Dynamic alternative DNA structures in biology and disease

Delineation of the DNA Structural Features of Eukaryotic Core Promoter Classes

(2022) Akkinepally Vanaja et al.   ACS Omega

A transposon‐introduced G‐quadruplex motif is selectively retained and constrained to downregulate CYP321A1

(2022) Zhongyuan Deng et al.   Insect Science

Stable G-quadruplex DNA structures promote replication-dependent genome instability

(2022) S. Dean Rider et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats

(2022) Ashkan Fakharzadeh et al.   NUCLEIC ACIDS RESEARCH

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

G4-quadruplex-binding proteins: review and insights into selectivity

(2022) Vanessa Meier-Stephenson   Biophysical Reviews

Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation

(2022) Guillaume Guilbaud et al.   NUCLEIC ACIDS RESEARCH

Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome

(2021) Wilfried M. Guiblet et al.   NUCLEIC ACIDS RESEARCH

Replication-independent instability of Friedreich’s ataxia GAA repeats during chronological aging

(2021) Alexander J. Neil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novel roles of an intragenic G-quadruplex in controlling microRNA expression and cardiac function

(2021) Min Zhu et al.   NUCLEIC ACIDS RESEARCH

Human Rev1 relies on insert-2 to promote selective binding and accurate replication of stabilized G-quadruplex motifs

(2021) Amit Ketkar et al.   NUCLEIC ACIDS RESEARCH

Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements

(2021) Kseniia Cheloshkina et al.   PLoS Computational Biology

Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp

(2021) Jianbo Yuan et al.   Communications Biology

Sequence, Chromatin and Evolution of Satellite DNA

(2021) Jitendra Thakur et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Sequence-dependent cost for Z-form shapes the torsion-driven B–Z transition via close interplay of Z-DNA and DNA bubble

(2021) Sook Ho Kim et al.   NUCLEIC ACIDS RESEARCH

Opposite roles of transcription elongation factors Spt4/5 and Elf1 in RNA polymerase II transcription through B-form versus non-B DNA structures

(2021) Jun Xu et al.   NUCLEIC ACIDS RESEARCH

Structural parameters of palindromic repeats determine the specificity of nuclease attack of secondary structures

(2021) Anissia Ait Saada et al.   NUCLEIC ACIDS RESEARCH

Position preference of essential genes in prokaryotic operons

(2021) Tao Liu et al.   PLoS One

Protection of the C. elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation

(2021) Bettina Meier et al.   PLoS One

ZBP1 not RIPK1 mediates tumor necroptosis in breast cancer

(2021) Jin Young Baik et al.   Nature Communications

Secondary structural choice of DNA and RNA associated with CGG/CCG trinucleotide repeat expansion rationalizes the RNA misprocessing in FXTAS

(2021) Yogeeshwar Ajjugal et al.   Scientific Reports

Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans

(2021) Kristina Krassovsky et al.   GENOME RESEARCH

Chemical profiling of DNA G-quadruplex-interacting proteins in live cells

(2021) Xiaoyun Zhang et al.   Nature Chemistry

Molecular mechanisms underlying nucleotide repeat expansion disorders

(2021) Indranil Malik et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structure specific DNA recognition by the SLX1–SLX4 endonuclease complex

(2021) Xiang Xu et al.   NUCLEIC ACIDS RESEARCH

Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome

(2021) Sara Lago et al.   Nature Communications

FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington’s disease

(2021) Robert Goold et al.   Cell Reports

DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regions

(2021) Vincent Rocher et al.   PLoS Computational Biology

Multiple G-quadruplex binding ligand induced transcriptomic map of cancer cell lines

(2021) Amjesh Revikumar et al.   Journal of Cell Communication and Signaling

pH-Responsive DNA Motif: From Rational Design to Analytical Applications

(2021) Lin Lin Zheng et al.   Frontiers in Chemistry

Transcription-Replication Collisions—A Series of Unfortunate Events

(2021) Commodore St Germain et al.   Biomolecules

A thermodynamic understanding of the salt-induced B-to-Z transition of DNA containing BZ junctions

(2021) Heyjin Son et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Defining R-loop classes and their contributions to genome instability

