Efforts to study the polymer physics of DNA confined in nanochannels have been stymied by a lack of consensus regarding its wall depletion length. We have measured this quantity in 38 nm wide, square silicon dioxide nanochannels for five different ionic strengths between 15 mM and 75 mM. Experiments used the Bionano Genomics Irys platform for massively parallel data acquisition, attenuating the effect of the sequence-dependent persistence length and finite-length effects by using nick-labeled E. coli genomic DNA with contour length separations of at least 30 µm (88 325 base pairs) between nick pairs. Over 5 × 106 measurements of the fractional extension were obtained from 39 291 labeled DNA molecules. Analyzing the stretching via Odijk’s theory for a strongly confined wormlike chain yielded a linear relationship between the depletion length and the Debye length. This simple linear fit to the experimental data exhibits the same qualitative trend as previously defined analytical models for the depletion length but now quantitatively captures the experimental data.
REFERENCES
1.
W.
Reisner
, K. J.
Morton
, R.
Riehn
, Y. M.
Wang
, Z.
Yu
, M.
Rosen
, J. C.
Sturm
, S. Y.
Chou
, E.
Frey
, and R. H.
Austin
, “Statics and dynamics of single DNA molecules confined in nanochannels
,” Phys. Rev. Lett.
94
, 196101
(2005
).2.
M.
Daoud
and P. G.
de Gennes
, “Statistics of macromolecular solutions trapped in small pores
,” J. Phys.
38
, 85
–93
(1977
).3.
T.
Odijk
, “The statistics and dynamics of confined or entangled stiff polymers
,” Macromolecules
16
, 1340
–1344
(1983
).4.
T.
Odijk
, “Scaling theory of DNA confined in nanochannels and nanoslits
,” Phys. Rev. E
77
, 060901
(2008
).5.
Y.
Wang
, D. R.
Tree
, and K. D.
Dorfman
, “Simulation of DNA extension in nanochannels
,” Macromolecules
44
, 6594
–6604
(2011
).6.
A.
Muralidhar
, D. R.
Tree
, Y.
Wang
, and K. D.
Dorfman
, “Interplay between chain stiffness and excluded volume of semiflexible polymers confined in nanochannels
,” J. Chem. Phys.
140
, 084905
(2014
).7.
L.
Dai
and P. S.
Doyle
, “Comparisons of a polymer in confinement versus applied force
,” Macromolecules
46
, 6336
–6344
(2013
).8.
L.
Dai
, J. R. C.
van der Maarel
, and P. S.
Doyle
, “Extended de Gennes regime of DNA confined in a nanochannel
,” Macromolecules
47
, 2445
–2450
(2014
).9.
A.
Muralidhar
, D. R.
Tree
, and K. D.
Dorfman
, “Backfolding of wormlike chains confined in nanochannels
,” Macromolecules
47
, 8446
–8458
(2014
).10.
A.
Muralidhar
and K. D.
Dorfman
, “Backfolding of DNA confined in nanotubes: Flory theory versus the two-state cooperativity model
,” Macromolecules
49
, 1120
–1126
(2016
).11.
A.
Muralidhar
, M. J.
Quevillon
, and K. D.
Dorfman
, “The backfolded Odijk regime for wormlike chains confined in rectangular nanochannels
,” Polymers
8
, 79
(2016
).12.
Y.
Yang
, T. W.
Burkhardt
, and G.
Gompper
, “Free energy and extension of a semiflexible polymer in cylindrical confining geometries
,” Phys. Rev. E
76
, 011804
(2007
).13.
T. W.
Burkhardt
, Y.
Yang
, and G.
Gompper
, “Fluctuations of a long, semiflexible polymer in a narrow channel
,” Phys. Rev. E
82
, 041801
(2010
).14.
E.
Werner
and B.
Mehlig
, “Confined polymers in the extended de Gennes regime
,” Phys. Rev. E
90
, 062602
(2014
).15.
E.
Werner
, G. K.
Cheong
, D.
Gupta
, K. D.
