Feng Pan

Works (9)

Updated: November 15th, 2024 05:01

2024 review

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

[Review of ]. BIOMOLECULES, 14(10).

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
Sources: Web Of Science, NC State University Libraries
Added: November 12, 2024

2023 journal article

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

JOURNAL OF MOLECULAR BIOLOGY, 435(10).

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
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)
UN Sustainable Development Goal Categories
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). JOURNAL OF PHYSICAL CHEMISTRY B.

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

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)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: October 10, 2023

2021 review

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

[Review of ]. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 19, 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
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: August 30, 2021

2021 journal article

The F19W mutation reduces the binding affinity of the transmembrane A beta(11-40) trimer to the membrane bilayer

RSC ADVANCES, 11(5), 2664–2676.

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

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)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: Web Of Science
Added: February 15, 2021

2020 journal article

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

NUCLEIC ACIDS RESEARCH, 48(17), 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
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)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: January 4, 2021

2018 journal article

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

JOURNAL OF PHYSICAL CHEMISTRY B, 122(16), 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
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)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2017 journal article

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

BIOPHYSICAL JOURNAL, 113(1), 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
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)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2016 journal article

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

JOURNAL OF CHEMICAL PHYSICS, 144(14).

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
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)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

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