Feng Pan

Works (9)

Updated: April 25th, 2025 17:34

2024 article

Structural and Dynamical Properties of Nucleic Acid Hairpins Implicated in Trinucleotide Repeat Expansion Diseases

Pan, F., Xu, P., Roland, C., Sagui, C., & Weninger, K. (2024, October 10). Biomolecules, Vol. 14.

By: F. Pan n, P. Xu n, C. Roland n , C. Sagui n  & K. Weninger n 

author keywords: trinucleotide repeats; expansion diseases; hairpin structure; single-molecule FRET; smFRET; molecular dynamics simulations; CAG and GAC; CTG and GTC
MeSH headings : Trinucleotide Repeat Expansion / genetics; Humans; Nucleic Acid Conformation; DNA / chemistry; DNA / metabolism; DNA / genetics; Molecular Dynamics Simulation; Trinucleotide Repeats / genetics; Fluorescence Resonance Energy Transfer
topics (OpenAlex): Genetic Neurodegenerative Diseases; Genetics and Neurodevelopmental Disorders; DNA Repair Mechanisms
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Sources: Web Of Science, NC State University Libraries
Added: November 12, 2024

2023 article

Frustration Between Preferred States of Complementary Trinucleotide Repeat DNA Hairpins Anticorrelates with Expansion Disease Propensity

Xu, P., Zhang, J., Pan, F., Mahn, C., Roland, C., Sagui, C., & Weninger, K. (2023, April 5). Journal of Molecular Biology, Vol. 435.

By: P. Xu  n, J. Zhang  n, F. Pan n, C. Mahn n, C. Roland n , C. Sagui n , K. Weninger n 

author keywords: single molecule FRET; hairpin slippage; molecular dynamics; kinetics; trinucleotide interrupts; Huntington's disease
MeSH headings : Humans; DNA / genetics; DNA / chemistry; DNA, Complementary; Nucleic Acid Conformation; Trinucleotide Repeat Expansion / genetics; Trinucleotide Repeats; Neurodegenerative Diseases / genetics
topics (OpenAlex): Genetic Neurodegenerative Diseases; RNA Research and Splicing; Mitochondrial Function and Pathology
TL;DR: Single molecule FRET experiments and molecular dynamics simulations are applied to determine conformational stabilities and slipping dynamics for CAG, CTG, GAC and GTC hairpins to determine Tetraloops and TTG interrupts near the loop in the CTG hairpin stabilize the hairpin against slipping. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: May 22, 2023

2023 article

Structure and Dynamics of DNA and RNA Double Helices Formed by d(CTG), d(GTC), r(CUG), and r(GUC) Trinucleotide Repeats and Associated DNA–RNA Hybrids

Fakharzadeh, A., Qu, J., Pan, F., Sagui, C., & Roland, C. (2023, September 8). The Journal of Physical Chemistry B, Vol. 9.

By: A. Fakharzadeh n, J. Qu n, F. Pan*, C. Sagui n  & C. Roland n 

MeSH headings : Adult; Humans; Trinucleotide Repeats; Biophysics; DNA; Hydrogen Bonding; RNA
topics (OpenAlex): Genetic Neurodegenerative Diseases; RNA Research and Splicing; RNA and protein synthesis mechanisms
TL;DR: Molecular dynamics simulations of homoduplexes associated with myotonic dystrophy type 1 found that the U·U and T·T mismatches are dynamic, favoring anti-anti conformations inside the helical core, followed by anti-syn and syn-syn conformations. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: October 10, 2023

2021 article

Molecular conformations and dynamics of nucleotide repeats associated with neurodegenerative diseases: double helices and CAG hairpin loops

Pan, F., Zhang, Y., Xu, P., Man, V. H., Roland, C., Weninger, K., & Sagui, C. (2021, January 1). Computational and Structural Biotechnology Journal, Vol. 19, pp. 2819–2832.

By: F. Pan*, Y. Zhang *, P. Xu n, V. Man n, C. Roland n , K. Weninger n , C. Sagui n 

author keywords: Trinucleotide hexanucleotide repeats; CAG; GAC; CTG; CUG; CCG; GGC; GGGGCC; GGCCCC; Hairpin loops; smFRET; Molecular dynamics
topics (OpenAlex): Genetic Neurodegenerative Diseases; Neurogenetic and Muscular Disorders Research; RNA Research and Splicing
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Added: August 30, 2021

2021 article

The F19W mutation reduces the binding affinity of the transmembrane Aβ11–40 trimer to the membrane bilayer

Tran, T. T., Pan, F., Tran, L., Roland, C., & Sagui, C. (2021, January 1). RSC Advances, Vol. 11, pp. 2664–2676.

