Yuan Zhang

Works (4)

Updated: July 14th, 2023 21:15

2017 journal article

E-motif formed by extrahelical cytosine bases in DNA homoduplexes of trinucleotide and hexanucleotide repeats

NUCLEIC ACIDS RESEARCH, 46(2), 942–955.

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

MeSH headings : Base Pairing; Base Sequence; Cytosine / chemistry; DNA / chemistry; DNA / genetics; Guanine / chemistry; Hydrogen Bonding; Microsatellite Repeats / genetics; Molecular Dynamics Simulation; Nucleic Acid Conformation; Nucleotide Motifs; Trinucleotide Repeats / genetics
TL;DR: Detailed molecular dynamics simulations of C-rich TR and HR DNA homoduplexes are performed in order to characterize the conformations, stability and dynamics of formation of the e-motif, where the mismatched cytosines symmetrically flip out in the minor groove, pointing their base moieties towards the 5′-direction in each strand. (via Semantic Scholar)
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Added: August 6, 2018

2017 journal article

Structural and Dynamical Characterization of DNA and RNA Quadruplexes Obtained from the GGGGCC and GGGCCT Hexanucleotide Repeats Associated with C9FTD/ALS and SCA36 Diseases

ACS CHEMICAL NEUROSCIENCE, 9(5), 1104–1117.

By: Y. Zhang n, C. Roland n & C. Sagui n

author keywords: Quadruplex; hexanucleotide repeats; DNA; RNA; G-quartets
MeSH headings : Amyotrophic Lateral Sclerosis / genetics; C9orf72 Protein / genetics; Circular Dichroism / methods; DNA / genetics; DNA Repeat Expansion / genetics; G-Quadruplexes / radiation effects; Humans; Models, Molecular; Nerve Tissue Proteins / genetics; Nuclear Proteins; Nucleic Acid Conformation / drug effects; RNA / genetics
TL;DR: A (GGGGCC) hexanucleotide repeat (HR) expansion in the C9ORF72 gene has been considered the major cause behind both frontotemporal dementia and amyotrophic lateral sclerosis, while a (GGGCCT) is associated with spinocerebellar ataxia 36. (via Semantic Scholar)
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2016 journal article

Structure and Dynamics of DNA and RNA Double Helices Obtained from the GGGGCC and CCCCGG Hexanucleotide Repeats That Are the Hallmark of C9FTD/ALS Diseases

ACS CHEMICAL NEUROSCIENCE, 8(3), 578–591.

By: Y. Zhang n, C. Roland n & C. Sagui n

author keywords: Nucleotide repeat disorder; hexanucleotide repeat; C-C and G-G mismatches; C9FTD; ALS; e-motif
MeSH headings : Amyotrophic Lateral Sclerosis / genetics; Base Pair Mismatch; C9orf72 Protein; Chromosomes, Human, Pair 9 / genetics; DNA / chemistry; DNA Repeat Expansion; Frontotemporal Dementia / genetics; Humans; Models, Molecular; Nucleic Acid Conformation; Principal Component Analysis; Proteins / genetics; RNA / chemistry; Repetitive Sequences, Nucleic Acid / genetics
TL;DR: Molecular dynamics simulations are performed to characterize the conformation and dynamics of the 12 duplexes that result from the three different reading frames in sense and antisense HRs for both DNA and RNA, showing atypical structures relevant for a molecular level understanding of these diseases. (via Semantic Scholar)
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2014 journal article

Secondary structure assignment for conformationally irregular peptides: Comparison between DSSP, STRIDE and KAKSI

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 55, 72–84.

By: Y. Zhang n & C. Sagui n

author keywords: Residual transient secondary structure; Intrinsically disordered proteins; gp41; Asparagine
MeSH headings : Amino Acid Sequence; Amino Acids / chemistry; Computer Simulation; Hydrogen Bonding; Peptides / chemistry; Protein Structure, Secondary; Software
TL;DR: Molecular Dynamics simulations of (relatively) disordered peptides, specifically gp41659-671 (ELLELDKWASLWN), the homopeptide polyasparagine (N18), and polyAsparagine dimers, are carried out and the resulting conformations with DSSP and STRIDE, based on hydrogen-bond patterns (and dihedral angles for STRIDE), and KAKSI, basedon α-Carbon distances are analyzed. (via Semantic Scholar)
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