Chemical Physics Letters

Transformation characteristic of A-DNA in salt solution revealed through molecular

dynamics simulation
--Manuscript Draft--

Manuscript Number: CPLETT-20-4648

Article Type: Research paper

Section/Category: Biomolecules

Keywords: A-DNA structure; Ionic valency; Temperature; Molecular dynamics simulations; Salt
solution

Abstract: In aqueous solution, A-DNA eventually will be the stable state on the B-form as time
goes on. The stability influence of ionic valence and temperature on the A-DNA
structure was explored through molecular dynamics (MD) simulations. The results
showed that A-DNA have better stability in high valent cationic solution. This has
something to do with electrostatic interaction between metal ions and DNA chains and
with the higher ionic valency is the stronger interaction force is. On the temperature
side, low temperature has a contribution to the stability of A-DNA structure in salt
solution.

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Highlights (for review)

Transformation characteristic of A-DNA in salt solution

revealed through molecular dynamics simulation

Highlights

 A-DNA have better stability in high valent cationic solution

 low temperature has a contribution to the stability of A-DNA
structure in salt solution
 Electrostatic interaction dominates the interaction between
metal ions and A-DNA
 The higer ionic valency is, more closely metal ions intergrate
with phosphate groups
Highlights (for review)

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The Manuscript Click here to view linked References
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7 Graphical Abstract
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9 Transformation characteristic of A-DNA in salt solution revealed through molecular dynam-
10 ics simulation
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12 Jingjing Xue,Xinpeng Li,Rongri Tan,Wenjun Zong
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7 Transformation characteristic of A-DNA in salt solution revealed
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9 through molecular dynamics simulation
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11 Jingjing Xue, Xinpeng Li, Rongri Tan∗ and Wenjun Zong∗
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13 Department of Physics, Jiangxi Science and Technology Normal University, NanChang,China
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16 ARTICLE INFO ABSTRACT
17 Keywords: In aqueous solution, A-DNA eventually will be the stable state on the B-form as time goes on.
18 A-DNA structure The stability influence of ionic valence and temperature on the A-DNA structure was explored
19 Bivalent metal ions through molecular dynamics (MD) simulations. The results showed that A-DNA have better
20 Molecular dynamics stability in high valent cationic solution. This has something to do with electrostatic interaction
21 Salt solution between metal ions and DNA chains and with the higher ionic valency is the stronger interaction
Concentration force is. On the temperature side, low temperature has a contribution to the stability of A-DNA
22 structure in salt solution.
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27 1. Introduction
28 As is known to all, Deoxyribonucleci Acid(DNA) is an important nucleic acid which concerns the life activi-
29 ties and the biodiversity.[1] DNA stores genetic information which is necessary to maintain normal physiological
30 activities.[2, 3] DNA is double-helix structure consisting of two antiparallel rotating polydeoxynucleotide chains.[4]
31 Three kinds of typical biologically active DNA structures are A-DNA, B-DNA and Z-DNA, and B-DNA is the com-
32 monest DNA structure in living cells.[5] A-DNA and B-DNA have similar structures and are all typical right-handed
33 double helix.[6] Compared to B-DNA, A-DNA has shorter and compacter double helix.[7] Z-DNA is left-hand double
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helix and its helical structure is indented.[8] In 1996, Cheatham and his colleagues studied the transition of A-DNA
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structure in pure water by molecular dynamics(MD) simulation.[9] They found the structure of A-DNA eventually
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37 stabilized at B-form in pure water.[10] Since then, the studies of A-DNA structure transition came to the attention
38 of researchers.[11] The stability of DNA structure is of importance to the regulation of biological functions and the
39 accuracy of genetic information.[12] The A-DNA structure studies have significant meanings for the fields of gene
40 therapy, DNA nanotechnology and so on.[13]
41 Metal ions are important components in every cell.[14] The existence of metal ions matters the stability and the
42 proper functioning of biological system.[15] In pure water enviroment, the A-DNA will translate to B-form as time
43 goes by, and eventually will stability on the B-DNA structure.[16] A large number of experiments indicate that metal
44 ions (like Na+ and Mg2+ ) are added in solution can stabilize A-DNA structure.[17] It is apparent different metal ions
45 have different stability effect on the A-DNA structure. Whether the valency of metal ions is one of the metal property
46 that can affect the stability of A-DNA structure? Whether the changes of temperature will affect the A-DNA structure
