Parminder Kaur

Works (39)

Updated: April 3rd, 2024 17:58

2023 journal article

Assembly path dependence of telomeric DNA compaction by TRF1, TIN2, and SA1

BIOPHYSICAL JOURNAL, 122(10), 1822–1832.

By: M. Liu  n, H. Pan n, P. Kaur n, L. Wang  n, M. Jin *, A. Detwiler *, P. Opresko *, Y. Tao *, H. Wang n , R. Riehn n 

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, ORCID, NC State University Libraries
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).

By: P. Kaur n, X. Lu *, Q. Xu *, E. Irvin n, C. Pappas n, H. Zhang *, I. Finkelstein *, Z. Shi * ...

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)
UN Sustainable Development Goal Categories
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.

By: N. Laspata*, P. Kaur*, S. Mersaoui *, D. Muoio *, Z. Liu *, M. Bannister *, H. Nguyen *, C. Curry* ...

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
Sources: Web Of Science, NC State University Libraries
Added: March 20, 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.

By: J. Wojtaszek *, K. Hoff*, M. Longley *, P. Kaur n, S. Andres *, H. Wang n , R. Williams *, W. Copeland *

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
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).

By: G. Leighton *, E. Irvin n, P. Kaur n, M. Liu n, C. You *, D. Bhattaram *, J. Piehler *, R. Riehn n  ...

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
14. Life Below Water (OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
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.

By: Z. Li *, P. Kaur n, C. Lo *, N. Chopra *, J. Smith*, H. Wang n , Y. Gao *

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
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).

By: H. Pan n, P. Kaur n, R. Barnes *, A. Detwiler *, S. Sanford *, M. Liu  n, P. Xu n, C. Mahn n ...

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
Sources: Web Of Science, NC State University Libraries
Added: October 26, 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.

By: P. Kaur n, R. Barnes *, H. Pan n, A. Detwiler *, M. Liu n, C. Mahn n, J. Hall n , Z. Messenger n ...

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
Sources: Web Of Science, NC State University Libraries, ORCID
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).

By: P. Kaur n, H. Pan n, M. Longley *, W. Copeland * & H. Wang n 

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
Source: Web Of Science
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.

By: H. Pan n, M. Jin *, A. Ghadiyaram n, P. Kaur n, H. Miller *, H. Ta *, M. Liu n, Y. Fan* ...

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
Sources: Web Of Science, ORCID, NC State University Libraries
Added: October 5, 2020

2020 journal article

DNA looping by two 5-methylcytosine-binding proteins quantified using nanofluidic devices

EPIGENETICS & CHROMATIN, 13(1).

By: M. Liu n, S. Movahed n, S. Dangi n, H. Pan n, P. Kaur n, S. Bilinovich *, E. Faison *, G. Leighton * ...

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
Sources: Web Of Science, NC State University Libraries
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.

By: P. Kaur n, M. Longley *, H. Pan n, W. Wang  n, P. Countryman n, H. Wang n , W. Copeland *

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
Source: Web Of Science
Added: May 18, 2020

2019 journal article

Cohesin SA2 and EWSR1 in R-Loop Regulation

Biophysical Journal, 116(3), 505a.

By: H. Wang n , A. Ghadiyaram n, H. Pan  n, Y. Fan*, P. Kaur n, A. Gorthi *, R. Riehn n , A. Bishop *, Y. Jane Tao *

Sources: Crossref, NC State University Libraries
Added: January 25, 2020

2019 journal article

Single-Molecule Study of TRF2 Mediated DNA Compaction using Physiologically Relevant Long Telomeric DNA

Biophysical Journal, 116(3), 505a.

By: P. Kaur n, R. Barnes *, H. Pan  n, P. Opresko *, R. Riehn n  & H. Wang n 

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.

By: H. Pan  n, S. Dangi n, P. Kaur n, P. Hao  n, K. Weninger n , R. Riehn n , P. Opresko *, H. Wang n 

Sources: Crossref, NC State University Libraries
Added: January 25, 2020

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.

By: P. Kaur n, M. Longley *, H. Pan n, H. Wang n  & W. Copeland *

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
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, 293(3), 1054–1069.

By: P. Countryman n, Y. Fan*, A. Gorthi *, H. Pan n, J. Strickland n, P. Kaur n, X. Wang  n, J. Lin  n ...

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
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

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.

By: H. Pan n, S. Bilinovich *, P. Kaur n, R. Riehn n , H. Wang n  & D. Williams *

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
14. Life Below Water (OpenAlex)
Sources: Web Of Science, NC State University Libraries
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.

