Some of our recent publications (updated in June 2009)

Papers, Ph.D. theses, monographs 

2009

  1. Aioanei, D., B. Samori and M. Brucale (2009). "Maximum likelihood estimation of protein kinetic parameters under weak assumptions from unfolding force spectroscopy experiments." Physical Review E 80(6): -.
  2. Altmann, K. H., J. Buchner, H. Kessler, F. Diederich, B. Krautler, S. Lippard, R. Liskamp, K. Muller, E. M. Nolan, B. Samori, G. Schneider, S. L. Schreiber, H. Schwalbe, C. Toniolo, C. A. A. van Boeckel, H. Waldmann and C. T. Walsh (2009). "The State of the Art of Chemical Biology." Chembiochem 10(1): 16-29.
  3. Brucale, M., M. Sandal, S. Di Maio, A. Rampioni, I. Tessari, L. Tosatto, M. Bisaglia, L. Bubacco and B. Samori (2009). "Pathogenic Mutations Shift the Equilibria of alpha-Synuclein Single Molecules towards Structured Conformers." Chembiochem 10(1): 176-183.
  4. Carrara, S., L. Benini, V. Bhalla, C. Stagni, A. Ferretti, A. Cavallini, B. Ricco and B. Samori (2009). "New insights for using self-assembly materials to improve the detection stability in label-free DNA-chip and immuno-sensors." Biosensors & Bioelectronics 24(12): 3425-3429.
  5. Carrara, S., V. Bhalla, C. Stagni, L. Benini, A. Ferretti, F. Valle, A. Gallotta, B. Ricco and B. Samori (2009). "Label-free cancer markers detection by capacitance biochip." Sensors and Actuators B-Chemical 136(1): 163-172.
  6. Carrara, S., V. Bhalla, C. Stagni and B. Samori (2009). "Nanoscale film structure related to capacitive effects in ethylene-glycol monolayers." Surface Science 603(13): L75-L77.
  7. Kapeliouchko, V., G. Palamone, T. Poggio, G. Zuccheri, R. Passeri, K. Sparnacci, D. Antonioli, S. Deregibus and M. Laus (2009). "PMMA-Based Core-Shell Nanoparticies with Various PTFE Cores." Journal of Polymer Science Part a-Polymer Chemistry 47(11): 2928-2937.
  8. Materassi, D., P. Baschieri, B. Tiribilli, G. Zuccheri and B. Samori (2009). "An open source/real-time atomic force microscope architecture to perform customizable force spectroscopy experiments." Review of Scientific Instruments 80(8): -.
  9. Samori, B. (2009). "Conformational Equilibria of Intrinsically Disordered Proteins Probed by Single Molecule Methodologies." Journal of Biomolecular Structure & Dynamics 26(6): 803-803.
  10. Sandal, M., F. Benedetti, M. Brucale, A. Gomez-Casado and B. Samori (2009). "Hooke: an open software platform for force spectroscopy." Bioinformatics 25(11): 1428-1430.
  11. Sorce, B., S. Sabella, M. Sandal, B. Samori, A. Santino, R. Cingolani, R. Rinaldi and P. P. Pompa (2009). "Single-Molecule Mechanical Unfolding of Amyloidogenic beta(2)-Microglobulin: The Force-Spectroscopy Approach." Chemphyschem 10(9-10): 1471-1477.
  12. Sparnacci, K., D. Antonioli, S. Deregibus, M. Laus, T. Poggio, V. Kapeliouchko, G. Palamone, G. Zuccheri and R. Passeri (2009).

2008

  1. "PTFE-Based Core-Soft Shell Nanospheres and Soft Matrix Nanocomposites." Macromolecules 42(10): 3518-3524.
  2. Carrara, S., V. V. Shumyantseva, A. I. Archakov and B. Samori (2008). "Screen-printed electrodes based on carbon nanotubes and cytochrome P450scc for highly sensitive cholesterol biosensors." Biosensors & Bioelectronics 24(1): 148-150.
  3. Sandal, M., F. Valle, I. Tessari, S. Mammi, E. Bergantino, F. Musiani, M. Brucale, L. Bubacco and B. Samori (2008). "Conformational equilibria in monomeric alpha-synuclein at the single-molecule level." Plos Biology 6(1): 99-108.
  4. Tessari, I., M. Bisaglia, F. Valle, B. Samori, E. Bergantino, S. Mammi and L. Bubacco (2008). "The reaction of alpha-synuclein with tyrosinase - Possible implications for Parkinson disease." Journal of Biological Chemistry 283(24): 16808-16817.
  5. Valle, F., G. Zuccheri, A. Bergia, L. Ayres, A. E. Rowan, R. J. M. Nolte and B. Samori (2008). "A polymeric molecular "Handle" for multiple AFM-based single-molecule force measurements." Angewandte Chemie-International Edition 47(13): 2431-2434.
  6. Vinelli, A., E. Primiceri, M. Brucale, G. Zuccheri, R. Rinaldi and B. Samori (2008). "Sample Preparation for the Quick Sizing of Metal Nanoparticles by Atomic Force Microscopy." Microscopy Research and Technique 71(12): 870-879.