47 in high concentration salt solution? And how? In this studies, we used the MD simulation method which can probe
48 motional details of the change of A-DNA structure to discuss the effect of ionic valency and temperature on the stability
49 of A-DNA structure.[18]
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52 2. Computational procedures
53 In our studies, the initial state of A-DNA duplex with a nucleotide sequence of CCCGGCCGGG is entry 1ZEX
54 from Protein Data Bank (PDB).[19] We chose this A-DNA model was because that the CG base-pair preferentially
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bounded metal ions compared to the AT base-pair.[20] Our all MD simulaltions were carried out by GROMACS 5.0.7
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program.[21] The interaction potential chose AMBER force fields.[22] The simulation cubic box (57 Åx57 Åx57
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Å, big enough to ensure DNA can not interact with its periodic images) contained one A-DNA model, metal ions
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59 and water molecules.[23] All MD simulations used standard molecular dynamics techniques included the velocity
60 ∗ Corresponding
author
61 rogertanr@hotmail.com (R. Tan); 13807065116@163.com (W. Zong)
62 ORCID (s):
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5 Short Title of the Article
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7 Table 1
8 (a) All performed simulations; (b) The properties of virtual ions.
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10 (a) MD Simulations
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The name of system Cations Anions Concentration(mol/L) Temperature(K)
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13 Na+ Na+ Cl- 3.00 300
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2+ 2+ -
15 Mg /300K Mg Cl 3.00 300
16 Al3+ Al3+ Cl- 3.00 300
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+ + -
18 X X Cl 3.00 300
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Z3+ Z3+ Cl- 3.00 300
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21 2+ -
280K Mg Cl 3.00 280
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23 330K Mg2+ Cl- 3.00 330
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(b) The Atom Details
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26 Mass Sigma Epsilon Charge
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28 X+ 24.305 0.141225 3.74342 1.00
29 Mg 2+
24.305 0.141225 3.74342 2.00
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31 Z3+ 24.305 0.141225 3.74342 3.00
32
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34 Verlet integrator and the periodic boundary conditions.[24] Long-rang electrostatic interactions were calculated by the
35 particle mesh Ewald summation method to avoid cutoff effects.[25] The energy minimization was run to ensure that
36 the system had a reasonable starting structure in terms of solvent and geometry. By NVT and NPT, the temperature
37 and pressure of system all reached a plateau at the desired value. All MD simulations were carried out at constant
38 pressure 1bar and constant temperature and run lasted 10ns at a time step of 2 fs.
39 As anions, Cl- ions were added into solution to kept all systems electric neutrality. In each system, a 1ZEX model
40 was solvated in the cubic box of water. To analyse the effect of ionic valency on the DNA structural stability, we
41 contrasted three different systems included NaCl salty solution, MgCl2 salty solution and AlCl3 salty solution. In
42 order to further make sure the effect of ionic valency, we also added two kinds of virtual ions information in force
43 fields to research and named them monovalent X+ and trivalent Z3+ . Their properties were exactly same as the Mg2+
44 except ionic valency (shown in table 1). In the aspect of temperature, in MgCl2 salty solution we ran and disscussed
45 three kinds of systems under different temperatures - 280K, 300K and 330K to figure out the effect of temperature on
46 the structural stability. It tured out that he presence and distribution of metal ions can affect the change of A-DNA
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structure in solution.
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50 3. Results and discussion
51 3.1. Ionic valency and A-DNA structural conformation
52 In our previous MD studies, we observed that the A-DNA will transform to B-form over time in pure water as
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previous reported studies. Under 300K temperature, we ran a series of MD simulations to contrast how the different
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valency metal ions impact the A-DNA structural stability. The three primary systems are
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56 • Na+ : 3M NaCl salt solution, included Na+ , Cl- and molecule of water
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58 • Mg2+ : 3M MgCl2 salt solution, included Mg2+ , Cl- and molecule of water
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• Al3+ : 3M AlCl3 salt solution, included Al3+ , Cl- and molecule of water.
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61 The addition of metal cations can help to stabilize the structure of A-form DNA. By our simulations, we found
62 the A-DNA stability is gradually improved with the increasing of ions concentration in salt solution about Na+ , Mg2+
