Fenfei Leng
Publications
selected publications
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Article
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2021A T5 Exonuclease-Based Assay for DNA Topoisomerases and DNA IntercalatorsFull Text via DOI: 10.1021/acsomega.1c00962 Web of Science: 000651520800042
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2021Trapped Ion Mobility Spectrometry of Native Macromolecular Assemblies. ANALYTICAL CHEMISTRY. 93:2933-2941.Full Text via DOI: 10.1021/acs.analchem.0c04556 Web of Science: 000618858500027
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2020Identification of HMGA2 inhibitors by AlphaScreen-based ultra-high-throughput screening assays. SCIENTIFIC REPORTS. 10.Full Text via DOI: 10.1038/s41598-020-75890-0 Web of Science: 000589618700022
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2020R-loops promote trinucleotide repeat deletion through DNA base excision repair enzymatic activities. JOURNAL OF BIOLOGICAL CHEMISTRY. 295:13902-13913.Full Text via DOI: 10.1074/jbc.RA120.014161 Web of Science: 000578444100016
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2019Fis protein forms DNA topological barriers to confine transcription-coupled DNA supercoiling in Escherichia coli. FEBS LETTERS. 594:791-798.Full Text via DOI: 10.1002/1873-3468.13643 Web of Science: 000496346800001
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2019Kinetic Study of DNA Topoisomerases by Supercoiling-Dependent Fluorescence Quenching. ACS OMEGA. 4:18413-18422.Full Text via DOI: 10.1021/acsomega.9b02676 Web of Science: 000495089100048
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2019Mechanism and resistance for antimycobacterial activity of a fluoroquinophenoxazine compound. PLOS ONE. 14.Full Text via DOI: 10.1371/journal.pone.0207733 Web of Science: 000459709100003
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2019Microheterogeneity of Topoisomerase IA/IB and Their DNA-Bound States. ACS OMEGA. 4:3619-3626.Full Text via DOI: 10.1021/acsomega.8b02887 Web of Science: 000460237300126
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2018Inhibition of the gyrA promoter by transcription-coupled DNA supercoiling in Escherichia coli. SCIENTIFIC REPORTS. 8.Full Text via DOI: 10.1038/s41598-018-33089-4 Web of Science: 000446339400043
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2018Differentiating Parallel and Antiparallel DNA Duplexes in the Gas Phase Using Trapped Ion Mobility Spectrometry. JOURNAL OF PHYSICAL CHEMISTRY B. 122.Full Text via DOI: 10.1021/acs.jpcb.7b12544 Web of Science: 000439002900001
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2018Peptide Sequence Influence on the Conformational Dynamics and DNA binding of the Intrinsically Disordered AT-Hook 3 Peptide. SCIENTIFIC REPORTS. 8.Full Text via DOI: 10.1038/s41598-018-28956-z Web of Science: 000438850200030
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2018Tailoring peptide conformational space with organic gas modifiers in TIMS-MS. INTERNATIONAL JOURNAL FOR ION MOBILITY SPECTROMETRY. 21.Full Text via DOI: 10.1007/s12127-018-0231-5 Web of Science: 000432547000005
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2018Protein-mediated loops in supercoiled DNA create large topological domains. NUCLEIC ACIDS RESEARCH. 46.Full Text via DOI: 10.1093/nar/gky153 Web of Science: 000433056900014
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2018Crystal structure and conformational analysis of doxorubicin nitrate. ACTA CRYSTALLOGRAPHICA SECTION E-CRYSTALLOGRAPHIC COMMUNICATIONS. 74.Full Text via DOI: 10.1107/S2056989018002955 Web of Science: 000426268200029
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2018Protein-mediated looping of DNA under tension requires supercoiling. NUCLEIC ACIDS RESEARCH. 46:2370-2379.
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2017Biochemical and biophysical properties of positively supercoiled DNA. BIOPHYSICAL CHEMISTRY. 230:68-73.
