Molecular Combing of DNA: Methods and Applications
DOI:
https://doi.org/10.13052/same2245-4551.116Keywords:
Molecular combing of DNA, DNA stretching, AFMAbstract
First proposed in 1994, molecular combing of DNA is a technique that allows
adsorption and alignment of DNA on the surface with no need for prior modi-
fication of the molecule. Since then, many variations of the original method
have been devised and used in a wide range of applications from genomic
studies to nanoelectronics. While molecular combing has been applied in a
variety of DNA-related studies, no comprehensive review has been published
on different combing methods proposed so far. In this review, the underly-
ing mechanisms of molecular combing of DNA are described followed by
discussion of the main methods in molecular combing as well as its major
applications in nanotechnology.
Downloads
References
L. B. Kish, Phys. Lett. A, 305, 144–149 (2002).
M. Lundstrom, Science, 299, 210–211 (2003).
A. M. van Oijen, J. J. Loparo, Annu. Rev. Biophys., 39, 429–448 (2010).
A. Stewart, Mol. Med. Today, 4, 2 (1998).
J. Herrick, A. Bensimon, Chromosome Res., 7, 409–423 (1999).
F. Zamora, M. P. Amo-Ochoa, P. J. Sanz Miguel, O. Castillo, Inorg. Chim. Acta., 362,
–706 (2009).
C. M. Niemeyer, Curr. Opin. Chem. Biol., 4, 609–618 (2004).
R. Chhabra, J. Sharma, Y. Liu, S. Rinker, H. Yan, Adv. Drug Deliver. Rev., 62, 617–625
(2010).
E. Farjami, L. Clima, K. Gothelf, E. E. Ferapontova, Anal. Chem., 83, 1594–1602
(2011).
C. G. Baumann, V. A. Bloomfield, S. B. Smith, C. Bustamante, M. D. Wang, S. M.
Block, Biophys. J., 78, 1965–1978 (2000).
H. Yokota, J. Sunwoo, M. Sarikaya, G. van den Engh, R. Aebersold, Anal. Chem., 71,
–4422 (1999).
L. M. Bellan, J. D. Cross, E. A. Strychalski, J. Moran-Mirabal, H. G. Craighead, Nano
Lett., 6, 2526–2530 (2006).
L. J. Guo, X. Cheng, C.-F. Chou, Nano Lett., 4, 69–73 (2004).
D. J. Doolittle, G. Muller, H. E. Scribner, Chem. Toxic., 25, 399–405 (1987).
D. Bensimon, A. J. Simon, V. Croquette, A. Bensimon, Phys. Rev. Lett., 74, 4754–4757
(1995).
A. Bensimon, A. Simon, A. Chiffaudel, V. Croquette, F. Heslot, D. Bensimon, Science,
, 2096–2097 (1994).
Z. Esmail Nazari, L. Gurevich, Beilstein J. Nanotechnol., in press (2013).
D. C. G. Klein, L. Gurevich, J. W. Janssen, L. P. Kouwenhoven, J. D. Carbeck, L. L.
Sohn, Appl. Phys. Lett., 78, 2396–2398 (2001).
A. Benke, M. Mertig, W. Pompe, Nanotechnology, 22, 035304 (2011).
J. F. Allemand, D. Bensimon, L. Jullien, A. Bensimon, V. Croquette, Biophys. J., 73,
–2070 (1997).
A. Cerf, C. Thibault, M. Genevi`eve, C. Vieu, Microelectron. Eng., 86, 1419–1423
(2009).
J. Guan, L. J. Lee, PNAS, 102, 18321–18325 (2005).
J. Herrick, A. Bensimon, Methods Mol. Biol., 521, 71–101 (2009).
J. Herrick, A. Bensimon, Biochimie, 81, 859–871 (1999).
Z.E. Nazari and L. Gurevich
S. B. Smith, Y. Cui, C. Bustamante, Science, 271, 795–799 (1996).
T. Strick, J. Allemand, V. Croquette, D. Bensimon, Prog. Biophys. Mol. Biol., 74, 115–
(2000).
M. Rief, H. Clausen-Schaumann, H. E. Gaub, Nat. Struct. Biol., 6, 346–349 (1999).
H. Clausen-Schaumann, M. Rief, C. Tolksdorf, H. E. Gaub, Biophys. J., 78, 1997–2007
(2000).