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7 and Al3+ . The properties difference of adding metal cations can affect the stability effect of A-DNA in solution. The
8 reason why higher concentration was not chosen is that obvious DNA structure changing contrast effect is unable to
9 show clear under too high concentration. And 3M is an suitable concentration to study and contrast the changing of
10 DNA structure, according to our simulations in aspect of ions concentration. The final DNA structures in different
11 systems shows in the figure 1(A). It is clear that the DNA structure in AlCl3 solution is most similar to the DNA
12 initial structure-1ZEX, the two structures have the best fitting results. The DNA final structure in NaCl solution is
13 very different from 1ZEX, especially the end of DNA chains. The root mean square coordinate deviation(RMSD) can
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represent the change of structures, because little changes of DNA structure will cause large RMSD values.[26] The
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larger RMSD means greater change of DNA structure. From the figure 1(B), the case of RMSDs is: Na+ > Mg2+ >
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Al3+ . A-DNA structure in solution will have autonomous changes over time. All RMSDs increased and gradually
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18 levelled out over time. With the increase of valency, the RMSD values are lower and the fluctuation ranges are smaller.
19 By the valency increase the DNA structures are more and more stablehave and have smaller change compared with
20 the staring structure. Especially the Al3+ , the RMSD values are basically stable and almost are only 0.27 nm. The
21 DNA structure was basically unchanged in AlCl3 solution, the whole structure remained stable. The RMSD of Na+
22 is very unstable and the highest RMSD value is even to 0.61nm. In NaCl solution, A-DNA structure basically can not
23 keep stable. Sugar pucker is the type of folded form of sugar group.[27] Sugar pucker can be taken as the important
24 judging basis for the kind of DNA structure. In real environments, sugar moiety is not a standard plane, C atom will
25 always offset from the plane of sugar moiety to form the sugar pucker.[28] When the C3 atom and C5 atom offset from
26 the plane of sugar moiety in the same direction, the type of sugar pucker is C3’-endo. The C3’-endo sugar pucker is
27 the representative sugar pucker of A-form DNA. The C2’-endo sugar pucker which means the C2 atom and C5 atom
28 offset from the plane of sugar moiety in the same direction is the representative sugar pucker of B-form DNA.[29]
29 Many literature says that the C1’-exo is also the typical sugar pucker of B-form DNA.[30] From the table 3, the sugar
30 puckers of 1ZEX are all C3’-endo and the sugar puckers of typical B-DNA with the d(CCCGGCCGGG) nucleotide
31 sequence (by 3DNA software) are all C1’-exo and C2’-endo.[31] For the three environments, the number of the C3’-
32 endo of DNA under AlCl3 solution which is 8 significantly outnumber the number under other solutions. The C3’-endo
33 numbers are: Al3+ > Mg2+ > Na+ . For typical A-DNA and typical B-DNA,they also have huge difference in the DNA
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groove size characteristics.[32] The groove size of B-DNA between minor and major has a bigger difference, the major
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groove width is much wider than the minor groove. The width of A-DNA major groove is close to its minor groove
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37 like 1ZEX whose major groove width(17.62Å) is really close to the minor groove(16.52Å). In the table 2, it is clearly
38 that the size of groove in AlCl3 solution performs best. In AlCl3 solution, the size of major groove is very close to
39 the minor groove and their size are all close to the size of 1ZEX PDB. From observing both the comparison of RMSD
40 values, combined with the analysis of the DNA structure parameters details, the stable function of cation ions on the
41 A-DNA is: Al3+ > Mg2+ > Na+ . In Al3+ system, the final DNA structure most resembled the 1ZEX structure.
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60 Figure 1: (A) The comparison between the 1ZEX structure (red) and the DNA overall averaged façade structure about
Na+ (yellow), Mg2+ (gray) and Al3+ (blue) three systems; (B) the RMSDs of the DNA trajectories with respect to the
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starting DNA structures.
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7 Table 2
8 The contrasts of DNA structure details
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10 Sugar Pucker
11 1ZEX Na+ Mg2+ Al3+
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Strand I Strand II Strand I Strand II Strand I Strand II Strand I Strand II
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14 C3’-endo C3’-endo C1’-exo O3’-endo C4’-exo C1’-exo
15 C3’-endo C3’-endo C1’-exo C4’-exo C1’-exo C1’-exo O4’-endo C3’-endo
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17 C3’-endo C3’-endo C1’-exo C2’-endo C1’-exo C2’-endo C2’-endo C2’-endo
18 C3’-endo C3’-endo C2’-endo O4’-endo O4’-endo C2’-endo C2’-exo C3’-endo
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C3’-endo C3’-endo C3’-exo C1’-exo C4’-exo C4’-exo C3’-endo C4’-exo
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21 C3’-endo C3’-endo C2’-endo C2’-endo C3’-endo O4’-endo C3’-endo C1’-exo