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2017Selective Inhibition of Escherichia coli RNA and DNA Topoisomerase I by Hoechst 33258 Derived Mono- and Bisbenzimidazoles. JOURNAL OF MEDICINAL CHEMISTRY. 60:4904-4922.
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2017Transient and dynamic DNA supercoiling potently stimulates the leu-500 promoter in Escherichia coli. JOURNAL OF BIOLOGICAL CHEMISTRY. 292:14566-14575.
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2016Characterization of an epoxide hydrolase from the Florida red tide dinoflagellate, Karenia brevis. PHYTOCHEMISTRY. 122:11-21.
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2016DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli. SCIENTIFIC REPORTS. 6.
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2016Direct observation of a 91 bp LacI-mediated, negatively supercoiled DNA loop by atomic force microscope. FEBS LETTERS. 590:613-618.
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2016Fluorescently labeled circular DNA molecules for DNA topology and topoisomerases. SCIENTIFIC REPORTS. 6.
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2016RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals. NUCLEIC ACIDS RESEARCH. 44:6335-6349.
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2015A rapid and sensitive high-throughput screening method to identify compounds targeting protein-nucleic acids interactions. NUCLEIC ACIDS RESEARCH. 43.
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2014Examination of bacterial inhibition using a catalytic DNAFull Text via DOI: 10.1371/journal.pone.0115640
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2014DNA supercoiling: A regulatory signal for the lambda repressor. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 111:15402-15407.
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2014Selective inhibition of bacterial topoisomerase I by alkynyl-bisbenzimidazoles. MEDCHEMCOMM. 5:816-825.
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2014lsomerization Kinetics of AT Hook Decapeptide Solution Structures. ANALYTICAL CHEMISTRY. 86:1210-1214.
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2013DNA Bending by Proteins: Utilizing Plasmid pBendAT as a Tool. DNA ELECTROPHORESIS: METHODS AND PROTOCOLS. 1054:267-282.
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2013HMGN1 Modulates Nucleosome Occupancy and DNase I Hypersensitivity at the CpG Island Promoters of Embryonic Stem Cells. MOLECULAR AND CELLULAR BIOLOGY. 33:3377-3389.
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2012Determining DNA supercoiling enthalpy by isothermal titration calorimetry. BIOCHIMIE. 94:2665-2672.
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2011A rapid procedure to purify Escherichia coli DNA topoisomerase I. PROTEIN EXPRESSION AND PURIFICATION. 77:214-219.
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2011Dividing a supercoiled DNA molecule into two independent topological domains. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 108:19973-19978.
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2010DNA Bending by the Mammalian High-Mobility Group Protein AT Hook 2. BIOCHEMISTRY. 49:1590-1595.
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2010DNA linking number change induced by sequence-specific DNA-binding proteins. NUCLEIC ACIDS RESEARCH. 38:3643-3654.
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2009Binding the Mammalian High Mobility Group Protein AT-hook 2 to AT-Rich Deoxyoligonucleotides: Enthalpy-Entropy Compensation. BIOPHYSICAL JOURNAL. 96:4144-4152.
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2008Inhibition of high-mobility-group A2 protein binding to DNA by netropsin: A biosensor-surface plasmon resonance assay. ANALYTICAL BIOCHEMISTRY. 374:7-15.
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2007Large scale preparation of the mammalian high mobility group protein A2 for biophysical studies. PROTEIN AND PEPTIDE LETTERS. 14:87-91.
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2007Specific recognition of AT-Rich DNA sequences by the mammalian high mobility group-protein AT-hook 2: A SELEX study. BIOCHEMISTRY. 46:13059-13066.
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2007Transcription-coupled hypernegative supercoiling of plasmid DNA by T7 RNA polymerase in Escherichia coli topoisomerase I-deficient strains. JOURNAL OF MOLECULAR BIOLOGY. 374:925-935.
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2005Energetics of binding the mammalian high mobility group protein HMGA2 to poly(dA-dT)(2) and poly(dA)-poly(dT). JOURNAL OF MOLECULAR BIOLOGY. 352:629-645.
