Elio A. Abbondanzieri, Ph.D. - Related publications

Stanford University, Palo Alto, CA 
biophysics, single molecules, motor proteins, transcription
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Wang H, Elber R. Catalytic Magnesium as a Door Stop for DNA Sliding. The Journal of Physical Chemistry. B. PMID 33819040 DOI: 10.1021/acs.jpcb.1c00122   
2021 Pauszek RF, Lamichhane R, Rajkarnikar Singh A, Millar DP. Single-molecule view of coordination in a multi-functional DNA polymerase. Elife. 10. PMID 33704066 DOI: 10.7554/eLife.62046   
2021 Loveless TB, Grotts JH, Schechter MW, Forouzmand E, Carlson CK, Agahi BS, Liang G, Ficht M, Liu B, Xie X, Liu CC. Lineage tracing and analog recording in mammalian cells by single-site DNA writing. Nature Chemical Biology. PMID 33753928 DOI: 10.1038/s41589-021-00769-8   
2021 Cohan B, Frappier L. Herpesvirus DNA Polymerase Processivity Factors: Not just for DNA Synthesis. Virus Research. 198394. PMID 33775751 DOI: 10.1016/j.virusres.2021.198394   
2021 Shen BW, Quispe JD, Luyten Y, McGough BE, Morgan RD, Stoddard BL. Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM. Structure (London, England : 1993). PMID 33826880 DOI: 10.1016/j.str.2021.03.012   
2021 Kapp JD, Green RE, Shapiro B. A fast and efficient single-stranded genomic library preparation method optimized for ancient DNA. The Journal of Heredity. PMID 33768239 DOI: 10.1093/jhered/esab012   
2021 Li D, Zhang Q, Liu G, Zhang L, Gu Z, Pan Y, Cui X, He P, Li X, Liu J, Liu G, Yang M, Tian X. Detection of residual E. coli host cell DNA by 23S ribosomal RNA gene-targeted quantitative polymerase chain reactions. Journal of Pharmaceutical and Biomedical Analysis. 198: 114000. PMID 33706144 DOI: 10.1016/j.jpba.2021.114000   
2021 Lu CH, Lan WH, Li HW. Single-Molecule Tethered Particle Motion Studies on the DNA Recombinase Filament Assembly and Disassembly. Methods in Molecular Biology (Clifton, N.J.). 2281: 135-149. PMID 33847956 DOI: 10.1007/978-1-0716-1290-3_8   
2021 Mo Y, Fizari M, Koharchik K, Smith DE. Determining Trap Compliances, Microsphere Size Variations, and Response Linearities in Single DNA Molecule Elasticity Measurements with Optical Tweezers. Frontiers in Molecular Biosciences. 8: 605102. PMID 33829038 DOI: 10.3389/fmolb.2021.605102   
2021 Mustafa M, Ali A, Siddiqui SA, Mir AR, Kausar T, Nayeem SM, Abidi M, Habib S. Biophysical characterization of structural and conformational changes in methylmethane sulfonate modified DNA leading to the frizzled backbone structure and strand breaks in DNA. Journal of Biomolecular Structure & Dynamics. 1-14. PMID 33719845 DOI: 10.1080/07391102.2021.1899051   
2021 Sui J, Gandotra N, Xie P, Lin Z, Scharfe C, Javanmard M. Multi-frequency impedance sensing for detection and sizing of DNA fragments. Scientific Reports. 11: 6490. PMID 33753781 DOI: 10.1038/s41598-021-85755-9   
2021 Dilley K, Pagan F, Chapman B. Methods for ensuring the highest DNA concentration and yield in future and retrospective trace DNA extracts. Science & Justice : Journal of the Forensic Science Society. 61: 193-197. PMID 33736853 DOI: 10.1016/j.scijus.2020.11.005   
2021 Jhan CR, Satange R, Wang SC, Zeng JY, Horng YC, Jin P, Neidle S, Hou MH. Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction. Nucleic Acids Research. PMID 33836081 DOI: 10.1093/nar/gkab227   
2021 Maity A, Winnerdy FR, Chen G, Phan AT. Duplexes Formed by GC Repeats Contain Alternate Slow- and Fast-Flipping G·G Base Pairs. Biochemistry. PMID 33750098 DOI: 10.1021/acs.biochem.0c00916   
2021 Gu C, Ming L, Tao S, Luo M, Guo H, Xie Y, Liu J, Shen Z. Transfected DNA is targeted by STING-mediated restriction. Biochemical and Biophysical Research Communications. 549: 207-213. PMID 33684697 DOI: 10.1016/j.bbrc.2021.02.109   
2021 Cheng M, Shu X, Cao J, Gao M, Xiang S, Wang F, Wang Y, Liu J. A Mutation-based Method for Pinpointing a DNA N6-methyladenine Methyltransferase's Modification Site at Single Base Resolution. Chembiochem : a European Journal of Chemical Biology. PMID 33779011 DOI: 10.1002/cbic.202100088   
2021 Galindo-Murillo R, Cheatham TE. Ethidium bromide interactions with DNA: an exploration of a classic DNA-ligand complex with unbiased molecular dynamics simulations. Nucleic Acids Research. PMID 33764383 DOI: 10.1093/nar/gkab143   
2021 Lo YMD, Han DSC, Jiang P, Chiu RWK. Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies. Science (New York, N.Y.). 372. PMID 33833097 DOI: 10.1126/science.aaw3616   
2021 Wan L, Lam SL, Lee HK, Guo P. Effects of Adenine Methylation on the Structure and Thermodynamic Stability of a DNA Minidumbbell. International Journal of Molecular Sciences. 22. PMID 33807305 DOI: 10.3390/ijms22073633   
2021 Emmanouilidis I, Fili N, Cook AW, Hari-Gupta Y, Dos Santos Á, Wang L, Martin-Fernandez ML, Ellis PJI, Toseland CP. A Targeted and Tuneable DNA Damage Tool Using CRISPR/Cas9. Biomolecules. 11. PMID 33672015 DOI: 10.3390/biom11020288   
2021 Ghosh D, Raghavan SC. 20 years of DNA Polymerase μ, the polymerase that still surprises. The Febs Journal. PMID 33786971 DOI: 10.1111/febs.15852   
2021 Gao X, Zhang K, Lu T, Zhao Y, Zhou H, Yu Y, Zellmer L, He Y, Huang H, Joshua Liao D. A reassessment of several erstwhile methods for isolating DNA fragments from agarose gels. 3 Biotech. 11: 138. PMID 33692931 DOI: 10.1007/s13205-021-02691-1   
2021 Jakhanwal S, Cress BF, Maguin P, Lobba MJ, Marraffini LA, Doudna JA. A CRISPR-Cas9-integrase complex generates precise DNA fragments for genome integration. Nucleic Acids Research. PMID 33693715 DOI: 10.1093/nar/gkab123   
2021 Neidle S. Beyond the double helix: DNA structural diversity and the PDB. The Journal of Biological Chemistry. 100553. PMID 33744292 DOI: 10.1016/j.jbc.2021.100553   
2021 Biber S, Wiesmüller L. Analysis of Replication Dynamics Using the Single-Molecule DNA Fiber Spreading Assay. Methods in Molecular Biology (Clifton, N.J.). 2267: 57-71. PMID 33786784 DOI: 10.1007/978-1-0716-1217-0_4   
2021 Unciuleac MC, Meir A, Xue C, Warren GM, Greene EC, Shuman S. Clutch mechanism of chemomechanical coupling in a DNA resecting motor nuclease. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33836607 DOI: 10.1073/pnas.2023955118   
2021 Hai H, Chen C, Chen D, Li P, Shan Y, Li J. A sensitive electrochemiluminescence DNA biosensor based on the signal amplification of ExoIII enzyme-assisted hybridization chain reaction combined with nanoparticle-loaded multiple probes. Mikrochimica Acta. 188: 125. PMID 33723966 DOI: 10.1007/s00604-021-04777-2   
2021 Schurr JM. A quantitative model of a cooperative two-state equilibrium in DNA: experimental tests, insights, and predictions. Quarterly Reviews of Biophysics. 54: e5. PMID 33722316 DOI: 10.1017/S0033583521000032   
2021 Zhou X, Chen X, An Y, Lu H, Wang L, Xu H, Tian B, Zhao Y, Hua Y. Biochemical characterization of a unique DNA polymerase A from the extreme radioresistant organism Deinococcus radiodurans. Biochimie. PMID 33727139 DOI: 10.1016/j.biochi.2021.02.014   
2021 Asrat TM, Cho W, Liu FA, Shapiro SM, Bracht JR, Zestos AG. Direct Detection of DNA and RNA on Carbon Fiber Microelectrodes Using Fast-Scan Cyclic Voltammetry. Acs Omega. 6: 6571-6581. PMID 33748569 DOI: 10.1021/acsomega.0c04845   
2021 Li Q, Edwards TC, Ponzar NL, Tavis JE. A mid-throughput HBV replication inhibition assay capable of detecting ribonuclease H inhibitors. Journal of Virological Methods. 114127. PMID 33766659 DOI: 10.1016/j.jviromet.2021.114127   
2021 Wang S, Zhang Q, Shen Z, He Y, Chen ZH, Li J, Huang DS. Predicting transcription factor binding sites using DNA shape features based on shared hybrid deep learning architecture. Molecular Therapy. Nucleic Acids. 24: 154-163. PMID 33767912 DOI: 10.1016/j.omtn.2021.02.014   
2021 Aparicio Casado T, Gautier J. DNA Damage Response in Xenopus laevis Cell-Free Extracts. Methods in Molecular Biology (Clifton, N.J.). 2267: 103-144. PMID 33786788 DOI: 10.1007/978-1-0716-1217-0_8   
2021 Petruseva I, Naumenko N, Kuper J, Anarbaev R, Kappenberger J, Kisker C, Lavrik O. The Interaction Efficiency of XPD-p44 With Bulky DNA Damages Depends on the Structure of the Damage. Frontiers in Cell and Developmental Biology. 9: 617160. PMID 33777931 DOI: 10.3389/fcell.2021.617160   
