Differential repair enzyme-substrate selection within dynamic DNA energy landscapes

Conformational and migrational dynamics of slipped-strand DNA three-way junctions containing trinucleotide repeats

(2021) Tianyu Hu et al.   Nature Communications

Coping with RNA damage with a focus on APE1, a BER enzyme at the crossroad between DNA damage repair and RNA processing/decay

(2021) Matilde Clarissa Malfatti et al.   DNA REPAIR

Molecular Mechanisms Regulating the DNA Repair Protein APE1: A Focus on Its Flexible N-Terminal Tail Domain

(2021) David J. López et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Submillisecond Conformational Transitions of Short Single-Stranded DNA Lattices by Photon Correlation Single-Molecule Förster Resonance Energy Transfer

(2021) Brett Israels et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamics of strand slippage in DNA hairpins formed by CAG repeats: roles of sequence parity and trinucleotide interrupts

(2020) Pengning Xu et al.   NUCLEIC ACIDS RESEARCH

Eukaryotic Base Excision Repair: New Approaches Shine Light on Mechanism

(2019) William A. Beard et al.   Annual Review of Biochemistry

Dynamic DNA Energy Landscapes and Substrate Complexity in Triplet Repeat Expansion and DNA Repair

(2019) Völker et al.   Biomolecules

DNA scanning by base excision repair enzymes and implications for pathway coordination

(2018) Michael J. Howard et al.   DNA REPAIR

Parity-dependent hairpin configurations of repetitive DNA sequence promote slippage associated with DNA expansion

(2017) Tze-Yun Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Capturing snapshots of APE1 processing DNA damage

(2015) Bret D Freudenthal et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface

(2015) Anita C. Jones et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Capturing snapshots of APE1 processing DNA damage

(2015) Bret D Freudenthal et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

APE1 Incision Activity at Abasic Sites in Tandem Repeat Sequences

(2014) Mengxia Li et al.   JOURNAL OF MOLECULAR BIOLOGY

Human Apurinic/Apyrimidinic Endonuclease 1

(2013) Mengxia Li et al.   ANTIOXIDANTS & REDOX SIGNALING

Impact of bulge loop size on DNA triplet repeat domains: Implications for DNA repair and expansion

(2013) Jens Völker et al.   BIOPOLYMERS

Bidirectional transcription of trinucleotide repeats: Roles for excision repair

(2013) Helen Budworth et al.   DNA REPAIR

Energy Landscapes of Dynamic Ensembles of Rolling Triplet Repeat Bulge Loops: Implications for DNA Expansion Associated with Disease States

(2012) Jens Völker et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Decoding the energy landscape: extracting structure, dynamics and thermodynamics

(2012) D. J. Wales   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Trinucleotide Repeat DNA Alters Structure To Minimize the Thermodynamic Impact of 8-Oxo-7,8-dihydroguanine

(2011) Catherine B. Volle et al.   BIOCHEMISTRY

Structure of Even/Odd Trinucleotide Repeat Sequences Modulates Persistence of Non-B Conformations and Conversion to Duplex

(2011) Amalia Ávila Figueroa et al.   BIOCHEMISTRY

Characterization of the Endoribonuclease Active Site of Human Apurinic/Apyrimidinic Endonuclease 1

(2011) Wan-Cheol Kim et al.   JOURNAL OF MOLECULAR BIOLOGY

Mechanisms of trinucleotide repeat instability during human development

(2010) Cynthia T. McMurray   NATURE REVIEWS GENETICS

DNA conformational changes at the primer-template junction regulate the fidelity of replication by DNA polymerase

(2010) K. Datta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure-Dependent DNA Damage and Repair in a Trinucleotide Repeat Sequence

(2009) Daniel A. Jarem et al.   BIOCHEMISTRY

DNA Hairpins Containing the Cytidine Analog Pyrrolo-dC: Structural, Thermodynamic, and Spectroscopic Studies

(2009) Xu Zhang et al.   BIOPHYSICAL JOURNAL

Energetic coupling between clustered lesions modulated by intervening triplet repeat bulge loops: Allosteric implications for DNA repair and triplet repeat expansion

(2009) Jens Völker et al.   BIOPOLYMERS

Local Conformations and Competitive Binding Affinities of Single- and Double-stranded Primer-Template DNA at the Polymerization and Editing Active Sites of DNA Polymerases

(2009) Kausiki Datta et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Spectroscopic studies of position-specific DNA "breathing" fluctuations at replication forks and primer-template junctions

(2009) D. Jose et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hijacking of the mismatch repair system to cause CAG expansion and cell death in neurodegenerative disease

(2008) Cynthia T. McMurray   DNA REPAIR

Characterization of Abasic Endonuclease Activity of Human Ape1 on Alternative Substrates, as Well as Effects of ATP and Sequence Context on AP Site Incision

(2008) Brian R. Berquist et al.   JOURNAL OF MOLECULAR BIOLOGY

Human abasic endonuclease action on multilesion abasic clusters: implications for radiation-induced biological damage

(2008) B. Paap et al.   NUCLEIC ACIDS RESEARCH

DNA energy landscapes via calorimetric detection of microstate ensembles of metastable macrostates and triplet repeat diseases

(2008) J. Volker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA