Adenine and cytosine methylation are two important epigenetic modifications of DNA sequences at the levels of the genome and transcriptome. To characterize the differential roles of methylating adenine or cytosine with respect to their hydration properties, we performed conventional MD simulations and free energy perturbation calculations for two particular DNA sequences, namely the brain-derived neurotrophic factor (BDNF) promoter and the R.DpnI-bound DNA that are known to undergo methylation of C5-methyl cytosine and N6-methyl adenine, respectively. We found that a single methylated cytosine has a clearly favorable hydration free energy over cytosine since the attached methyl group has a slightly polar character. In contrast, capping the strongly polar N6 of adenine with a methyl group gives a slightly unfavorable contribution to its free energy of solvation. Performing the same demethylation in the context of a DNA double-strand gave quite similar results for the more solvent-accessible cytosine but much more unfavorable results for the rather buried adenine. Interestingly, the same demethylation reactions are far more unfavorable when performed in the context of the opposite (BDNF or R.DpnI target) sequence. This suggests a natural preference for methylation in a specific sequence context. In addition, free energy calculations for demethylating adenine or cytosine in the context of B-DNA vs. Z-DNA suggest that the conformational B-Z transition of DNA transition is rather a property of cytosine methylated sequences but is not preferable for the adenine-methylated sequences investigated here.

1.
Bennett
,
C. H.
, “
Efficient estimation of free-energy differences from Monte-Carlo data
,”
J. Comput. Phys.
22
,
245
268
(
1976
).
2.
Braaten
,
B. A.
,
Nou
,
X.
,
Kaltenbach
,
L. S.
, and
Low
,
D. A.
, “
Methylation patterns in pap regulatory DNA control pyelonephritis-associated pili phase variation in E. coli
,”
Cell
76
,
577
588
(
1994
).
3.
Chen
,
W. G.
,
Chang
,
Q.
,
Lin
,
Y.
,
Meissner
,
A.
,
West
,
A. E.
,
Griffith
,
E. C.
,
Jaenisch
,
R.
, and
Greenberg
,
M. E.
, “
Derepression of BDNF transcription involves calcium-dependent phosphorylation of MeCP2
,”
Science
302
,
885
889
(
2003
).
4.
Darden
,
T.
,
York
,
D.
, and
Pedersen
,
L. G.
, “
Particle mesh Ewald: An N?log(N) method for Ewald sums in large systems
,”
J. Chem. Phys.
98
,
10089
(
1993
).
5.
Eisenhaber
,
F.
and
Lijnzaad
,
P.
, “
The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies
,”
J. Comput. Chem.
16
,
273
284
(
1995
).
6.
Fatemi
,
M.
,
Pao
,
M. M.
,
Jeong
,
S.
,
Gal-Yam
,
E. N.
,
Egger
,
G.
,
Weisenberger
,
D. J.
, and
Jones
,
P. A.
, “
Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level
,”
Nucleic Acids Res.
33
,
e176
(
2005
).
7.
Foloppe
,
N.
and
MacKerell
,
A. D.
, “
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
,”
J. Comput. Chem.
21
,
86
104
(
2000
).
8.
Frisch
,
M. J.
,
Trucks
,
G. W.
,
Schlegel
,
H. B.
 et al, Gaussian 03, Revision 03, Gaussian, Inc., Wallingford, CT,
2004
.
9.
Furmanchuk
,
A.
,
Shishkin
,
O. V.
,
Issayev
,
O.
,
Gorb
,
L.
, and
Leszczynski
,
J.
, “
New insight on structural properties of hydrated nucleic acid bases from ab initio molecular dynamics
,”
Phys. Chem. Chem. Phys.
12
,
9945
9954
(
2010
).
10.
Hess
,
B.
,
Kutzner
,
C.
,
van der Spoel
,
D.
, and
Lindahl
,
E.
, “
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
,”
J. Chem. Theory Comput.
4
,
435
447
(
2008
).
11.
Hornak
,
V.
and
Simmerling
,
C.
, “
Development of softcore potential functions for overcoming steric barriers in molecular dynamics simulations
,”
J. Molec. Graph. Model.
22
,
405
413
(
2004
).
12.
Jana
,
B.
,
Pal
,
S.
, and
Bagchi
,
B.
, “
Enhanced tetrahedral ordering of water molecules in minor grooves of DNA: Relative role of DNA rigidity, nanoconfinement, and surface specific interactions
,”
J. Phys. Chem.
114
,
3633
3638
(
2010
).
13.
Jorgensen
,
W. L.
,
Chandrasekhar
,
J.
,
Madura
,
J. D.
,
Impey
,
R. W.
, and
Klein
,
M. L.
, “
Comparison of simple potential functions for simulating liquid water
,”
J. Chem. Phys.
79
,
926
935
(
1983
).
14.
Kovacs
,
H.
,
Mark
,
A. E.
, and
van Gunsteren
,
W. F.
, “
Solvent structure at a hydrophobic protein surface
,”
Proteins
27
,
395
404
(
1997
).
15.
Kumar
,
P.
,
Buldyrev
,
S. V.
, and
Stanley
,
H. E.
, “
A tetrahedral entropy for water
,”
Proc. Natl. Acad. Sci. U.S.A.
106
,
22130
22134
(
2009
).
16.
Kypr
,
J.
,
Kejnovská
,
I.
,
Renčiuk
,
D.
, and
Vorlíčková
,
M.
Circular dichroism and conformational polymorphism of DNA
,”
Nucleic Acids Res.
37
,
1713
1725
(
2009
).
17.
Lacks
,
S. A.
,
Mannarelli
,
B. M.
,
Springhorn
,
S. S.
, and
Greenberg
,
B.
, “
Genetic basis of the complementary DpnI and DpnII restriction systems of S. pneumoniae: an intercellular cassette mechanism
,”
Cell
46
,
993
1000
(
1986
).
18.
Liu
,
H.
,
Mulholland
,
N.
,
Fu
,
H. Q.
, and
Zhao
,
K.
, “
Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling
,”
Mol. Cell. Biol.
26
,
2550
2559
(
2006
).
19.
Liu
,
J.
,
Yue
,
Y.
,
Han
,
D.
,
Wang
,
X.
,
Fu
,
Y.
,
Zhang
,
L.
,
Jia
,
G.
,
Yu
,
M.
,
Lu
,
Z.
,
Deng
,
X.
, et al, “
A METTL3 METTL14 complex mediates mammalian nuclear RNA N-6-adenosine methylation
,”
Natur. Chem. Bio.
10
,
93
95
(
2014
).
20.
Lu
,
X. J.
and
Olson
,
W. O.
, “
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures
,”
Nat. Protoc.
3
,
1213
1227
(
2008
).
21.
Mayer-Jung
,
C.
,
Moras
,
D.
, and
Timsit
,
Y.
, “
Hydration and recognition of methylated CpG steps in DNA
,”
EMBO J.
17
,
2709
2718
(
1998
).
22.
Meyer
,
K. D.
and
Jaffrey
,
S. R.
, “
The dynamic epitranscriptome: N-6-methyladenosine and gene expression control
,”
Nat. Rev. Mol. Cell Bio.
15
,
313
326
(
2014
).
23.
Mobley
,
D. L.
,
Chodera
,
J. D.
, and
Dill
,
K. A.
, “
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
,”
J. Chem. Phys.
125
,
084902
(
2006
).
24.
Pohorille
,
A.
,
Jarzynski
,
C.
, and
Chipot
,
C.
, “
Good Practices in Free-Energy Calculations
,”
J. Phys. Chem. B
114
,
10235
10253
(
2010
).
25.
Pruunsild
,
P.
,
Kazantseva
,
A.
,
Aid
,
T.
,
Palm
,
K.
, and
Timmusk
,
T.
, “
Dissecting the human BDNF locus: Bidirectional transcription, complex splicing, and multiple promoters
,”
Genomics
90
,
397
406
(
2007
).
26.
Ratel
,
D.
,
Ravanat
,
J. L.
,
Berger
,
F.
, and
Wion
,
D.
, “
N6-methyladenine: The other methylated base of DNA
,”
Bioessays
28
,
309
315
(
2006
).
27.
Siwek
,
W.
,
Czapinska
,
H.
,
Bochtler
,
M.
,
Bujnicki
,
J. M.
, and
Skowronek
,
K.
, “
Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI
,”
Nucleic Acids Res.
40
,
7563
7572
(
2012
).
28.
van Gunsteren
,
W. F.
and
Berendsen
,
H. G. C.
, “
A leap-frog algorithm for stochastic dynamics
,”
Mol. Simul.
1
,
173
185
(
1988
).
29.
Vanommeslaeghe
,
K.
,
Hatcher
,
E.
,
Acharya
,
C.
,
Kundu
,
S.
,
Zhong
,
S.
,
Shim
,
J.
,
Darian
,
E.
,
Guvench
,
O.
,
Lopes
,
P.
,
Vorobyov
,
I.
 et al “
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
,”
J. Comput. Chem.
31
,
671
690
(
2010
).
30.
Wilson
,
G. G.
, “
Organization of restriction-modification systems
,”
Nucleic Acids Res.
19
,
2539
2566
(
1991
).
You do not currently have access to this content.