2021 Kim S, Ha G, Gang J. Characterizing Fluorescence Emissions of Hairpin DNA-Templated Silver Nanoclusters by cDNA Hybridization. Journal of Nanoscience and Nanotechnology. 21: 4134-4138. PMID 33714292 DOI: 10.1166/jnn.2021.19377   
2021 Pellanda P, Dalsass M, Filipuzzi M, Loffreda A, Verrecchia A, Castillo Cano V, Thabussot H, Doni M, Morelli MJ, Soucek L, Kress T, Mazza D, Mapelli M, Beaulieu ME, Amati B, et al. Integrated requirement of non-specific and sequence-specific DNA binding in Myc-driven transcription. The Embo Journal. e105464. PMID 33792944 DOI: 10.15252/embj.2020105464   
2021 Westwood MN, Ljunggren KD, Boyd B, Becker J, Dwyer TJ, Meints GA. Single-Base Lesions and Mismatches Alter the Backbone Conformational Dynamics in DNA. Biochemistry. PMID 33689312 DOI: 10.1021/acs.biochem.0c00784   
2021 Ji Y, Dai D, Luo H, Shen S, Fan J, Wang Z, Chen M, Wan J, Li J, Ma H, Liu G. C-S Coupling of DNA-Conjugated Aryl Iodides for DNA-Encoded Chemical Library Synthesis. Bioconjugate Chemistry. PMID 33720689 DOI: 10.1021/acs.bioconjchem.1c00076   
2021 Shendi AM, Davenport A. The difference between delivered and prescribed dialysate sodium in haemodialysis machines. Clinical Kidney Journal. 14: 863-868. PMID 33777369 DOI: 10.1093/ckj/sfaa022   
2021 Ming X, Zhu B, Zhang Z. Simultaneously measuring the methylation of parent and daughter strands of replicated DNA at the single-molecule level by Hammer-seq. Nature Protocols. PMID 33686219 DOI: 10.1038/s41596-020-00488-9   
2021 Ueda S, Yamashita S, Watanabe SI, Wakabayashi M, Motoi N, Noguchi M, Sekine S, Sato Y, Ushijima T. Influence of degree of DNA degradation in formalin-fixed and paraffin-embedded tissue samples on accuracy of genome-wide DNA methylation analysis. Epigenomics. PMID 33820444 DOI: 10.2217/epi-2020-0431   
2021 Yu Q, Zhang J, Qiu W, Li K, Qian L, Zhang X, Liu G. Gold nanorods-based lateral flow biosensors for sensitive detection of nucleic acids. Mikrochimica Acta. 188: 133. PMID 33745096 DOI: 10.1007/s00604-021-04788-z   
2021 Ma N, Dai L, Chen Z, Ji M, Wang Y, Tian Y. Environment-Resistant DNA Origami Crystals Bridged by Rigid DNA Rods with Adjustable Unit Cells. Nano Letters. PMID 33821653 DOI: 10.1021/acs.nanolett.1c00607   
2021 Bigman LS, Greenblatt HM, Levy Y. What Are the Molecular Requirements for Protein Sliding along DNA? The Journal of Physical Chemistry. B. 125: 3119-3131. PMID 33754737 DOI: 10.1021/acs.jpcb.1c00757   
2021 Leitner M, Brummeir J, Oswald Plaimer G, Kefer I, Poturnayova A, Hianik T, Ebner A. DNA building blocks for AFM tip functionalization: an easy, fast and stable strategy. Methods (San Diego, Calif.). PMID 33677061 DOI: 10.1016/j.ymeth.2021.02.021   
2021 Wang J, Yang L, Diao Y, Liu J, Li J, Li R, Zheng L, Zhang K, Ma Y, Hao X. Circulating tumour DNA methylation in hepatocellular carcinoma diagnosis using digital droplet PCR. The Journal of International Medical Research. 49: 300060521992962. PMID 33750234 DOI: 10.1177/0300060521992962   
2021 Bhowmik D, Zhu F. Evasion of Intracellular DNA Sensing by Human Herpesviruses. Frontiers in Cellular and Infection Microbiology. 11: 647992. PMID 33791247 DOI: 10.3389/fcimb.2021.647992   
2021 Shrivastava P, Jain T, Kumawat RK. Direct PCR amplification from saliva sample using non-direct multiplex STR kits for forensic DNA typing. Scientific Reports. 11: 7112. PMID 33782478 DOI: 10.1038/s41598-021-86633-0   
2021 Waldern JM, Smith D, Piazza CL, Bailey EJ, Schiraldi NJ, Nemati R, Fabris D, Belfort M, Novikova O. Methylation of rRNA as a host defense against rampant group II intron retrotransposition. Mobile Dna. 12: 9. PMID 33678171 DOI: 10.1186/s13100-021-00237-z   
2021 Li Y, Gao H, Qi Z, Huang Z, Ma L, Liu J. Freezing-assisted Conjugation of Unmodified Diblock DNA to Hydrogel Nanoparticles and Monoliths for DNA and Hg2+ Sensing. Angewandte Chemie (International Ed. in English). PMID 33792133 DOI: 10.1002/anie.202102330