References
1. Soisson SM, MacDougall-Shackleton B, Schleif R, Wolberger C. Structural basis for ligand-regulated oligomerization of AraC.Science . 1997;276:421–425. DOI:10.1126/science.276.5311.421.
2. Weldon JE, Rodgers ME, Larkin C, Schleif RF. Structure and Properties of a Truly Apo Form of AraC Dimerization Domain. PROTEINS: Structure, Function, and Bioinformatics 2007;66:646–654.
3. Rodgers ME, Schleif R. Solution structure of the DNA binding domain of AraC protein.Proteins 2009;77: 202-208.
4. Schleif R. AraC protein, regulation of the L-arabinose operon inEscherichia coli and the light switch mechanism of AraC action.FEMS 2010;34:779-796. DOI:10.1111/j.1574-6976.2010.00226.x
5. Lobell R and Schleif RF. DNA Looping and Unlooping by AraC Protein.Science 1990;250:528-532.
6. Carra JH, Schleif RF. Variation of half-site organization and DNA looping by AraC protein. The EMBO Journal 1993;12(1):35-44.
7. Saviola B, Seabold RR, Schleif RF. DNA Bending by AraC: a Negative Mutant. J. Bacteriology 1998;180 (16):4227-4232.
8. Brunelle A, Schleif R. Determining residue-base interactions between AraC protein and araI DNA. J. Mol. Biol. 1989;209:607-622.
9. Schleif R. 2021. A Career’s Work, the L-Arabinose Operon: How it functions and how we learned it. EcoSal Plus 2021. https://doi.org/10.1128/ecosalplus.ESP-0012-2021
10. Greenfield L, Boone T, Wilcox G. DNA sequence of the araBAD promoter in Escherichia coli B/r. Proc. Nati. Acad. Sci. USA1978;75(10):4724-4728.
11. Main KHS, Provan JI, Haynes PJ, Wells G, Hartley JA, Pyne ALP. Atomic force microscopy—A tool for structural and translational DNA research. APL Bioeng. 2021:5:031504. DOI:10.1063/5.0054294
12. Rivetti C, Guthold M, Bustamante C. Scanning Force Microscopy of DNA Deposited onto Mica: Equilibration versus Kinetic Trapping Studied by Statistical Polymer Chain Analysis. J. Mol. Biol.1996;264:919–932.
13. Tessmer I, Yang Y, Zhai J, Du C, Hsieh P, Hingorani MM, Erie DA. Mechanism of MutS Searching for DNA Mismatches and Signaling Repair.J. Biological Chemistry 2008;283(52):36646–36654.
14. Erie, DA, Yang G, Schultz HC, Bustamante C. DNA Bending by Cro Protein in Specific and Nonspecific Complexes: Implications for Protein Site Recognition and Specificity. Science 1994;266:1562-1566.
15. Mysiak, ME, Wyman C, Holthuizen PE, van der Vliet PC. NFI and Oct-1 bend the Ad5 origin in the same direction leading to optimal DNA replication. Nucl. Acids Res. 2004;32:6218-6225.
16. Dutta S, Rivetti C, Gassman NR, Young CG, Jones BT, Scarpinato K, Guthold M. Analysis of single, cisplatin-induced DNA bends by atomic force microscopy and simulations. Journal of Molecular Recognition 2018; 31(10):e32731, 11 pages total, DOI: 10.1002/jmr.2731
17. Yan Y, Tao H, He J, Huang S-Y. The HDOCK server for integrated protein–protein docking. Nat. Protoc.  2020;15:1829-1852. DOI:10.1038/s41596-020-0312-x
18. Rodgers ME, Schleif R. Heterodimers reveal that two arabinose molecules are required for the normal arabinose response of AraC.Biochemistry 2012;51:8085−8091.
19. Pastre D, Pietrement O, Fusil S, Landousy F, Jeusset J, David MO, Hamon L, Le Cam E, Zozime A. Adsorption of DNA to Mica Mediated by Divalent Counterions: A Theoretical and Experimental Study.Biophysical Journal 2003;85:2507–2518.