(2021) Daisy Castillo-Guzman et al.   DNA REPAIR

DNA polymerase θ promotes CAG•CTG repeat expansions in Huntington’s disease via insertion sequences of its catalytic domain

(2021) Kara Y. Chan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Translesion polymerase eta both facilitates DNA replication and promotes increased human genetic variation at common fragile sites

(2021) Shyam Twayana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer

(2021) Yuan Yin et al.   Nature Communications

FAN1 exo- not endo-nuclease pausing on disease-associated slipped-DNA repeats: A mechanism of repeat instability

(2021) Amit Laxmikant Deshmukh et al.   Cell Reports

Mechanisms of Genome Instability in the Fragile X-Related Disorders

(2021) Bruce E. Hayward et al.   Genes

G4detector: Convolutional Neural Network to Predict DNA G-Quadruplexes

(2021) Mira Barshai et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A slipped-CAG DNA-binding small molecule induces trinucleotide-repeat contractions in vivo

(2020) Masayuki Nakamori et al.   NATURE GENETICS

DNA unwinding mechanism of a eukaryotic replicative CMG helicase

(2020) Zuanning Yuan et al.   Nature Communications

Distinct DNA repair pathways cause genomic instability at alternative DNA structures

(2020) Jennifer A. McKinney et al.   Nature Communications

Yeast Genome Maintenance by the Multifunctional PIF1 DNA Helicase Family

(2020) Julius Muellner et al.   Genes

Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction

(2020) Paul R. Marshall et al.   NATURE NEUROSCIENCE

The regulation and functions of DNA and RNA G-quadruplexes

(2020) Dhaval Varshney et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop ‘G4 Kissing’ interaction

(2020) Jonathan D Williams et al.   NUCLEIC ACIDS RESEARCH

E. coli Rep helicase and RecA recombinase unwind G4 DNA and are important for resistance to G4-stabilizing ligands

(2020) Tapas Paul et al.   NUCLEIC ACIDS RESEARCH

Endogenous oxidized DNA bases and APE1 regulate the formation of G-quadruplex structures in the genome

(2020) Shrabasti Roychoudhury et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts

(2020) Ilias Georgakopoulos-Soares et al.   Nature Communications

Cruciform DNA Sequences in Gene Promoters Can Impact Transcription upon Oxidative Modification of 2′-Deoxyguanosine

(2020) Aaron M. Fleming et al.   BIOCHEMISTRY

Single-molecule visualization of DNA G-quadruplex formation in live cells

(2020) Marco Di Antonio et al.   Nature Chemistry

Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction

(2020) Xiaojun Xu et al.   NUCLEIC ACIDS RESEARCH

ALU non-B-DNA conformations, flipons, binary codes and evolution

(2020) Alan Herbert   Royal Society Open Science

Remodeling Chromatin Induces Z-DNA Conformation Detected through Fourier Transform Infrared Spectroscopy

(2020) Yalin Li et al.   ANALYTICAL CHEMISTRY

The DEAH helicase DHX36 and its role in G-quadruplex-dependent processes

(2020) Philipp Schult et al.   BIOLOGICAL CHEMISTRY

Replication stress at microsatellites causes DNA double strand breaks and break induced replication

(2020) Rujuta Yashodhan Gadgil et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Insights into the Kinetic Partitioning Folding Dynamics of the Human Telomeric G-Quadruplex from Molecular Simulations and Machine Learning

(2020) Yunqiang Bian et al.   Journal of Chemical Theory and Computation

Repeat expansions confer WRN dependence in microsatellite-unstable cancers

(2020) Niek van Wietmarschen et al.   NATURE

Demystifying the D-loop during DNA recombination

(2020) Upasana Roy et al.   NATURE

Cruciform DNA in mouse growing oocytes: Its dynamics and its relationship with DNA transcription

(2020) Xie Feng et al.   PLoS One

Warsaw Breakage Syndrome associated DDX11 helicase resolves G-quadruplex structures to support sister chromatid cohesion

(2020) Janne J. M. van Schie et al.   Nature Communications

Responses of DNA Mismatch Repair Proteins to a Stable G-Quadruplex Embedded into a DNA Duplex Structure