2007

  1. Kolaric, B., M. Sliwa, M. Brucale, R. A. L. Vallee, G. Zuccheri, B. Samori, J. Hofkens and F. C. De Schryver (2007). "Single molecule fluorescence spectroscopy of pH sensitive oligonucleotide switches." Photochemical & Photobiological Sciences 6(6): 614-618.
  2. Mazzocchetti, L., S. Sandri, M. Scandola, A. Bergia and G. Zuccheri (2007). "Radiopaque organic-inorganic hybrids based on poly(D,L-lactide)." Biomacromolecules 8(2): 672-678.
  3. Valle, F., M. Sandal and B. Samori (2007). "The interplay between chemistry and mechanics in the transduction of a mechanical signal into a biochemical function." Physics of Life Reviews 4(3): 157-188.

2006

  1. Brucale, M., G. Zuccheri, L. Rossi, A. Bazzani, G. Castellani and B. Samori (2006). "Characterization and modulation of the hierarchical self-assembly of nanostructured DNA tiles into supramolecular polymers." Organic & Biomolecular Chemistry 4(18): 3427-3434.
  2. Brucale, M., G. Zuccheri and B. Samori (2006). "Mastering the complexity of DNA nanostructures." Trends in Biotechnology 24(5): 235-243.
  3. Grandi, F., M. Sandal, G. Guarguaglini, E. Capriotti, R. Casadio and B. Samori (2006). "Hierarchical mechanochemical switches in angiostatin." Chembiochem 7(11): 1774-1782.
  4. Sandal, M., F. Grandi and B. Samori (2006). "Single molecule force spectroscopy discovers mechanochemical switches in biology: The case of the disulfide bond." Polymer 47(7): 2571-2579.
  5. Scipioni, A., S. Pisano, A. Bergia, M. Savino, B. Samori and P. De Santis (2006). "Recognition on the nanoscale of a DNA sequence by an inorganic crystal surface." Chembiochem 7(11): 1645-+.
  6. Stagni, C., C. Guiducci, L. Benini, B. Ricco, S. Carrara, B. Samori, C. Paulus, M. Schienle, M. Augustyniak and R. Thewes (2006). "CMOS DNA sensor array with integratedA/D conversion based on label-free capacitance measurement." Ieee Journal of Solid-State Circuits 41(12): 2956-2964.

2005

  1. Brucale, M., G. Zuccheri and B. Samori (2005). "The dynamic properties of an intramolecular transition from DNA duplex to cytosine-thymine motif triplex." Organic & Biomolecular Chemistry 3(4): 575-577.
  2. Ficarra, E., L. Benini, E. Macii and G. Zuccheri (2005). "Automated DNA fragments recognition and sizing through AFM image processing." Ieee Transactions on Information Technology in Biomedicine 9(4): 508-517.
  3. Ficarra, E., D. Masotti, E. Macii, L. Benini, G. Zuccheri and B. Samori (2005). "Automatic intrinsic DNA curvature computation from AFM images." Ieee Transactions on Biomedical Engineering 52(12): 2074-2086.
  4. Samori, B. and G. Zuccheri (2005). "DNA codes for nanoscience." Angewandte Chemie-International Edition 44(8): 1166-1181.
  5. Samori, B., G. Zuccheri and P. Baschieri (2005). "Protein unfolding and refolding under force: Methodologies for nanomechanics." Chemphyschem 6(1): 29-34.
  6. Zuccheri, G., M. Brucale and B. Samori (2005). "The tube or the helix? This is the question: Towards the fully controlled DNA-directed assembly of carbon nanotubes." Small 1(6): 590-592.