Dorfman
, and B.
Mehlig
, “One-parameter scaling theory for DNA extension in a nanochannel
,” Phys. Rev. Lett.
119
, 268102
(2017
).16.
J. Z.
Chen
, “Self-avoiding wormlike chain confined in a cylindrical tube: Scaling behavior
,” Phys. Rev. Lett.
121
, 037801
(2018
).17.
W.
Reisner
, J. P.
Beech
, N. B.
Larsen
, H.
Flyvbjerg
, A.
Kristensen
, and J. O.
Tegenfeldt
, “Nanoconfinement-enhanced conformational response of single DNA molecules to changes in ionic environment
,” Phys. Rev. Lett.
99
, 058302
(2007
).18.
F.
Persson
, P.
Utko
, W.
Reisner
, N. B.
Larsen
, and A.
Kristensen
, “Confinement spectroscopy: Probing single DNA molecules with tapered nanochannels
,” Nano Lett.
9
, 1382
–1385
(2009
).19.
V.
Iarko
, E.
Werner
, L.
Nyberg
, V.
Müller
, J.
Fritzsche
, T.
Ambjörnsson
, J.
Beech
, J.
Tegenfeldt
, K.
Mehlig
, F.
Westerlund
, and B.
Mehlig
, “Extension of nanoconfined DNA: Quantitative comparison between experiment and theory
,” Phys. Rev. E
92
, 062701
(2015
).20.
D.
Gupta
, J.
Sheats
, A.
Muralidhar
, J. J.
Miller
, D. E.
Huang
, S.
Mahshid
, K. D.
Dorfman
, and W.
Reisner
, “Mixed confinement regimes during equilibrium confinement spectroscopy of DNA
,” J. Chem. Phys.
140
, 214901
(2014
).21.
D.
Gupta
, J. J.
Miller
, A.
Muralidhar
, S.
Mahshid
, W.
Reisner
, and K. D.
Dorfman
, “Experimental evidence of weak excluded volume effects for nanochannel confined DNA
,” ACS Macro Lett.
4
, 759
–763
(2015
).22.
W. F.
Reinhart
, J. G.
Reifenberger
, D.
Gupta
, A.
Muralidhar
, J.
Sheats
, H.
Cao
, and K. D.
Dorfman
, “Distribution of distances between DNA barcode labels in nanochannels close to the persistence length
,” J. Chem. Phys.
142
, 064902
(2015
).23.
D.
Gupta
, A. B.
Bhandari
, and K. D.
Dorfman
, “Evaluation of Blob theory for the diffusion of DNA in nanochannels
,” Macromolecules
51
, 1748
–1755
(2018
).24.
E. T.
Lam
, A.
Hastie
, C.
Lin
, D.
Ehrlich
, S. K.
Das
, M. D.
Austin
, P.
Deshpande
, H.
Cao
, N.
Nagarajan
, M.
Xiao
, and P.-Y.
Kwok
, “Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly
,” Nat. Biotechnol.
30
, 771
(2012
).25.
A. V.
Dobrynin
, “Electrostatic persistence length of semiflexible and flexible polyelectrolytes
,” Macromolecules
38
, 9304
–9314
(2005
).26.
D.
Stigter
, “Interactions of highly charged colloidal cylinders with applications to double-stranded DNA
,” Biopolymers
16
, 1435
–1448
(1977
).27.
D. R.
Tree
, A.
Muralidhar
, P. S.
Doyle
, and K. D.
Dorfman
, “Is DNA a good model polymer?
,” Macromolecules
46
, 8369
–8382
(2013
).28.
W.
Reisner
, J. N.
Pedersen
, and R. H.
Austin
, “DNA confinement in nanochannels: Physics and biological applications
,” Rep. Prog. Phys.
75
, 106601
(2012
).29.
J.
Sheats
, J. G.
Reifenberger
, H.
Cao
, and K. D.
Dorfman
, “Measurements of DNA barcode label separations in nanochannels from time-series data
,” Biomicrofluidics
9
, 064119
(2015
).30.