(2020) Anzhela V. Pavlova et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

DNA fragility in the parallel evolution of pelvic reduction in stickleback fish

(2019) Kathleen T. Xie et al.   SCIENCE

Replication of G Quadruplex DNA

(2019) Leticia Koch Lerner et al.   Genes

G-quadruplex DNA drives genomic instability and represents a targetable molecular abnormality in ATRX-deficient malignant glioma

(2019) Yuxiang Wang et al.   Nature Communications

Whole genome experimental maps of DNA G-quadruplexes in multiple species

(2019) Giovanni Marsico et al.   NUCLEIC ACIDS RESEARCH

Mycobacterium tuberculosis UvrD1 and UvrD2 helicases unwind G‐quadruplex DNA

(2019) Tias Saha et al.   FEBS Journal

G4Hunter web application: a web server for G-quadruplex prediction

(2019) Václav Brázda et al.   BIOINFORMATICS

Tissue-specific impact of stem-loops and quadruplexes on cancer breakpoints formation

(2019) Kseniia Cheloshkina et al.   BMC CANCER

Cooperation between non-essential DNA polymerases contributes to genome stability in Saccharomyces cerevisiae

(2019) Damon Meyer et al.   DNA REPAIR

Integrative characterization of G-Quadruplexes in the three-dimensional chromatin structure

(2019) Yue Hou et al.   Epigenetics

Mammalian DNA Polymerase Kappa Activity and Specificity

(2019) Hannah R. Stern et al.   MOLECULES

Involvement of G-quadruplex regions in mammalian replication origin activity

(2019) Paulina Prorok et al.   Nature Communications

Modulation of DNA structure formation using small molecules

(2019) Imee M.A. del Mundo et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

DDX5 helicase resolves G-quadruplex and is involved in MYC gene transcriptional activation

(2019) Guanhui Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synergistic Coordination of Chromatin Torsional Mechanics and Topoisomerase Activity

(2019) Tung T. Le et al.   CELL

Transcription-mediated organization of the replication initiation program across large genes sets common fragile sites genome-wide

(2019) Olivier Brison et al.   Nature Communications

Requirement or exclusion of inverted repeat sequences with cruciform-forming potential in Escherichia coli revealed by genome-wide analyses

(2018) Osamu Miura et al.   CURRENT GENETICS

Non-B-Form DNA Is Enriched at Centromeres

(2018) Sivakanthan Kasinathan et al.   MOLECULAR BIOLOGY AND EVOLUTION

BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes

(2018) Niek van Wietmarschen et al.   Nature Communications

Distinct Mechanisms of Nuclease-Directed DNA-Structure-Induced Genetic Instability in Cancer Genomes

(2018) Junhua Zhao et al.   Cell Reports

A Live-Cell Imaging Approach for Measuring DNA Replication Rates

(2018) Daniel Dovrat et al.   Cell Reports

Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis

(2018) Ilias Georgakopoulos-Soares et al.   GENOME RESEARCH

A strong structural correlation between short inverted repeat sequences and the polyadenylation signal in yeast and nucleosome exclusion by these inverted repeats

(2018) Osamu Miura et al.   CURRENT GENETICS

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate

(2018) Wilfried M. Guiblet et al.   GENOME RESEARCH

Escherichia coli DNA polymerase I can disrupt G-quadruplex structures during DNA replication

(2017) Fang-Yuan Teng et al.   FEBS Journal

The G-quadruplex (G4) resolvase DHX36 efficiently and specifically disrupts DNA G4s via a translocation-based helicase mechanism

(2017) Philip M. Yangyuoru et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DNA repair in the trinucleotide repeat disorders

(2017) Lesley Jones et al.   LANCET NEUROLOGY

Topological impact of noncanonical DNA structures on Klenow fragment of DNA polymerase

(2017) Shuntaro Takahashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oxidative DNA damage is epigenetic by regulating gene transcription via base excision repair

(2017) Aaron M. Fleming et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours

(2017) Hong Xu et al.   Nature Communications

Effects of Replication and Transcription on DNA Structure-Related Genetic Instability