2004

  1. Giro, A., A. Bergia, G. Zuccheri, H. H. J. Bink, C. W. A. Pleij and B. Samori (2004). "Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA." Microscopy Research and Technique 65(4-5): 235-245.
  2. Guiducci, C., C. Stagni, G. Zuccheri, A. Bogliolo, L. Benini, B. Samori and B. Ricco (2004). "DNA detection by integrable electronics." Biosensors & Bioelectronics 19(8): 781-787.
  3. Samori, B., F. Grandi, G. Guarguaglini, M. Sandal, R. Casadio and E. Capriotti (2004). "Mechanochemistry of human angiostatin." Abstracts of Papers of the American Chemical Society 227: U470-U470.

older papers

  1. Arciola, C. R., Y. Bustanji, M. Conti, D. Campoccia, L. Baldassarri, B. Samori and L. Montanaro (2003). "Staphylococcus epidermidis - fibronectin binding and its inhibition by heparin." Biomaterials 24(18): 3013-3019.
  2. Bustanji, Y., C. R. Arciola, M. Conti, E. Mandello, L. Montanaro and B. Samori (2003). "Dynamics of the interaction between a fibronectin molecule and a living bacterium under mechanical force." Proceedings of the National Academy of Sciences of the United States of America 100(23): 13292-13297.
  3. Barna, M., T. Merghoub, J. A. Costoya, D. Ruggero, M. Branford, A. Bergia, B. Samori and P. P. Pandolfi (2002). "Plzf mediates transcriptional repression of HoxD gene expression through chromatin remodeling." Developmental Cell 3(4): 499-510.
  4. Bustanji, Y. and B. Samori (2002). "The mechanical properties of human angiostatin can be modulated by means of its disulfide bonds: A single-molecule force-spectroscopy study." Angewandte Chemie-International Edition 41(9): 1546-1548.
  5. Conti, M., G. Donati, G. Cianciolo, S. Stefoni and B. Samori (2002). "Force spectroscopy study of the adhesion of plasma proteins to the surface of a dialysis membrane: Role of the nanoscale surface hydrophobicity and topography." Journal of Biomedical Materials Research 61(3): 370-379.
  6. Nagami, F., G. Zuccheri, B. Samori and R. Kuroda (2002). "Time-lapse imaging of conformational changes in supercoiled DNA by scanning force microscopy." Analytical Biochemistry 300(2): 170-176.
  7. Sampaolese, B., A. Bergia, A. Scipioni, G. Zuccheri, M. Savino, B. Samori and P. De Santis (2002). "Recognition of the DNA sequence by an inorganic crystal surface." Proceedings of the National Academy of Sciences of the United States of America 99(21): 13566-13570.
  8. Scipioni, A., C. Anselmi, G. Zuccheri, B. Samori and P. De Santis (2002). "Sequence-dependent DNA curvature and flexibility from scanning force microscopy images." Biophysical Journal 83(5): 2408-2418.
  9. Scipioni, A., G. Zuccheri, C. Anselmi, A. Bergia, B. Samori and P. De Santis (2002). "Sequence-dependent DNA dynamics by scanning force microscopy time-resolved imaging." Chemistry & Biology 9(12): 1315-1321.
  10. Zuccheri, G. and B. Samori (2002). "Scanning force microscopy studies on the structure and dynamics of single DNA molecules." Atomic Force Microscopy in Cell Biology 68: 357-395.
  11. Conti, M., Y. Bustanji, G. Falini, P. Ferruti, S. Stefoni and B. Samori (2001). "The desorption process of macromolecules adsorbed on interfaces: The force spectroscopy approach." Chemphyschem 2(10): 610-613.
  12. Laus, M., K. Sparnacci, B. Ensoli, S. Butto, A. Caputo, I. Mantovani, G. Zuccheri, B. Samori and L. Tondelli (2001). "Complex associates of plasmid DNA and a novel class of block copolymers with PEG and cationic segments as new vectors for gene delivery." Journal of Biomaterials Science-Polymer Edition 12(2): 209-228.
  13. Zuccheri, G., A. Bergia, G. Gallinella, M. Musiani and B. Samori (2001). "Scanning force microscopy study on a single-stranded DNA: The genome of parvovirus B19." Chembiochem 2(3): 199-204.
  14. Zuccheri, G., A. Scipioni, V. Cavaliere, G. Gargiulo, P. De Santis and B. Samori (2001). "Mapping the intrinsic curvature and flexibility along the DNA chain." Proceedings of the National Academy of Sciences of the United States of America 98(6): 3074-3079.
  15. Zuccheri, G., A. Sciponi, V. Cavaliere, G. Gargiulo, P. De Santis and B. Samori (2001). "Mapping the intrinsic curvature and flexibility along the DNA chain (vol 98, pg 3074, 2001)." Proceedings of the National Academy of Sciences of the United States of America 98(9): 5368-5368.
  16. Barbieri, L., P. Valbonesi, F. Righi, G. Zuccheri, F. Monti, P. Gorini, B. Samori and F. Stirpe (2000). "Polynucleotide : adenosine glycosidase is the sole activity of ribosome-inactivating proteins on DNA." Journal of Biochemistry 128(5): 883-889.
  17. Conti, M., G. Falini and B. Samori (2000). "How strong is the coordination bond between a histidine tag and Ni-nitrilotriacetate? An experiment of mechanochemistry on single molecules." Angewandte Chemie-International Edition 39(1): 215-+.
  18. Samori, B. (2000). "Stretching single molecules along unbinding and unfolding pathways with the scanning force microscope." Chemistry-a European Journal 6(23): 4249-4255.
