DNA base pair resolution by single molecule force spectroscopy.

The forces that hold complementary strands of DNA together in a double helix, and the role of base mismatches in these, are examined by single molecule force spectroscopy using an atomic force microscope (AFM). These forces are important when considering the binding of proteins to DNA, since these proteins often mechanically stretch the DNA during their action. In AFM measurement of forces, there is an inherent instrumental limitation that makes it difficult to compare results from different experimental runs. This is circumvented by using an oligonucleotide microarray, which allowed a direct comparison of the forces between perfectly matched short oligonucleotides and those containing a single or double mismatch. Through this greatly increased sensitivity, the force contribution of a single AT base pair was derived. The results indicate that the contribution to forces from the stacking interactions is more important than that from hydrogen bonding.

[1]  J. Sader,et al.  Method for the calibration of atomic force microscope cantilevers , 1995 .

[2]  I. Rouzina,et al.  Heat capacity effects on the melting of DNA. 1. General aspects. , 1999, Biophysical journal.

[3]  A J Bard,et al.  Monitoring DNA immobilization and hybridization on surfaces by atomic force microscopy force measurements. , 2001, Analytical chemistry.

[4]  J. Bechhoefer,et al.  Calibration of atomic‐force microscope tips , 1993 .

[5]  I. Rouzina,et al.  Heat capacity effects on the melting of DNA. 2. Analysis of nearest-neighbor base pair effects. , 1999, Biophysical journal.

[6]  M. Hegner,et al.  Molecular Recognition and Adhesion of Individual DNA Strands Studied by Dynamic Force Microscopy , 2001 .

[7]  J. SantaLucia,et al.  Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. , 1999, Biochemistry.

[8]  J. SantaLucia,et al.  A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Timothy Senden,et al.  Experimental Determination of Spring Constants in Atomic Force Microscopy , 1994 .

[10]  Z. Ou-Yang,et al.  Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions. , 2001, Biophysical journal.

[11]  Gil U. Lee,et al.  Direct measurement of the forces between complementary strands of DNA. , 1994, Science.

[12]  P. Hansma,et al.  A nondestructive method for determining the spring constant of cantilevers for scanning force microscopy , 1993 .

[13]  J. Völker,et al.  A more unified picture for the thermodynamics of nucleic acid duplex melting: a characterization by calorimetric and volumetric techniques. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[14]  H. Güntherodt,et al.  Dynamic force spectroscopy of single DNA molecules. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Charles M. Lieber,et al.  Stretching and breaking duplex DNA by chemical force microscopy. , 1997, Chemistry & biology.

[16]  H. Blöcker,et al.  Predicting DNA duplex stability from the base sequence. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[17]  J. Essigmann,et al.  High-fidelity in vivo replication of DNA base shape mimics without Watson–Crick hydrogen bonds , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Ulrich Bockelmann,et al.  MOLECULAR STICK-SLIP MOTION REVEALED BY OPENING DNA WITH PICONEWTON FORCES , 1997 .

[19]  Elizabeth M. Boon,et al.  Morphology of 15-mer Duplexes Tethered to Au(111) Probed Using Scanning Probe Microscopy , 2001 .

[20]  N. Mourougou-Candoni,et al.  Adsorption of Thiolated Oligonucleotides on Gold Surfaces: An Atomic Force Microscopy Study , 2003 .

[21]  E. Evans,et al.  Strength of a weak bond connecting flexible polymer chains. , 1999, Biophysical journal.

[22]  B D Ratner,et al.  Direct measurement of hydrogen bonding in DNA nucleotide bases by atomic force microscopy. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[23]  E. Kool,et al.  Hydrogen bonding, base stacking, and steric effects in dna replication. , 2001, Annual review of biophysics and biomolecular structure.

[24]  M. Rief,et al.  Sequence-dependent mechanics of single DNA molecules , 1999, Nature Structural Biology.

[25]  Hans-Jürgen Butt,et al.  Calculation of thermal noise in atomic force microscopy , 1995 .

[26]  M. Rief,et al.  Mechanical stability of single DNA molecules. , 2000, Biophysical journal.

[27]  M. Hegner,et al.  Temperature dependence of unbinding forces between complementary DNA strands. , 2002, Biophysical journal.

[28]  K. Breslauer.  Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions. , 1995, Methods in Enzymology.

[29]  U. Bockelmann,et al.  Unzipping DNA with optical tweezers: high sequence sensitivity and force flips. , 2002, Biophysical journal.

[30]  I. Rouzina,et al.  Force-induced melting of the DNA double helix 1. Thermodynamic analysis. , 2001, Biophysical journal.

[31]  S. Smith,et al.  Single-molecule studies of DNA mechanics. , 2000, Current opinion in structural biology.

[32]  M. Davies,et al.  Force-induced melting of a short DNA double helix , 2001, European Biophysics Journal.

[33]  Sverre Myhra,et al.  Determination of the spring constants of probes for force microscopy/spectroscopy , 1996 .

[34]  Gil U. Lee,et al.  Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads , 1999, European Biophysics Journal.

[35]  P. Markiewicz,et al.  Identifying locations on a substrate for the repeated positioning of AFM samples , 1997 .