J. H. Kim, W.-X. Shi, R. G. Larson, Langmuir, 23, 755–764 (2007).
T. R. Strick, J.-F. Allemand, D. Bensimon, V. Croquette, Biophys. J., 74, 2016–2028
(1998).
H.-Z. Zheng, D.-W. Pang, Z.-X. Lu, Z.-L. Zhang, Z.-X. Xie, Biophys. Chem., 112, 27–33
(2004).
H. Yokota, F. Johnson, H. Lu, R. M. Robinson, A. M. Belu, M. D. Garrison, B. D. Ratner,
B. J. Trask, D. L. Miller, Nucleic Acids Res., 25, 1064–1070 (1997).
X. Michalet, R. Ekong, F. Fougerousse, S. Rousseaux, C. Schurra, N. Hornigold, M. van
Slegtenhorst, J. Wolfe, S. Povey, J. S. Beckmann, A. Bensimon, Science, 277, 1518–1523
(1997).
K. J. Kwak, S. Yoda, M. Fujihira, Appl. Surf. Sci., 210, 73–78 (2003).
J. Li, C. Bai, C. Wang, C. Zhu, Z. Lin, Q. Li, E. Cao, Nucleic Acids Res., 26, 4785–4786
(1998).
Z. Deng, C. Mao, Nano Lett., 3, 1545–1548 (2003).
T. Heim, T. M ́elin, D. Deresmes, D. Vuillaume, Appl. Phys. Lett., 85, 2637–2639 (2004).
M. Oshige, K. Yamaguchi, S.-I. Matsuura, H. Kurita, A. Mizuno, S. Katsura, Anal.
Biochem., 400, 145–147 (2010).
H. Nakao, H. Hayashi, T. Yoshino, S. Sugiyama, K. Otobe, T. Ohtani, Nano Lett., 2,
–479 (2002).
G. Liu, J. Zhao, Langmuir , 22, 2923–2926 (2006).
J. Zhang, Y. Ma, S. Stachura, H. He, Langmuir , 21, 4180–4184 (2005).
Z. Esmail Nazari, L. Gurevich, In preparation.
C.-H. Hsu, C. Chen, M.-L. Jou, A. Y.-L. Lee, Y.-C. Lin, Y.-P. Yu, W.-T. Huang, S.-H.
Wu, Nucleic Acids Res., 33, 4053–4064 (2005).
W. Zhang, J. P. Bond, C. F. Anderson, T. M. Lohman, M. T. Record, PNAS, 93, 2511–
(1996).
L. Gurevich, T. W. Poulsen, O. Z. Andersen, N. L. Kildeby, P. Fojan, J. Nanosci.
Nanotechnol., 10, 1–5 (2010).
P. Fojan, K. Jensen, L. Gurevich, IEEE Xplore 2011, DOI 10.1109/Wireless-
vitae.2011.5940906.
D. Nyamjav, A. Ivanisevic, Adv. Mater., 15, 1805–1809 (2003).
D. Nyamjav, A. Ivanisevic, Biomaterials, 26, 2749–2757 (2005).
H. Nakao, M. Gad, S. Sugiyama, K. Otobe, T. Ohtani, J. Am. Chem. Soc., 125, 7162–
(2003).
M. Gad, S. Sugiyama, T. Ohtani, J. Biomol. Struct. Dyn., 21, 387–393 (2003).
J. Opitz, F. Braun, R. Seidel, W. Pompe, B. Voit, M. Mertig, Nanotechnology, 15, 717–
(2004).
H. Kudo, K. Suga, M. Fujihira, Colloids Surf. A., 313, 651–654 (2008).
Molecular Combing of DNA: Methods and Applications 147
S. Gad, A. Aurias, N. Puget, A. Mairal, C. Schurra, M. Montagna, S. Pages, V. Caux,
S. Mazoyer, A. Bensimon, D. Stoppa-lyonnet, Genes, Chromosomes Cancer, 31, 75–84
(2001).
A. V. de Barros, T. S. Sczepanski, J. Cabrero, J. P. M. Camacho, M. R. Vicari, R. F.
Artoni, Aquaculture, 322, 47–50 (2011).