  19. Samori, B. (1998). "Stretching, tearing, and dissecting single molecules of DNA." Angewandte Chemie-International Edition 37(16): 2198-2200.
  20. Zuccheri, G., R. T. Dame, M. Aquila, I. Muzzalupo and B. Samori (1998). "Conformational fluctuations of supercoiled DNA molecules observed in real time with a scanning force microscope." Applied Physics a-Materials Science & Processing 66: S585-S589.
  21. Bustamante, C., G. Zuccheri, S. H. Leuba, G. L. Yang and B. Samori (1997). "Visualization and analysis of chromatin by scanning force microscopy." Methods-a Companion to Methods in Enzymology 12(1): 73-83.
  22. Samori, B., C. Nigro, A. Gordano, I. Muzzalupo and C. Quagliariello (1996). "Trapping and imaging molecular dynamics by combining scanning force microscopy with topology." Angewandte Chemie-International Edition in English 35(5): 529-530.
  23. Muzzalupo, I., C. Nigro, G. Zuccheri, B. Samori, C. Quagliariello and M. Buttinelli (1995). "Deposition on Mica and Scanning Force Microscopy Imaging of DNA-Molecules Whose Original B-Structure Is Retained." Journal of Vacuum Science & Technology a-Vacuum Surfaces and Films 13(3): 1752-1754.
  24. Solimani, R., F. Bayon, I. Domini, P. G. Pifferi, P. E. Todesco, G. Marconi and B. Samori (1995). "Flavonoid-DNA Interaction Studied with Flow Linear Dichroism Technique." Journal of Agricultural and Food Chemistry 43(4): 876-882.
  25. Zuccheri, G., G. A. Ranieri, C. Nigro and B. Samori (1995). "Writhing Number of Supercoiled DNA from Its Scanning Force Microscopy Imaging." Journal of Vacuum Science & Technology B 13(1): 158-160.
  26. Leuba, S. H., G. L. Yang, C. Robert, B. Samori, K. Vanholde, J. Zlatanova and C. Bustamante (1994). "3-Dimensional Structure of Extended Chromatin Fibers as Revealed by Tapping-Mode Scanning Force Microscopy." Proceedings of the National Academy of Sciences of the United States of America 91(24): 11621-11625.
  27. Siligardi, G., B. Samori, S. Melandri, M. Visconti and A. F. Drake (1994). "Correlations between Biological-Activities and Conformational Properties for Human, Salmon, Eel, Porcine Calcitonins and Elcatonin Elucidated by Cd Spectroscopy." European Journal of Biochemistry 221(3): 1117-1125.
  28. Samori, B., S. Masiero, G. R. Luckhurst, S. K. Heeks, B. A. Timimi and P. Mariani (1993). "Chemical-Reactivity within a Smectic-B Liquid-Crystalline Phase - a Model of Enzyme Catalysis." Liquid Crystals 15(2): 217-231.
  29. Samori, B., C. Nigro, V. Armentano, S. Cimieri, G. Zuccheri and C. Quagliariello (1993). "DNA Supercoiling Imaged in 3 Dimensions by Scanning Force Microscopy." Angewandte Chemie-International Edition in English 32(10): 1461-1463.
  30. Samori, B., M. A. Osipov, I. Domini and A. Bartolini (1993). "Transverse Dipoles Added to DNA Chains by Drug-Binding Can Induce Inversion of the Long-Range Chirality of DNA Condensates." International Journal of Biological Macromolecules 15(6): 353-359.
  31. Samori, B., G. Siligardi, C. Quagliariello, A. L. Weisenhorn, J. Vesenka and C. J. Bustamante (1993). "Chirality of DNA Supercoiling Assigned by Scanning Force Microscopy." Proceedings of the National Academy of Sciences of the United States of America 90(8): 3598-3601.
  32. Erokhin, V., B. Popov, B. Samori and A. Yakovlev (1992). "Immobilization of DNA Fragments by Langmuir - Blodgett Technique." Molecular Crystals and Liquid Crystals 215: 213-220.
  33. Lenaz, G., B. Samori, R. Fato, M. Battino, G. P. Castelli and I. Domini (1992). "Localization and Preferred Orientations of Ubiquinone Homologs in Model Bilayers." Biochemistry and Cell Biology-Biochimie Et Biologie Cellulaire 70(6): 504-514.
  34. Samori, B., G. Lenaz, M. Battino, G. Marconi and I. Domini (1992). "On Coenzyme-Q Orientation in Membranes - a Linear Dichroism Study of Ubiquinones in a Model Bilayer." Journal of Membrane Biology 128(3): 193-203.
  35. Bustamante, C., B. Samori and E. Builes (1991). "Daunomycin Inverts the Long-Range Chirality of DNA Condensed States." Biochemistry 30(23): 5661-5666.
  36. Capobianco, M. L., F. P. Colonna, A. Forni, A. Garbesi, S. Iotti, I. Moretti, B. Samori and L. Tondelli (1991). "Interactions of Nucleic-Acids with Distamycins - Binding of Dst-3 to D(Cgtttaaacg)2 and D(Cgtacgtacg)2." Nucleic Acids Research 19(7): 1695-1698.
  37. Chiesa, M., I. Domini, B. Samori, S. Eriksson, M. Kubista and B. Norden (1990). "Multisite Distributions of Solute Molecules in Micelles - Benzene in a Nematic Phase of Potassium Laurate Decanol Water." Gazzetta Chimica Italiana 120(11): 667-670.
  38. Samori, B., I. D. Pellerano, A. Rossi, D. Grasso and G. Albertini (1990). "Preparation and Electron-Microscopy of Liquid-Crystalline Condensates of DNA." Nuovo Cimento Della Societa Italiana Di Fisica D-Condensed Matter Atomic Molecular and Chemical Physics Fluids Plasmas Biophysics 12(9): 1317-1324.