By: N. Adkins*, S. Swygert *, P. Kaur n, H. Niu *, S. Grigoryev *, P. Sung *, H. Wang  n, C. Peterson *

MeSH headings : Chromatin Assembly and Disassembly / genetics; DNA Breaks, Double-Stranded; DNA Repair / genetics; DNA, Single-Stranded / metabolism; Genomic Instability; Histones / metabolism; Nucleosomes / metabolism; Protein Processing, Post-Translational; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae Proteins / metabolism; Transcription Factors / metabolism
TL;DR: It is demonstrated that histones are not evicted from ssDNA after in vitro chromatin resection, indicating that ssNucs may be a hallmark of processes that generate ssDNA, and that posttranslational modification of ssNUCs may generate novel signaling platforms involved in genome stability. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2017 journal article

Single Molecule Fluorescence and Atomic Force Microscopy Studies of DNA Repair

Biophysical Journal, 112(3), 7a.

By: D. Erie *, K. Bradford *, H. Wilkins*, J. Bower *, Z. Wang *, J. Gauer*, M. Satusky *, R. Qiu n ...

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

DNA Repair Enzymes: Structure, Biophysics, and Mechanism, 592, 187–212.

By: S. LeBlanc, H. Wilkins, Z. Li, P. Kaur, H. Wang  & D. Erie

Source: NC State University Libraries
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.

By: S. Bilinovich *, H. Pan  n, P. Kaur n, H. Wang n  & D. Williams *

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).

By: P. Kaur n, D. Wu n, J. Lin n, P. Countryman n, K. Bradford *, D. Erie *, R. Riehn n , P. Opresko *, H. Wang n 

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
Sources: Crossref, NC State University Libraries, NC State University Libraries
Added: August 6, 2018

2016 journal article

Functional interplay between SA1 and TRF1 in telomeric DNA binding and DNA-DNA pairing

NUCLEIC ACIDS RESEARCH, 44(13), 6363–6376.

By: J. Lin n, P. Countryman n, H. Chen *, H. Pan n, Y. Fan*, Y. Jiang *, P. Kaur n, W. Miao * ...

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
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, 61(2), 274–286.

By: D. Benarroch-Popivker*, S. Pisano*, A. Mendez-Bermudez, L. Lototska*, P. Kaur*, S. Bauwens *, N. Djerbi *, C. Latrick * ...

MeSH headings : Ataxia Telangiectasia Mutated Proteins / metabolism; Base Pairing; DNA / chemistry; DNA / metabolism; DNA Damage; DNA End-Joining Repair; HeLa Cells; Humans; Lysine / metabolism; Models, Molecular; Mutation; Nucleic Acid Conformation; Protein Structure, Tertiary; Shelterin Complex; Signal Transduction; Telomere / metabolism; Telomere-Binding Proteins / metabolism; Telomeric Repeat Binding Protein 2 / chemistry; Telomeric Repeat Binding Protein 2 / metabolism
TL;DR: It is concluded that a distinctive topological state of telomeric DNA, controlled by the TRF2-dependent DNA wrapping and linked to t-loop formation, inhibits both ATM activation and NHEJ. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Crossref, 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.

By: D. Wu *, P. Kaur n, Z. Li *, K. Bradford *, H. Wang n  & D. Erie *

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
Source: Web Of Science
Added: August 6, 2018

2015 journal article

Comparison of Ensemble and Single Molecule Methods for Particle Characterization and Binding Analysis of a PEGylated Single-Domain Antibody

Journal of Pharmaceutical Sciences, 104(12), 4015–4024.

By: L. Schneeweis *, L. Obenauer-Kutner*, P. Kaur*, A. Yamniuk*, J. Tamura *, N. Jaffe*, B. O’Mara *, S. Lindsay *, M. Doyle *, J. Bryson *

author keywords: proteins; PEGylation; microscopy; light scattering (static); calorimetry (ITC)
MeSH headings : Antibodies / chemistry; Biological Assay / methods; Half-Life; Kinetics; Microscopy, Atomic Force / methods; Polyethylene Glycols / chemistry; Protein Binding / drug effects; Proteins / chemistry; Surface Plasmon Resonance / methods
TL;DR: This study has used AFM single-molecule studies to determine the mechanism of PEG-dependent reductions in the effectiveness of the dAb observed by SPR kinetic studies, and helps explain the disconnect between the SPR, determined kinetically, and the force microscopy and ITC results that demonstrated that PEG does not change the binding energy. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: Crossref
Added: February 24, 2020

2015 journal article

Determining the DNA Diffusion Behavior of SA2 on Various DNA Substrates

Biophysical Journal, 108(2), 397a.

By: P. Countryman n, J. Lin  n, P. Kaur n, E. Brennan  n, H. Chen *, C. You *, J. Piehler *, Y. Tao *, H. Wang n 

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

Enhanced Electrostatic Force Microscopy Imaging Reveals Mechanism of TRF2 Mediated DNA Compaction

Biophysical Journal, 108(2), 166a.