(2017) Guliang Wang et al.   Genes

Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome

(2017) Fedor Kouzine et al.   Cell Systems

CGG Repeats in the 5’UTR of FMR1 RNA Regulate Translation of Other RNAs Localized in the Same RNA Granules

(2017) René Rovozzo et al.   PLoS One

The Interplay between G-quadruplex and Transcription

(2017) Nayun Kim   CURRENT MEDICINAL CHEMISTRY

Histone Acetylation Induced Transformation of B-DNA to Z-DNA in Cells Probed through FT-IR Spectroscopy

(2016) Fengqiu Zhang et al.   ANALYTICAL CHEMISTRY

Human Translesion Polymerase κ Exhibits Enhanced Activity and Reduced Fidelity Two Nucleotides from G-Quadruplex DNA

(2016) Sarah Eddy et al.   BIOCHEMISTRY

A Comparative Study of G-Quadruplex Unfolding and DNA Reeling Activities of Human RECQ5 Helicase

(2016) Jagat B. Budhathoki et al.   BIOPHYSICAL JOURNAL

MutSβ promotes trinucleotide repeat expansion by recruiting DNA polymerase β to nascent (CAG)n or (CTG)n hairpins for error-prone DNA synthesis

(2016) Jinzhen Guo et al.   CELL RESEARCH

DNA replication origins—where do we begin?

(2016) Marie-Noëlle Prioleau et al.   GENES & DEVELOPMENT

The nature of mutations induced by replication–transcription collisions

(2016) T. Sabari Sankar et al.   NATURE

Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences

(2016) Albino Bacolla et al.   NUCLEIC ACIDS RESEARCH

G-Quadruplexes in DNA Replication: A Problem or a Necessity?

(2016) Anne-Laure Valton et al.   TRENDS IN GENETICS

Replication intermediates that escape Dna2 activity are processed by Holliday junction resolvase Yen1

(2016) Gizem Ölmezer et al.   Nature Communications

Crosstalk between MSH2–MSH3 and polβ promotes trinucleotide repeat expansion during base excision repair

(2016) Yanhao Lai et al.   Nature Communications

Detection of cis- and trans-acting Factors in DNA Structure-Induced Genetic Instability Using In silico and Cellular Approaches

(2016) Guliang Wang et al.   Frontiers in Genetics

DNA Triplet Repeat Expansion and Mismatch Repair

(2015) Ravi R. Iyer et al.   Annual Review of Biochemistry

DNA Replication Stress as a Hallmark of Cancer

(2015) Morgane Macheret et al.   Annual Review of Pathology-Mechanisms of Disease

Evidence for the Kinetic Partitioning of Polymerase Activity on G-Quadruplex DNA

(2015) Sarah Eddy et al.   BIOCHEMISTRY

Spectrum of variations in dog-1/FANCJ and mdf-1/MAD1 defective Caenorhabditis elegans strains after long-term propagation

(2015) Maja Tarailo-Graovac et al.   BMC GENOMICS

DNA Secondary Structure at Chromosomal Fragile Sites in Human Disease

(2015) Ryan G. Thys et al.   CURRENT GENOMICS

Chromatin, DNA structure and alternative splicing

(2015) Nicolás Nieto Moreno et al.   FEBS LETTERS

A Role for Non-B DNA Forming Sequences in Mediating Microlesions Causing Human Inherited Disease

(2015) Mihir Anant Kamat et al.   HUMAN MUTATION

The Structure of theCyprinid herpesvirus 3ORF112-Zα·Z-DNA Complex Reveals a Mechanism of Nucleic Acids Recognition Conserved with E3L, a Poxvirus Inhibitor of Interferon Response

(2015) Krzysztof Kuś et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Rif1 binds to G quadruplexes and suppresses replication over long distances

(2015) Yutaka Kanoh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription blockage by stable H-DNA analogs in vitro

(2015) Shristi Pandey et al.   NUCLEIC ACIDS RESEARCH

The NEIL glycosylases remove oxidized guanine lesions from telomeric and promoter quadruplex DNA structures