S. Caburet, C. Conti, A. Bensimon, Trends Biotechnol., 20, 344–350 (2002).
D. M. Czajkowsky, J. Liu, J. L. Hamlin, Z. Shao, J. Mol. Biol., 375, 12–19 (2008).
J. N. Bianco, J. Poli, J. Saksouk, J. Bacal, M. J. Silva, K. Yoshida, Y.-L. Lin, H. Tourri`ere,
A. Lengronne, P. Pasero, Methods, 57, 149–157 (2012).
K. Koutroumpas, J. Lygeros, Automatica, 47, 1156–1164 (2011).
R. Lebofsky, R. Heilig, M. Sonnleitner, J. Weissenbach, A. Bensimon, Mol. Biol. Cell.,
, 5337–5345 (2006).
L. Fu, L. Cao, Y. Liu, D. Zhu, Adv. Colloid Interface Sci., 111, 133–157 (2004).
T. H. Labean, H. Li, Nano Today, 2, 26–35 (2007).
H. Li, J. D. Carter, T. H. LaBean, Materials Today, 12, 24–32 (2009).
A. J. Storm, J. van Noort, S. de Vries, C. Dekker, Appl. Phys. Lett., 79, 3881–3883
(2001).
C. G ́omez-Navarro, F. Moreno-Herrero, P. J. de Pablo, J. Colchero, J. G ́omez-Herrero,
A. M. Bar ́o, PNAS, 99, 8484–8487 (2002).
P. J. de Pablo, F. Moreno-Herrero, J. Colchero, J. G ́omez Herrero, P. Herrero, A. M.
Bar ́o, P. Ordej ́on, J. M. Soler, E. Artacho, Phys. Rev. Lett., 85, 4992–4995 (2000).
K. Iguchi, Int. J. Mod. Phys. B, 17, 2565–2578 (2003).
H.-W. Fink, C. Sch ̈onenberger, Nature, 398, 407–410 (1999).
O. Legrand, D. Cˆote, U. Bockelmann, Phys. Rev. E, 73, 0319251–6 (2006).
L. Cai, H. Tabata, T. Kawai, Appl. Phys. Lett., 77, 3105–3106 (2000).
Y. Okahata, T. Kobayashi, H. Nakayama, K. Tanaka, Supramol. Sci., 5, 317–320 (1998).
A. Y. Kasumov, M. Kociak, S. Gu ́eron, B. Reulet, V. T. Volkov, D. V Klinov, H. Bouchiat,
Science, 291, 280–282 (2001).
M. Taniguchi, T. Kawai, Physica E, 33, 1–12 (2006).
F. Moreno-Herrero, P. Herrero, J. Colchero, C. G ́omez-Navarro, J. G ́omez-Herrero, A.
M. Bar ́o, Nanotechnology, 14, 128–133 (2003).
H. Yang, K. L. Metera, H. F. Sleiman, Coord. Chem. Rev., 254, 2403–2415 (2010).
A. D. Chepelianskii, D. Klinov, A. Kasumov, S. Gu ́eron, O. Pietrement, S. Lyonnais, H.
Bouchiat, New J. Phys., 13, 063046 (2011).
M. Bockrath, N. Markovic, A. Shepard, M. Tinkham, L. Gurevich, L. P. Kouwenhoven,
M. W. Wu, L. L. Sohn, Nano Lett., 2, 187–190 (2002).
L. Cai, H. Tabata, T. Kawai, Nanotechnology, 12, 211–216 (2001).
P. Maragakis, R. L. Barnett, E. Kaxiras, M. Elstner, T. Frauenheim, Phys. Rev. B, 66,
–1–4 (2002).
C.-H. Hsu, C. Chen, M.-L. Jou, A. Y.-L. Lee, Y.-C. Lin, Y.-P. Yu, W.-T. Huang, S.-H.
Wu, Nucleic Acids Res., 33, 4053–4064 (2005).
H. Yokota, D. A. Nickerson, B. J. Trask, G. van den Engh, M. Hirst, I. Sadowski, R.
Aebersold, Anal. Biochem., 264, 158–164 (1998).
H. Nakao, H. Shiigi, Y. Yamamoto, S. Tokonami, T. Nagaoka, S. Sugiyama, T. Ohtani,
Nano Lett., 3, 1391–1394 (2003).
Z.E. Nazari and L. Gurevich
K. Keren, M. Krueger, R. Gilad, G. Ben-Yoseph, U. Sivan, E. Braun, Science, 297, 72–75
(2002).
K. Keren, R. S. Berman, E. Buchstab, U. Sivan, E. Braun, Science, 302, 1380–1382
(2003).
H. Cohen, T. Sapir, N. Borovok, T. Molotsky, R. Di Felice, A. B. Kotlyar, D. Porath,
Nano Letters 7, 981–986 (2007)