J. G.
Reifenberger
, K. D.
Dorfman
, and H.
Cao
, “Topological events in single molecules of E. coli DNA confined in nanochannels
,” Analyst
140
, 4887
–4894
(2015
).31.
A.
Jain
, J.
Sheats
, J. G.
Reifenberger
, H.
Cao
, and K. D.
Dorfman
, “Modeling the relaxation of internal DNA segments during genome mapping in nanochannels
,” Biomicrofluidics
10
, 054117
(2016
).32.
H.-M.
Chuang
, J. G.
Reifenberger
, H.
Cao
, and K. D.
Dorfman
, “Sequence-dependent persistence length of long DNA
,” Phys. Rev. Lett.
119
, 227802
(2017
).33.
J. G.
Reifenberger
, H.
Cao
, and K. D.
Dorfman
, “Odijk excluded volume interactions during the unfolding of DNA confined in a nanochannel
,” Macromolecules
51
, 1172
–1180
(2018
).34.
R. H.
Doremus
, “Diffusion of water in silica glass
,” J. Mater. Res.
10
, 2379
–2389
(1995
).35.
G. A.
Parks
, “The isoelectric points of solid oxides, solid hydroxides, and aqueous hydroxo complex systems
,” Chem. Rev.
65
, 177
–198
(1965
).36.
H.
Chang
, F.
Kosari
, G.
Andreadakis
, M.
Alam
, G.
Vasmatzis
, and R.
Bashir
, “DNA-mediated fluctuations in ionic current through silicon oxide nanopore channels
,” Nano Lett.
4
, 1551
–1556
(2004
).37.
D.
Stigter
, “The charged colloidal cylinder with a Gouy double layer
,” J. Colloid Interface Sci.
53
, 296
–306
(1975
).38.
G. S.
Manning
, “Limiting laws and counterion condensation in polyelectrolyte solutions. I. Colligative properties
,” J. Chem. Phys.
51
, 924
–933
(1969
).39.
J. A.
Schellman
and D.
Stigter
, “Electrical double layer, zeta potential, and electrophoretic charge of double-stranded DNA
,” Biopolymers
16
, 1415
–1434
(1977
).40.
S. H.
Behrens
and D. G.
Grier
, “The charge of glass and silica surfaces
,” J. Chem. Phys.
115
, 6716
–6721
(2001
).41.
42.
T.
Hiemstra
, J.
De Wit
, and W.
Van Riemsdijk
, “Multisite proton adsorption at the soil/solution interface of (hydr) oxides: A new approach. II. Application to various important (hydr) oxides
,” J. Colloid Interface Sci.
133
, 105
–117
(1989
).43.
L. H.
Thamdrup
, A.
Klukowska
, and A.
Kristensen
, “Stretching DNA in polymer nanochannels fabricated by thermal imprint in PMMA
,” Nanotechnology
19
, 125301
(2008
).44.
P.
Utko
, F.
Persson
, A.
Kristensen
, and N. B.
Larsen
, “Injection molded nanofluidic chips: Fabrication method and functional tests using single-molecule DNA experiments
,” Lab Chip
11
, 303
–308
(2011
).45.
E.
Werner
, F.
Persson
, F.
Westerlund
, J. O.
Tegenfeldt
, and B.
Mehlig
, “Orientational correlations in confined DNA
,” Phys. Rev. E
86
, 041802
(2012
).46.
M.
Alizadehheidari
, E.
Werner
, C.
Noble
, M.
Reiter-Schad
, L. K.
Nyberg
, J.
Fritzsche
, B.
Mehlig
, J. O.
Tegenfeldt
, T.
Ambjörnsson
, F.
Persson
, and F.
Westerlund
, “Nanoconfined circular and linear DNA: Equilibrium conformations and unfolding kinetics
,” Macromolecules
48
, 871
–878
(2015
).47.
A. R.
Hastie
, L.
Dong
, A.
Smith
, J.
Finklestein
, E. T.
Lam
, N.
Huo
, H.
Cao
, P.-Y.
Kwok
, K. R.
Deal
, J.
Dvorak
, M.-C.
Luo
, Y.
Gu
, and M.
Xiao
, “Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome
,” PLoS One
8
, e55864
(2013
).48.
A. C. Y.
Mak
, Y. Y. Y.
Lai
, E. T.
Lam
, T.-P.
Kwok
, A. K. Y.
Leung
, A.
Poon
, Y.
Mostovoy
, A. R.
Hastie
, W.
Stedman
, T.
Anantharaman
, W.
Andrews
, X.
Zhou
, A. W. C.
Pang
, H.
Dai
, C.
Chu
, C.
Lin
, J. J. K.
Wu
, C. M. L.
Li
, J.-W.
Li
, A. K. Y.
Yim
, S.
Chan
, J.
Sibert
, Ž.
Džakula
, H.
Cao
, S.-M.
Yiu
, T.-F.
Chan
, K. Y.
Yip
, M.
Xiao
, and P.-Y.
Kwok
, “Genome-wide structural variation detection by genome mapping on nanochannel arrays
,” Genetics
202
, 351
–362
(2016
).49.
S. K.
Das
, M. D.
Austin
, M. C.
Akana
, P.
Deshpande
, H.
Cao
, and M.
Xiao
, “Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes
,” Nucleic Acids Res.
38
, e177
(2010
).50.
T.
Su
, S. K.
Das
, M.
Xiao
, and P. K.
Purohit
, “Transition between two regimes describing internal fluctuation of DNA in a nanochannel
,” PLoS One
6
, e16890
(2011
).51.
A.
Valouev
, Shotgun Optical Mapping: A Comprehensive Statistical and Computational Analysis
(University of Southern California
, 2006
).52.
U.
Dobrindt
, F.
Agerer
, K.
Michaelis
, A.
Janka
, C.
Buchrieser
, M.
Samuelson
, C.
Svanborg
, G.
Gottschalk
, H.
Karch
, and J.
Hacker
, “Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays
,” J. Bacteriol.
185
, 1831
–1840
(2003
).53.
T. M.
Conrad
, A. R.
Joyce
, M. K.
Applebee
, C. L.
Barrett
, B.
Xie
, Y.
Gao
, and B. Ø.
Palsson
, “Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations
,” Genome Biol.
10
, R118
(2009
).54.
P. L.
Freddolino
, S.
Amini
, and S.
Tavazoie
, “Newly identified genetic variations in common Escherichia coli MG1655 stock cultures
,” J. Bacteriol.
194
, 303
–306
(2012
).55.
C.-C.
Hsieh
, A.
Balducci
, and P. S.
Doyle
, “Ionic effects on the equilibrium dynamics of DNA confined in nanoslits
,” Nano Lett.
8
, 1683
–1688
(2008
).56.
B.
Kundukad
, J.
Yan
, and P. S.
Doyle
, “Effect of YOYO-1 on the mechanical properties of DNA
,” Soft Matter
10
, 9721
–9728
(2014
).57.
K.
Günther
, M.
Mertig
, and R.
Seidel
, “Mechanical and structural properties of YOYO-1 complexed DNA
,” Nucleic Acids Res.
38
, 6526
–6532
(2010
).58.
K. D.
Dorfman
, “The statistical segment length of DNA: Opportunities for biomechanical modeling in polymer physics and next-generation genomics
,” J. Biomech. Eng.
140
, 020801
(2018
).59.
Y.
Wang
, W. F.
Reinhart
, D. R.
Tree
, and K. D.
Dorfman
, “Resolution limit for DNA barcodes in the Odijk regime
,” Biomicrofluidics
6
, 014101
(2012
).60.
R.
Van der Hofstad
, F.
Den Hollander
, and W.
König
, “Weak interaction limits for one-dimensional random polymers
,” Probab. Theory Relat. Fields
125
, 483
–521
(2003
).61.
K.
Jo
, D. M.
Dhingra
, T.
Odijk
, J. J.
de Pablo
, M. D.
