: September 23, 2021
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