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2004Coupling DNA supercoiling to transcription in defined protein systemsFull Text via DOI: 10.1074/jbc.M403798200
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2003Energetics of echinomycin binding to DNA. NUCLEIC ACIDS RESEARCH. 31.Full Text via DOI: 10.1093/nar/gkg826 Web of Science: 000186312300023
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1998Chemical cross-linking of ethidium to DNA by glyoxalFull Text via DOI: 10.1016/S0167-4781(98)00122-5
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1998Ultratight DNA binding of a new bisintercalating anthracycline antibioticFull Text via DOI: 10.1021/bi9720742
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1997Structure-based design of a new bisintercalating anthracycline antibioticFull Text via DOI: 10.1021/jm9607414
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1996Base specific and regioselective chemical cross-linking of daunorubicin to DNAFull Text via DOI: 10.1021/ja9542606
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Correction
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2018HMGN1 Modulates Nucleosome Occupancy and DNase I Hypersensitivity at the CpG Island Promoters of Embryonic Stem Cells (vol 33, pg 337, 2013). MOLECULAR AND CELLULAR BIOLOGY.Full Text via DOI: 10.1128/MCB.00185-18 Web of Science: 000433419600004
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Meeting Abstract
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2019Insights on the structural integrity of knot proteins using trapped ion mobility spectrometry - mass spectrometry. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY.Web of Science: 000478860500229
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2019Tight Binding of Natural Polyphenols to the Intrinsically Disordered Mammalian High Mobility Group Protein At-Hook 2. BIOPHYSICAL JOURNAL. 482A-482A.Web of Science: 000460779802421
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2018Identification of Suramin as a Potent and Specific Inhibitor of the Mammalian High Mobility Group Protein at-Hook 2 (HMGA2)-DNA Interactions. BIOPHYSICAL JOURNAL.Web of Science: 000430450000709
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2017Chemical cross-linking of doxorubicin to synthetic oligonucleotides by formaldehyde. FASEB JOURNAL.Web of Science: 000405461402327
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2017Protein-Mediated Loops in Supercoiled DNA Create Large Topological Domains. BIOPHYSICAL JOURNAL. 170A-170A.Full Text via DOI: 10.1016/j.bpj.2016.11.938 Web of Science: 000402328000837
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2016Design and Construct a Type of Fluorescently Labeled Circular DNA Molecules to Study DNA Topology and Topoisomerases by Fluorescence Resonance Energy Transfer (FRET). BIOPHYSICAL JOURNAL. 564A-564A.Full Text via DOI: 10.1016/j.bpj.2015.11.3019 Web of Science: 000375143000250
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2016Effect of FIS on Transcription-Coupled DNA Supercoiling in E. coli. BIOPHYSICAL JOURNAL. 233A-234A.Full Text via DOI: 10.1016/j.bpj.2015.11.1287 Web of Science: 000375141600138
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2016HU Protein and DNA Supercoiling Dramatically Enhance Lac-Repressor-Mediated DNA Looping. BIOPHYSICAL JOURNAL. 236A-236A.Full Text via DOI: 10.1016/j.bpj.2015.11.1302 Web of Science: 000375141600151
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2014Activating the Prokaryotic leu-500 Promoter by Transient, Dynamic DNA Supercoiling in Escherichia Coli. BIOPHYSICAL JOURNAL. 487A-488A.Full Text via DOI: 10.1016/j.bpj.2013.11.4476 Web of Science: 000337000402702
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2014Biochemical and Biophysical Properties of Positively Supercoiled DNA. BIOPHYSICAL JOURNAL. 66A-66A.Full Text via DOI: 10.1016/j.bpj.2013.11.444 Web of Science: 000337000400340
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2013Lactose Repressor Functions as a DNA Topological Barrier in Escherichia Coli Lactose Operon. BIOPHYSICAL JOURNAL. 417A-418A.Full Text via DOI: 10.1016/j.bpj.2012.11.2326 Web of Science: 000316074304126