By: P. Kaur n

TL;DR: The results clearly demonstrate the electrostatic changes in TRF2-DNA complexes upon oligomerizaton of proteins and DNA compaction, and underscore the importance of developing new electrostatic force microscopy imaging techniques for studying biological systems. (via Semantic Scholar)
Source: Crossref
Added: December 31, 2020

2015 journal article

Revealing Structure and Dynamics of Telomere Maintenance Proteins on DNA: One Molecule at a Time

Biophysical Journal, 108(2), 7a.

By: H. Wang n , J. Lin  n, P. Kaur n, P. Countryman n, P. Opresko *, S. Smith *, J. Tao*

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.

By: J. Lin  n, H. Chen *, P. Kaur n, W. Miao  n, P. Countryman n, C. You *, J. Piehler *, Y. Tao *, S. Smith *, H. Wang n 

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

2014 journal article

Probing transient protein-mediated DNA linkages using nanoconfinement

Biomicrofluidics, 8(3), 034113.

By: M. Roushan n, P. Kaur n, A. Karpusenko n, P. Countryman n, C. Ortiz n, S. Fang Lim  n, H. Wang n , R. Riehn n 

Contributors: M. Roushan n, P. Kaur n, A. Karpusenko n, P. Countryman n, C. Ortiz n, S. Lim n , H. Wang 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 conference paper

Single-molecule imaging reveals DNA-binding properties of cohesin proteins SA1 and SA2.

Environmental and Molecular Mutagenesis, 55, S29–29.

By: J. Lin, P. Kaur, H. Chen, P. Countryman, M. Roushan, D. Flaherty, E. Brennan, C. You ...

Source: NC State University Libraries
Added: August 6, 2018

2014 journal article

Solution-state conformation and stoichiometry of yeast Sir3 heterochromatin fibres

Nature Communications, 5(1).

By: S. Swygert *, B. Manning*, S. Senapati *, P. Kaur*, S. Lindsay *, B. Demeler *, C. Peterson *

MeSH headings : Algorithms; Heterochromatin / chemistry; Heterochromatin / metabolism; Microscopy, Atomic Force; Monte Carlo Method; Nucleosomes / chemistry; Nucleosomes / genetics; Nucleosomes / metabolism; Protein Multimerization; Silent Information Regulator Proteins, Saccharomyces cerevisiae / chemistry; Silent Information Regulator Proteins, Saccharomyces cerevisiae / genetics; Silent Information Regulator Proteins, Saccharomyces cerevisiae / metabolism; Ultracentrifugation
TL;DR: Sygert et al. show that Sir3 - a key factor in the formation of heterochromatin - promotes a chromatin structure distinct from the canonical 30 nm fibre. (via Semantic Scholar)
Source: Crossref
Added: August 28, 2020

2014 journal article

Unraveling secrets of telomeres: One molecule at a time

DNA REPAIR, 20, 142–153.

By: J. Lin n, P. Kaur n, P. Countryman n, P. Opresko * & H. Wang n 

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
Source: Web Of Science
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.

By: J. Lormand *, N. Buncher *, C. Murphy*, P. Kaur*, M. Lee*, P. Burgers *, H. Wang* , T. Kunkel *, P. Opresko *

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
Source: Web Of Science
Added: August 6, 2018

2013 review

Investigating bioconjugation by atomic force microscopy

[Review of ]. Journal of Anobiotechnology, 11.

By: I. Tessmer, P. Kaur, J. Lin & H. Wang 

Source: NC State University Libraries
Added: August 6, 2018

2013 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.

By: J. Lin n, P. Countryman n, N. Buncher  n, P. Kaur n, E. Longjiang  n, Y. Zhang n, G. Gibson  n, C. You  n ...

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
7. Affordable and Clean Energy (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2011 journal article

Antibody-Unfolding and Metastable-State Binding in Force Spectroscopy and Recognition Imaging

Biophysical Journal, 100(1), 243–250.

By: P. Kaur*, Qiang-Fu, A. Fuhrmann*, R. Ros *, L. Kutner*, L. Schneeweis *, R. Navoa*, K. Steger* ...

MeSH headings : Humans; Imaging, Three-Dimensional / methods; Immunoglobulin G / chemistry; Immunoglobulin G / metabolism; Kinetics; Protein Binding; Protein Conformation; Protein Unfolding; Spectrum Analysis / methods
TL;DR: Recognition imaging is nonetheless a powerful tool for interpreting complex atomic force microscopy images, so long as specificity is calibrated in situ, and not inferred from equilibrium binding kinetics. (via Semantic Scholar)
Source: Crossref
Added: August 28, 2020

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