By: T. Tran *, F. Pan*, L. Tran *, C. Roland n  & C. Sagui n 

topics (OpenAlex): Lipid Membrane Structure and Behavior; Cellular transport and secretion; Glycosylation and Glycoproteins Research
TL;DR: Experiments show that F19 mutations influence the aggregation rate, but maintain the fibril structures in the 3Aβ11–40 trimer immersed in DPPC lipid bilayers submerged in aqueous solution, suggesting the impact of mutations can be assessed, at least partially, by evaluating the interaction of the mutated peptides with the lipid membranes. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: February 15, 2021

2020 article

Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich’s ataxia: DNA triplexes and RNA/DNA hybrids

Zhang, J., Fakharzadeh, A., Pan, F., Roland, C., & Sagui, C. (2020, August 5). Nucleic Acids Research, Vol. 48, pp. 9899–9917.

By: J. Zhang n, A. Fakharzadeh n, F. Pan n, C. Roland n  & C. Sagui n 

MeSH headings : DNA / chemistry; Friedreich Ataxia / genetics; Humans; Nucleic Acid Heteroduplexes / chemistry; R-Loop Structures; Trinucleotide Repeats
topics (OpenAlex): Genetic Neurodegenerative Diseases; DNA Repair Mechanisms; Mitochondrial Function and Pathology
TL;DR: A systematic in silico characterization of the possible DNA triplexes that could be assembled with GAA and TTC strands contributes to a systematic structural basis for the emerging field of quantitative R-loop biology. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: January 4, 2021

2018 article

Structure and Dynamics of DNA and RNA Double Helices Obtained from the CCG and GGC Trinucleotide Repeats

Pan, F., Man, V. H., Roland, C., & Sagui, C. (2018, April 4). The Journal of Physical Chemistry B, Vol. 122, pp. 4491–4512.

By: F. Pan n, V. Man  n, C. Roland n  & C. Sagui n 

MeSH headings : DNA / chemistry; Molecular Dynamics Simulation; Nucleic Acid Conformation; RNA / chemistry; Trinucleotide Repeats
topics (OpenAlex): RNA and protein synthesis mechanisms; RNA Research and Splicing; DNA and Nucleic Acid Chemistry
TL;DR: Molecular dynamics simulations of (GCC) n and (GGC) n homoduplexes are performed in order to characterize their conformations, stability, and dynamics, and a novel technique based on fast melting by means of an infrared laser pulse is used to classify the relative stability of the different DNA-CCG and -GGC homodups. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2017 article

Structure and Dynamics of DNA and RNA Double Helices of CAG and GAC Trinucleotide Repeats

Pan, F., Man, V. H., Roland, C., & Sagui, C. (2017, July 1). Biophysical Journal, Vol. 113, pp. 19–36.

By: F. Pan n, V. Man n, C. Roland n  & C. Sagui n 

MeSH headings : Cations / chemistry; DNA / chemistry; Hydrogen-Ion Concentration; Molecular Dynamics Simulation; Nucleic Acid Conformation; Principal Component Analysis; RNA / chemistry; Sodium / chemistry; Trinucleotide Repeats
topics (OpenAlex): Genetic Neurodegenerative Diseases; RNA and protein synthesis mechanisms; RNA Research and Splicing
TL;DR: Free energy and molecular dynamics studies are carried out to determine the preferred conformations of the A-A noncanonical pairs in (CAG)n and (GAC)n trinucleotide repeats and the consequent changes in the overall structure of the RNA and DNA duplexes, finding that the global free energy minimum corresponds to A- A pairs stacked inside the core of the helix with anti-anti conformations in RNA and (high-anti)-( high-anti) (via Semantic Scholar)
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7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2016 article

Comparative melting and healing of B-DNA and Z-DNA by an infrared laser pulse

Man, V. H., Pan, F., Sagui, C., & Roland, C. (2016, April 12). The Journal of Chemical Physics, Vol. 144.

By: V. Man n, F. Pan n, C. Sagui n  & C. Roland n 

MeSH headings : DNA, B-Form / chemistry; DNA, Z-Form / chemistry; Lasers; Molecular Dynamics Simulation; Thermodynamics
topics (OpenAlex): Ion-surface interactions and analysis; Nanopore and Nanochannel Transport Studies; Fusion materials and technologies
TL;DR: It is proposed that fast melting by an infrared laser pulse could be used as a technique for a fast comparison of relative stabilities of same-sequence oligonucleotides with different secondary structures with full atomistic detail of the structures and solvent. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

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