(2015) Jia Zhou et al.   NUCLEIC ACIDS RESEARCH

Human RECQ1 helicase-driven DNA unwinding, annealing, and branch migration: Insights from DNA complex structures

(2015) Ashley C. W. Pike et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contribution of a mutational hot spot to hemoglobin adaptation in high-altitude Andean house wrens

(2015) Spencer C. Galen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Structural Variation: Mechanisms of Chromosome Rearrangements

(2015) Brooke Weckselblatt et al.   TRENDS IN GENETICS

Allele-specific analysis of DNA replication origins in mammalian cells

(2015) Boris Bartholdy et al.   Nature Communications

Mutagenic consequences of a single G-quadruplex demonstrate mitotic inheritance of DNA replication fork barriers

(2015) Bennie Lemmens et al.   Nature Communications

Rif1 binds to G quadruplexes and suppresses replication over long distances

(2015) Yutaka Kanoh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Short Inverted Repeats Are Hotspots for Genetic Instability: Relevance to Cancer Genomes

(2015) Steve Lu et al.   Cell Reports

In the Sense of Transcription Regulation by G-Quadruplexes: Asymmetric Effects in Sense and Antisense Strands

(2014) Tani Agarwal et al.   BIOCHEMISTRY

Impact of alternative DNA structures on DNA damage, DNA repair, and genetic instability

(2014) Guliang Wang et al.   DNA REPAIR

G4 motifs affect origin positioning and efficiency in two vertebrate replicators

(2014) A.-L. Valton et al.   EMBO JOURNAL

The intrinsically disordered amino-terminal region of human RecQL4: multiple DNA-binding domains confer annealing, strand exchange and G4 DNA binding

(2014) Heidi Keller et al.   NUCLEIC ACIDS RESEARCH

Base Excision Repair of Chemotherapeutically-Induced Alkylated DNA Damage Predominantly Causes Contractions of Expanded GAA Repeats Associated with Friedreich's Ataxia

(2014) Yanhao Lai et al.   PLoS One

detectIR: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation

(2014) Congting Ye et al.   PLoS One

A Polymerase Theta-dependent repair pathway suppresses extensive genomic instability at endogenous G4 DNA sites

(2014) Wouter Koole et al.   Nature Communications

Transcription-Associated R-Loop Formation across the Human FMR1 CGG-Repeat Region

(2014) Erick W. Loomis et al.   PLoS Genetics

Targeting Non-B-Form DNA in Living Cells

(2013) Yuhao Du et al.   CHEMICAL RECORD

Human Origin Recognition Complex Binds Preferentially to G-quadruplex-preferable RNA and Single-stranded DNA

(2013) Shoko Hoshina et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Human Specialized DNA Polymerases and Non-B DNA: Vital Relationships to Preserve Genome Integrity

(2013) Anne-Sophie Boyer et al.   JOURNAL OF MOLECULAR BIOLOGY

Methods to detect replication-dependent and replication-independent DNA structure-induced genetic instability

(2013) Guliang Wang et al.   METHODS

Triplex-forming oligonucleotides targeting c-MYCpotentiate the anti-tumor activity of gemcitabine in a mouse model of human cancer

(2013) Stephen B. Boulware et al.   MOLECULAR CARCINOGENESIS

Coordinated Actions of SLX1-SLX4 and MUS81-EME1 for Holliday Junction Resolution in Human Cells

(2013) Haley D.M. Wyatt et al.   MOLECULAR CELL

XPD-dependent activation of apoptosis in response to triplex-induced DNA damage

(2013) Meetu Kaushik Tiwari et al.   NUCLEIC ACIDS RESEARCH

DNA polymerase δ stalls on telomeric lagging strand templates independently from G-quadruplex formation

(2013) Justin D. Lormand et al.   NUCLEIC ACIDS RESEARCH

Associations between intronic non-B DNA structures and exon skipping

(2013) Z. T.-Y. Tsai et al.   NUCLEIC ACIDS RESEARCH

DHX9 helicase is involved in preventing genomic instability induced by alternatively structured DNA in human cells

