Probing biopolymers with the atomic force microscope: A review

This short review presents an overview of atomic force microscopy (AFM) of biopolymers and specific examples of some of the biopolymers that have been analyzed by AFM. These specific examples include extracellular polymeric substances on the surfaces of bacterial biofilms, condensed DNA, DNA constructs, and DNA-protein interactions. In addition, two examples are presented for AFM analyses of proteins: laminin flexing its arms in solution and neurofilaments entropically brushing away the space around themselves.

[1]  L. Pietrasanta,et al.  DNA toroids: stages in condensation. , 1999, Biochemistry.

[2]  O. Stemmann,et al.  Probing the Saccharomyces cerevisiae centromeric DNA (CEN DNA)-binding factor 3 (CBF3) kinetochore complex by using atomic force microscopy. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[3]  C. le Grimellec,et al.  Visualization of trp repressor and its complexes with DNA by atomic force microscopy. , 1998, Biophysical journal.

[4]  G. Georgiou,et al.  Molecular determinants of bacterial adhesion monitored by atomic force microscopy. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[5]  N. Seeman,et al.  Ligation of DNA Triangles Containing Double Crossover Molecules , 1998 .

[6]  N. Seeman,et al.  Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.

[7]  J. Hoh,et al.  Functional protein domains from the thermally driven motion of polypeptide chains: A proposal , 1998, Proteins.

[8]  Z. Shao,et al.  Submolecular resolution of single macromolecules with atomic force microscopy , 1998, FEBS letters.

[9]  A. Engel,et al.  Mapping flexible protein domains at subnanometer resolution with the atomic force microscope , 1998, FEBS letters.

[10]  G. Semenza,et al.  Measuring elasticity of biological materials by atomic force microscopy , 1998, FEBS letters.

[11]  C. H. Chen,et al.  Structures and dynamic motion of laminin-1 as observed by atomic force microscopy. , 1998, Biochemistry.

[12]  B. D. de Grooth,et al.  Direct visualization of dynamic protein-DNA interactions with a dedicated atomic force microscope. , 1998, Biophysical journal.

[13]  Jason Cleveland,et al.  Energy dissipation in tapping-mode atomic force microscopy , 1998 .

[14]  H. Hansma,et al.  DNA condensation for gene therapy as monitored by atomic force microscopy. , 1998, Nucleic acids research.

[15]  R. Marchant,et al.  Atomic force microscopy for characterization of the biomaterial interface. , 1998, Biomaterials.

[16]  R. Levinsky,et al.  Lipid-mediated enhancement of transfection by a nonviral integrin-targeting vector. , 1998, Human gene therapy.

[17]  T. Furuno,et al.  Atomic force microscopy for studying gene transfection mediated by cationic liposomes with a cationic cholesterol derivative , 1998, FEBS letters.

[18]  M. Firestone,et al.  Toluene diffusion and reaction in unsaturated Pseudomonas putida biofilms. , 1997, Biotechnology and bioengineering.

[19]  J. Hoh,et al.  Entropic exclusion by neurofilament sidearms: a mechanism for maintaining interfilament spacing. , 1997, Biochemistry.

[20]  H. Hansma,et al.  Phase imaging of moving DNA molecules and DNA molecules replicated in the atomic force microscope. , 1997, Nucleic acids research.

[21]  M. Lieber,et al.  Interaction of DNA‐dependent protein kinase with DNA and with Ku: biochemical and atomic‐force microscopy studies , 1997, The EMBO journal.

[22]  L. Monaco,et al.  Nanoscopic structure of DNA condensed for gene delivery. , 1997, Nucleic acids research.

[23]  P. V. von Hippel,et al.  Transcriptional activation via DNA-looping: visualization of intermediates in the activation pathway of E. coli RNA polymerase x sigma 54 holoenzyme by scanning force microscopy. , 1997, Journal of molecular biology.

[24]  R Balhorn,et al.  AFM analysis of DNA-protamine complexes bound to mica. , 1997, Nucleic acids research.

[25]  M J Doktycz,et al.  Mapping individual cosmid DNAs by direct AFM imaging. , 1997, Genomics.

[26]  J. Wang,et al.  DNA looping by Ku and the DNA-dependent protein kinase. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[27]  M. Jung,et al.  Ku proteins join DNA fragments as shown by atomic force microscopy. , 1997, Cancer research.

[28]  A. Engel,et al.  High resolution imaging of native biological sample surfaces using scanning probe microscopy. , 1997, Current opinion in structural biology.

[29]  Myung-Hwan Whangbo,et al.  Phase imaging and stiffness in tapping-mode atomic force microscopy , 1997 .

[30]  S. Kustu,et al.  Unusual Oligomerization Required for Activity of NtrC, a Bacterial Enhancer-Binding Protein , 1997, Science.

[31]  P K Hansma,et al.  Escherichia coli RNA polymerase activity observed using atomic force microscopy. , 1997, Biochemistry.

[32]  A. P. Gunning,et al.  Comparative imaging of Pseudomonas putida bacterial biofilms by scanning electron microscopy and both DC contact and AC non‐contact atomic force microscopy , 1996 .

[33]  M. Wolfert,et al.  Atomic force microscopic analysis of the influence of the molecular weight of poly(L)lysine on the size of polyelectrolyte complexes formed with DNA. , 1996, Gene therapy.

[34]  Z. Shao,et al.  High‐resolution atomic‐force microscopy of DNA: the pitch of the double helix , 1995, FEBS letters.

[35]  H. Hansma,et al.  Applications for atomic force microscopy of DNA. , 1995, Biophysical journal.

[36]  P. Hansma,et al.  Lattice resolution and solution kinetics on surfaces of amino acid crystals: an atomic force microscope study , 1993 .

[37]  C F Quate,et al.  Imaging crystals, polymers, and processes in water with the atomic force microscope. , 1989, Science.

[38]  Louis Hellemans,et al.  Molecular resolution images of amino acid crystals with the atomic force microscope , 1988, Nature.

[39]  Y. Varshavsky,et al.  A compact form of double‐stranded DNA in solution , 1972, FEBS letters.

[40]  J. Hoh,et al.  Surface-directed DNA condensation in the absence of soluble multivalent cations. , 1998, Nucleic acids research.

[41]  H. Hansma,et al.  Atomic force microscopy and other scanning probe microscopies. , 1998, Current opinion in chemical biology.

[42]  I. Beech.  The potential use of atomic force microscopy for studying corrosion of metals in the presence of bacterial biofilms — an overview , 1996 .

[43]  A. Steele,et al.  An atomic force microscopy study of the biodeterioration of stainless steel in the presence of bacterial biofilms , 1994 .

[44]  N C Seeman,et al.  DNA branched junctions. , 1994, Annual review of biophysics and biomolecular structure.

[45]  C F Quate,et al.  Atomic force microscopy of an organic monolayer. , 1988, Science.