Graham
, R.
Runnheim
, D.
Forrest
, and D. C.
Schwartz
, “A single-molecule barcoding system using nanoslits for DNA analysis
,” Proc. Natl. Acad. Sci. U. S. A.
104
, 2673
–2678
(2007
).62.
C.
Zhang
, F.
Zhang
, J. A.
van Kan
, and J. R. C.
van der Maarel
, “Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel
,” J. Chem. Phys.
128
, 225109
(2008
).63.
D. J.
Bonthuis
, C.
Meyer
, D.
Stein
, and C.
Dekker
, “Conformation and dynamics of DNA confined in slitlike nanofluidic channels
,” Phys. Rev. Lett.
101
, 108303
(2008
).64.
Y.
Kim
, K. S.
Kim
, K. L.
Kounovsky
, R.
Chang
, G. Y.
Jung
, J. J.
de Pablo
, K.
Jo
, and D. C.
Schwartz
, “Nanochannel confinement: DNA stretch approaching full contour length
,” Lab Chip
11
, 1721
–1729
(2011
).65.
P.-k.
Lin
, C.-C.
Hsieh
, Y.-L.
Chen
, and C.-F.
Chou
, “Effects of topology and ionic strength on double-stranded DNA confined in nanoslits
,” Macromolecules
45
, 2920
–2927
(2012
).66.
K. L.
Kounovsky-Shafer
, J. P.
Hernández-Ortiz
, K.
Jo
, T.
Odijk
, J. J.
De Pablo
, and D. C.
Schwartz
, “Presentation of large DNA molecules for analysis as nanoconfined dumbbells
,” Macromolecules
46
, 8356
–8368
(2013
).67.
J.
Lee
, S.
Kim
, H.
Jeong
, G. Y.
Jung
, R.
Chang
, Y.-L.
Chen
, and K.
Jo
, “Nanoslit confined DNA at low ionic strengths
,” ACS Macro Lett.
3
, 926
–930
(2014
).68.
K. L.
Kounovsky-Shafer
, J. P.
Hernandez-Ortiz
, K.
Potamousis
, G.
Tsvid
, M.
Place
, P.
Ravindran
, K.
Jo
, S.
Zhou
, T.
Odijk
, J. J.
de Pablo
, and D. C.
Schwartz
, “Electrostatic confinement and manipulation of DNA molecules for genome analysis
,” Proc. Natl. Acad. Sci. U. S. A.
114
, 13400
–13405
(2017
).69.
G. K.
Cheong
, X.
Li
, and K. D.
Dorfman
, “Wall depletion length of a channel-confined polymer
,” Phys. Rev. E
95
, 022501
(2017
).70.
S. R.
Quake
, H.
Babcock
, and S.
Chu
, “The dynamics of partially extended single molecules of DNA
,” Nature
388
, 151
(1997
).71.
T.
Berge
, N. S.
Jenkins
, R. B.
Hopkirk
, M. J.
Waring
, J. M.
Edwardson
, and R. M.
Henderson
, “Structural perturbations in DNA caused by bis-intercalation of ditercalinium visualised by atomic force microscopy
,” Nucleic Acids Res.
30
, 2980
–2986
(2002
).72.
A.
Sischka
, K.
Toensing
, R.
Eckel
, S. D.
Wilking
, N.
Sewald
, R.
Ros
, and D.
Anselmetti
, “Molecular mechanisms and kinetics between DNA and DNA binding ligands
,” Biophys. J.
88
, 404
–411
(2005
).73.
M.
Maaloum
, P.
Muller
, and S.
Harlepp
, “DNA-intercalator interactions: Structural and physical analysis using atomic force microscopy in solution
,” Soft Matter
9
, 11233
–11240
(2013
).74.
N.
Shi
and V. M.
Ugaz
, “An entropic force microscope enables nano-scale conformational probing of biomolecules
,” Small
10
, 2553
–2557
(2014
).© 2018 Author(s).
2018
Author(s)
You do not currently have access to this content.