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2009Protein-Induced DNA Unwinding is An Intrinsic Feature of Certain Sequence-Specific DNA-Binding Proteins. BIOPHYSICAL JOURNAL. 414A-414A.Web of Science: 000426354000211
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2007Binding the mammalian high mobility group protein AT-hook 2 to AT-rich deoxyoligonucleotides: enthalpy-entropy compensation. BIOPHYSICAL JOURNAL. 233A-233A.Web of Science: 000243972401296
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2007The Mammalian high mobility group protein AT-hook 2 (HMGA2) is a sequence-specific DNA-binding protein. BIOPHYSICAL JOURNAL. 55A-55A.Web of Science: 000243972400255
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2006A new method to purify the Mammalian High Mobility Group Protein HGMA2. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY.Web of Science: 000238125901627
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2005Energetics of mammalian high mobility group protein HMGA2 recognizing DNA minor groove. BIOPHYSICAL JOURNAL. 62A-62A.Web of Science: 000226378500306
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Review
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2020The Mammalian High Mobility Group Protein AT-Hook 2 (HMGA2): Biochemical and Biophysical Properties, and Its Association with Adipogenesis. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES.Full Text via DOI: 10.3390/ijms21103710 Web of Science: 000539312100306
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2016Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects. 123-133.Full Text via DOI: 10.1007/s12551-016-0239-1
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2016Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects. 197-207.Full Text via DOI: 10.1007/s12551-016-0204-z
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2013Transcription-coupled DNA supercoiling in defined protein systems and in E. coli topA mutant strains. IUBMB LIFE. 615-622.
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chaired theses and dissertations
- Zhi, Xiaoduo, Transcription-Coupled DNA Supercoiling in Escherichia Coli: Mechanisms and Biological Functions 2012
- Xu, Xiaozhou, Kinetics of E. coli Topoisomerase I and Energetic Studies of DNA Supercoiling by Isothermal Titration Calorimetry 2010
- Cui, Tengjiao, Specific binding of mammalian high mobility group protein at-hook 2 to the minor groove of at-rich DNAS : thermodynamic and specificity studies 2007
- Edwards, Lorraine Katy, Biochemical characterization of mammalian high mobility group protein A2 2006
Research
principal investigator on
- Targeting transcription-coupled DNA supercoiling for discovering antibiotics against bacterial DNA gyrase awarded by National Institutes of Health 2017 - 2019
- Transcription-coupled DNA Supercoiling awarded by National Institutes of Health 2014 - 2018
- DOR Bridge Funding awarded by FIU Division of Research 2013 - 2014
- Mechanisms of Transcription-Coupled DNA Supercoiling awarded by Eunice Kennedy Shriver National Institute of Child Health and Human Development 2009 - 2014
co-principal investigator on
investigator on
Teaching
teaching activities
- BCH7930-U01: Biochemistry Graduate Seminar Spring Term 2019
- CHM4304-U02: Biological Chemistry I Fall Term 2019
- CHM4910-U03: Undergraduate Research in Chemistry Spring Term 2019
- CHM4910-U14: Undergraduate Research in Chemistry Fall Term 2019
- CHM7910-U15: Dissertation Research Fall Term 2019
- CHM7980-U02: PH.D. Dissertation Fall Term 2019
- CHM7980-U13: PH.D. Dissertation Spring Term 2019
Contact
full name
- Fenfei Leng
visualizations
Recent publications and grants in Scholars@FIU
publication subject areas
- Biochemistry & Molecular Biology
- Biophysics
- Biotechnology & Applied Microbiology
- Cell Biology
- Chemistry
- Crystallography
- Genetics & Heredity
- Life Sciences & Biomedicine - Other Topics
- Pharmacology & Pharmacy
- Plant Sciences
- Science & Technology - Other Topics
- Spectroscopy