Hai Pan

Works (13)

Updated: July 10th, 2023 08:50

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
Added: April 21, 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
Added: August 29, 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, ORCID
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, 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*, H. Pan*, M. Longley, W. Copeland & H. Wang* 

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
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, 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.

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

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.

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, ORCID
Added: August 6, 2018

2018 journal article

Optical Temperature Sensing With Infrared Excited Upconversion Nanoparticles

FRONTIERS IN CHEMISTRY, 6.

By: K. Green n, K. Huang *, H. Pan n, G. Han * & S. Lim n 

author keywords: upconversion thermal sensing; pulsed excitation; 800 nm; 980 nm; local thermal heating; DNA denaturation
TL;DR: These studies provide evidence for the feasibility of exploring protein-DNA interactions at the single molecule scale, using UCNPs as a reporter, and confirm the applicability of infrared imaging at excitation intensities compatible with single nanoparticle tracking. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, ORCID
Added: October 16, 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.

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, ORCID
Added: February 11, 2019

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, 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, 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, ORCID
Added: August 6, 2018

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