(2013) A. Jain et al.   NUCLEIC ACIDS RESEARCH

The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli

(2013) Xiangjun Du et al.   NUCLEIC ACIDS RESEARCH

DNA polymerases ζ and Rev1 mediate error-prone bypass of non-B DNA structures

(2013) Matthew R. Northam et al.   NUCLEIC ACIDS RESEARCH

Structure-specific endonucleases: guardians of fragile site stability

(2013) Sheroy Minocherhomji et al.   TRENDS IN CELL BIOLOGY

Combinatorial Regulation of Meiotic Holliday Junction Resolution in C. elegans by HIM-6 (BLM) Helicase, SLX-4, and the SLX-1, MUS-81 and XPF-1 Nucleases

(2013) Ana Agostinho et al.   PLoS Genetics

G-quadruplex recognition activities of E. Coli MutS

(2012) Edward A Ehrat et al.   BMC MOLECULAR BIOLOGY

Inhibition of RNA Polymerase I as a Therapeutic Strategy to Promote Cancer-Specific Activation of p53

(2012) Megan J. Bywater et al.   CANCER CELL

RTEL1 Dismantles T Loops and Counteracts Telomeric G4-DNA to Maintain Telomere Integrity

(2012) Jean-Baptiste Vannier et al.   CELL

Small inverted repeats drive mitochondrial genome evolution in Lake Baikal sponges

(2012) Dennis V. Lavrov et al.   GENE

Mechanism of Replicative DNA Polymerase Delta Pausing and a Potential Role for DNA Polymerase Kappa in Common Fragile Site Replication

(2012) Erin Walsh et al.   JOURNAL OF MOLECULAR BIOLOGY

Altered Replication in Human Cells Promotes DMPK (CTG)n {middle dot} (CAG)n Repeat Instability

(2012) G. Liu et al.   MOLECULAR AND CELLULAR BIOLOGY

DNA secondary structures: stability and function of G-quadruplex structures

(2012) Matthew L. Bochman et al.   NATURE REVIEWS GENETICS

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools

(2012) Regina Z. Cer et al.   NUCLEIC ACIDS RESEARCH

Role of DNA Polymerases in Repeat-Mediated Genome Instability

(2012) Kartik A. Shah et al.   Cell Reports

Cruciform structures are a common DNA feature important for regulating biological processes

(2011) Václav Brázda et al.   BMC MOLECULAR BIOLOGY

DNA Replication through G-Quadruplex Motifs Is Promoted by the Saccharomyces cerevisiae Pif1 DNA Helicase

(2011) Katrin Paeschke et al.   CELL

Conformational changes of non-B DNA

(2011) Jungkweon Choi et al.   CHEMICAL SOCIETY REVIEWS

The in vitro fidelity of yeast DNA polymerase δ and polymerase ɛ holoenzymes during dinucleotide microsatellite DNA synthesis

(2011) Amy L. Abdulovic et al.   DNA REPAIR

G-quadruplex-induced instability during leading-strand replication

(2011) Judith Lopes et al.   EMBO JOURNAL

Pathways for Holliday Junction Processing during Homologous Recombination in Saccharomyces cerevisiae

(2011) T. M. Ashton et al.   MOLECULAR AND CELLULAR BIOLOGY

Collisions between Replication and Transcription Complexes Cause Common Fragile Site Instability at the Longest Human Genes

(2011) Anne Helmrich et al.   MOLECULAR CELL

Pif1 overcomes a quadruplex hurdle

(2011) Alison Schuldt   NATURE REVIEWS MOLECULAR CELL BIOLOGY

G-quadruplex formation at the 3' end of telomere DNA inhibits its extension by telomerase, polymerase and unwinding by helicase

(2011) Q. Wang et al.   NUCLEIC ACIDS RESEARCH

Overcoming natural replication barriers: differential helicase requirements

(2011) Ranjith P. Anand et al.   NUCLEIC ACIDS RESEARCH

Holliday junction-containing DNA structures persist in cells lacking Sgs1 or Top3 following exposure to DNA damage

(2011) H. W. Mankouri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expanded CAG/CTG Repeat DNA Induces a Checkpoint Response That Impacts Cell Proliferation in Saccharomyces cerevisiae