Ph.D. Theses of our students

Dr. Andrea Giro's "AFM nello studio di strutture nanometriche di acidi nucleici di interesse
biologico e nanobiotecnologico"

Dr. Fabio Grandi's "Mechanochemical Switches in Angiostatin Revealed by Single Molecule Force Spectroscopy Tecniques"

Dr. Marco Brucale's "Design, Synthesis And Characterization of DNA Supramolecular Nanostructures"

 

Monographical papers in books

  1. R. Passeri, M. Brucale, G. Zuccheri, B. Samorì. (2008). DNA-based Parallelograms: a Retrospective or a Perspective?.
    In WOLFGANG FRITZSCHE, FRANK BIER. DNA-Based Nanodevices: international symposium on DNA-based Nanodevices. (pp. 58 - 64). ISBN: 978-0-7354-0592-9. MELVILLE,NEW YORK: American Institute of Physics.
  2. B. Samorì, G. Zuccheri, A. Scipioni, P. De Santis. (2006). Towards an Increase of the Hierarchy in the Construction of DNA-Based Nanostructures Through the Integration of Inorganic Materials.
    in JUNGHUEI CHEN, NATAŠA JONOSKA, GRZEGORZ ROZENBERG. Nanotechnology: Science and Computation. (pp. 249 - 260). ISBN: 3-540-30295-6. NEW YORK: Springer.
  3. F. Valle, G. Zuccheri, B. Samorì. (2006). Dalle Cellule alle Molecole: alla scoperta della Struttura delle Molecole Biologiche e delle loro Interazioni con la Microscopia a Forza Atomica.
    In D. QUAGLINO, E. FALCIERI, M. CATALANO, A. DIASPRO, A. MONTONE, P. MENGUCCI, C. PELLICCIARI. 1956/2006 Cinquanta anni di microscopia in Italia tra storia, progresso ed innovazione. (pp. 207 - 218). ISBN: 9788879632157. ROMA: Società Italiana di Scienze Microscopiche.
  4. Zuccheri G., Brucale M., Vinelli A., Samorì B. (2006). DNA-based Artificial Nanostructures.
    In VARIOUS AUTHORS. Annual Review of Nano Research. (pp. *). WASHINGTON: G. Cao, C. J. Brinker.
  5. M. Sandal, G. Zuccheri, B. Samorì. (2005). Inside the small length and energy scales of the world of the individual biological molecules.
    In V. EVANGELISTA, L. BARSANTI, V. PASSARELLI, P. GUALTIERI. From Cells to Proteins: Imaging Nature across Dimensions. (pp. 111 - 137). VERLAG: Springer.