20. Hsueh C, Chen H, Gimzewski JK, Reed J, Abdel-Fattah TM. Localized Nanoscopic Surface Measurements of Nickel-Modified Mica for Single Molecule DNA Sequence Sampling. ACS Appl. Mater. Interfaces2010;2(11): 3249–3256. DOI:10.1021/am100697z
21. Nečas D, Klapetek P. Gwyddion: an open-source software for SPM data analysis. Cent. Eur. J. Phys.  2012;10(1):181-188. Also see http://gwyddion.net/ .
22. Margeat E, Le Grimellec C, Royer CA. Visualization of trp Repressor and its Complexes with DNA by Atomic Force Microscopy. Biophysical Journal 1998;75:2712-2720.
23. Li S, Olson WK, Lu XJ. Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures. Nucleic Acids Research 2019;47:W26-W34. DOI: 10.1093/nar/gkz394
24. Calladine CR, Drew H, Luisi B, Travers A. Understanding DNA: The Molecule and How it Works. New York: Elsevier Academic Press; 2004. 72-78 p.
25. Stefl R, Wu H, Ravindranathan S, Sklenář V, Feigon J. DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum. Proc. Natl. Acad. Sci. 2004;101(5):1177-1182. DOI:10.1073/pnas.0308143100
26. Huang S-Y, Zou X. A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method. Nucleic Acids Research 2014;42(7):e55. DOI:10.1093/nar/gku077
27. Hendrickson W, Schleif RF. Regulation of the Escherichiu coli L-Arabinose Operon Studied by Gel Electrophoresis DNA Binding Assay.J. Mol. Biol. 1984;174:611-628.
28. Perez-Martin J, Espinosa M. Protein-induced Bending as a Transcriptional Switch. Science 1993;260(5109):805-807.
29. Zhang X, Reeder T, Schleif R. Transcription Activation Parameters atara pBAD . J. Mol. Biol. 1996;258:14–24.
30. Zhang X, Schleif R. Catabolite gene activator protein mutations affecting activity of the araBAD Promoter. J Bacteriology1998;180:195-200.
31. Benoff B, Yang H, Lawson CL, Parkinson G, Liu J, Blatter E, Ebright YW, Berman HM, Ebright RH. Structural Basis of Transcription Activation: The CAP-αCTD-DNA Complex. Science 2002;297(5586):1562-1566.
32. Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M, Zhang X. Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation. Molecular Cell 2018;70: 1111–1120. DOI:10.1016/j.molcel.2018.05.021
33. Lee J, Borukhov S. Bacterial RNA Polymerase-DNA Interaction-The Driving Force of Gene Expression and the Target for Drug Action.Front. Mol. Biosci. , 2016;3:73. DOI: 10.3389/fmolb.2016.00073
34. Wang JC. Helical repeat of DNA in solution. Proc. Natl. Acad. Sci. 1979;76(1):200-203.
35. Lee D, Schleif R. In vivo DNA Loops in araCBAD : Size Limit and Helical Repeat. Proc. Nat. Acad. Sci. 1989;86:476-480.
36. He J, Tao H, Huang SY. Protein-ensemble–RNA docking by efficient consideration of protein flexibility through homology models.Bioinformatics 2019; 35(23):4994–5002.
37. Pinzi L, Rastelli G. Molecular Docking: Shifting Paradigms in Drug Discovery. Int. J. Mol. Sci. 2019;20: 4331. DOI:10.3390/ijms20184331
38. Pagadala NS, Syed K, Tuszynski J. oftware for molecular docking: a review. Biophys Rev 2017;9:91–102. DOI 10.1007/s12551-016-0247-1
39. Sanchez-Sevilla A, Thimonier J, Marilley M, Rocca-Serra J, Barbet J. Accuracy of AFM measurements of the contour length of DNA fragments adsorbed on mica in air and in aqueous buffer. Ultramicroscopy2002;92:151–158.
40. Japaridze, A., Vobornik D, Lipiec E, Cerreta A, Szczerbinski J, Zenobi R, Dietler G. Toward an Effective Control of DNA’s Submolecular Conformation on a Surface. Macromolecules 2016;49:643−652. DOI: 10.1021/acs.macromol.5b01827