(2011) Rangapriya Sundararajan et al.   PLoS Genetics

G-quadruplex nucleic acids and human disease

(2010) Yuliang Wu et al.   FEBS Journal

Epigenetic Instability due to Defective Replication of Structured DNA

(2010) Peter Sarkies et al.   MOLECULAR CELL

Replication-dependent instability at (CTG)•(CAG) repeat hairpins in human cells

(2010) Guoqi Liu et al.   Nature Chemical Biology

Mechanisms of trinucleotide repeat instability during human development

(2010) Cynthia T. McMurray   NATURE REVIEWS GENETICS

Secondary structure formation and DNA instability at fragile site FRA16B

(2010) Allison A. Burrow et al.   NUCLEIC ACIDS RESEARCH

Mechanisms and implications of transcription blockage by guanine-rich DNA sequences

(2010) B. P. Belotserkovskii et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TTS Mapping: integrative WEB tool for analysis of triplex formation target DNA Sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome

(2009) Piroon Jenjaroenpun et al.   BMC GENOMICS

DNA Repair and DNA Triplet Repeat Expansion: The Impact of Abasic Lesions on Triplet Repeat DNA Energetics

(2009) Jens Völker et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Stable G-quadruplexes are found outside nucleosome-bound regions

(2009) Han Min Wong et al.   Molecular BioSystems

Role of TLS DNA polymerases eta and kappa in processing naturally occurring structured DNA in human cells

(2009) Rémy Bétous et al.   MOLECULAR CARCINOGENESIS

Large-Scale Expansions of Friedreich's Ataxia GAA Repeats in Yeast

(2009) Alexander A. Shishkin et al.   MOLECULAR CELL

dUTP incorporation into genomic DNA is linked to transcription in yeast

(2009) Nayun Kim et al.   NATURE

SRS2 and SGS1 prevent chromosomal breaks and stabilize triplet repeats by restraining recombination

(2009) Alix Kerrest et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Replisome stalling and stabilization at CGG repeats, which are responsible for chromosomal fragility

(2009) Irina Voineagu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DNA structure and the Werner protein modulate human DNA polymerase delta-dependent replication dynamics within the common fragile site FRA16D

(2009) Sandeep N. Shah et al.   NUCLEIC ACIDS RESEARCH

Mismatch repair and nucleotide excision repair proteins cooperate in the recognition of DNA interstrand crosslinks

(2009) Junhua Zhao et al.   NUCLEIC ACIDS RESEARCH

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Chromosome fragility at GAA tracts in yeast depends on repeat orientation and requires mismatch repair

(2008) Hyun-Min Kim et al.   EMBO JOURNAL

Processing of G4 DNA by Dna2 Helicase/Nuclease and Replication Protein A (RPA) Provides Insights into the Mechanism of Dna2/RPA Substrate Recognition

(2008) Taro Masuda-Sasa et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Friedreich's Ataxia GAA·TTC Duplex and GAA·GAA·TTC Triplex Structures Exclude Nucleosome Assembly

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(2008) Y. Wu et al.   MOLECULAR AND CELLULAR BIOLOGY

Mus81-Dependent Double-Strand DNA Breaks at In Vivo-Generated Cruciform Structures in S. cerevisiae

(2008) Atina G. Coté et al.   MOLECULAR CELL

SbcCD Causes a Double-Strand Break at a DNA Palindrome in the Escherichia coli Chromosome

(2008) John K. Eykelenboom et al.   MOLECULAR CELL

Inhibitory effect of a short Z-DNA forming sequence on transcription elongation by T7 RNA polymerase

(2008) J. V. Ditlevson et al.   NUCLEIC ACIDS RESEARCH

Stability and kinetics of G-quadruplex structures

(2008) A. N. Lane et al.   NUCLEIC ACIDS RESEARCH

Activities of human exonuclease 1 that promote cleavage of transcribed immunoglobulin switch regions

(2008) A. C. Vallur et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Replication stalling at unstable inverted repeats: Interplay between DNA hairpins and fork stabilizing proteins

(2008) I. Voineagu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA reveals an unusual binding mode to Z-DNA

(2008) S. C. Ha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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