22 C3’-endo C3’-endo O4’-endo C1’-exo C3’-endo C3’-exo C3’-endo C3’-endo
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24 C3’-endo C3’-endo C1’-exo O4’-endo C3’-endo C1’-exo C4’-exo C3’-endo
25 C3’-endo C3’-endo C1’-exo C2’-endo C2’-endo C1’-exo C1’-exo C3’-endo
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C3’-endo C3’-endo C1’-exo C4’-exo C4’-exo C4’-exo
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28 Groove Width (Å)
29 +
Na Mg2+ Al3+ 1ZEX
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31 Minor Groove 12.40 15.25 16.42 17.52
32 Major Groove 20.08 20.74 18.92 17.62
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34
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From the discussions above, we speculated that the stability of A-form DNA in salt solution is gradually improved
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with the increase of ionic valency. But different metal ions have different properties like mass, size and so on, these
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38 properties difference all can affect the interaction between ions and DNA. So we want to discuss wheather ionic valency
39 is an important factor affecting A-DNA structure change in salt solution when the other properties of metal ions are
40 same. In 3M concentration MgCl2 solution,the stability of A-DNA structure has a better performance. To further
41 confirm the effect of ionic valency on the A-DNA structure, we chose to take Mg2+ system as a reference system.[33]
42 To further confirm the effect of ionic valency on the A-DNA structure, we chose to take Mg2+ system as a reference
43 system. Based on the properties of magnesium ion, we made two kinds of virtual ions - monovalent X+ and divalent
44 Z3+ . Except for ionic valency, X+ ions and Z3+ ions have exactly same properties as the magnesium ion. We contrasted
45 and analyzed the three systems(X+ , Mg2+ , and Z3+ ) results to further determine the relationship between ionic valency
46 and the stability of A-DNA structure. From the figure 2(B), the X+ system RMSD values are clearly the most fluctuation
47 and highest and continue to grow by the time. And the RMSD values of Z3+ system are basically stable. In ZCl3
48 solution the DNA is basically unchanged compared with staring structure. By observing the fitting between final
49 structure and the 1ZEX, it is obviously that the DNA in ZCl3 is most similar to the staring 1ZEX structure. Combined
50 with the analyses of RMSDs, we found that with the increase of ionic valency the DNA structure in solution is more
51 stable. In terms of the sugar pucker, Z3+ system had the most number of C3’-endo which is 9. The C3’-endo content
52 of DNA obvious decreased by the decrease of ionic valency. X+ system did not even have C3’-endo and are all
53 C1’-exo and C2’-endo which are all the typical sugar pucker of B-DNA (shown in table 5). The figure 2(C) shows
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the comparison of DNA structure details in salt solution and the table 3 shows their concrete data. The standard A-
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DNA structure and the standard B-DNA structure with the d(CCCGGCCGGG) nucleotide sequence were generated
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57 by 3DNA. The data of Z3+ system is the most similar to the 1ZEX structure. The DNA structure changing trend is
58 obviously. For the X+ system, the DNA structure datas are more similar with the standard B-DNA. And with the
59 increase of ionic valency, the DNA structure datas are more and more close to the standard A-DNA. By summarizing
60 all our analyses, the different of ionic valency can affect the A-form DNA structure stability in salt solution. And the
61 metal ions are increasingly more effective for the structure stability of A-form DNA along with the increase of ionic
62 valency.This is has to do with interaction force between metal ions in solution and DNA chains.
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7 Table 3
8 The basepair sugar pucker of DNA structures
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10 Sugar Pucker
+
11 1ZEX X Mg2+ Z3+
12 Strand I Strand II Strand I Strand II Strand I Strand II Strand I Strand II
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C3’-endo C3’-endo C1’-exo C2’-endo C4’-exo O4’-endo
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15 C3’-endo C3’-endo C1’-exo C1’-exo C1’-exo C1’-exo C2’-endo C1’-exo
16 C3’-endo C3’-endo O4’-endo C1’-exo C1’-exo C2’-endo O4’-endo C1’-exo
17 C3’-endo C3’-endo C1’-exo C1’-exo O4’-endo C2’-endo C2’-endo C1’-exo
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C3’-endo C3’-endo C4’-endo C4’-endo C4’-exo C4’-exo C3’-endo C2’-endo
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20 C3’-endo C3’-endo C1’-exo C1’-exo C3’-endo O4’-endo C3’-endo C3’-endo
21 C3’-endo C3’-endo C2’-endo C2’-endo C3’-endo C3’-exo C3’-endo C3’-endo
22 C3’-endo C3’-endo C1’-exo O4’-endo C3’-endo C1’-exo C3’-endo C3’-endo
23 C3’-endo C3’-endo C2’-endo C4’-exo C2’-endo C1’-exo C3’-endo O4’-endo
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25 C3’-endo C3’-endo O4’-endo C2’-endo C3’-endo C1’-exo
26 DNA structure parameters (Å)
27 X+ Mg2+ Z3+ 1ZEX standard-A standard-B
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29 Minor Groove 11.88 15.25 15.88 17.52 18.36 12.58
30 Major Groove 23.96 20.74 19.98 17.62 16.62 16.50
31 X-disp -2.27 -3.54 -5.93 -4.68 -4.49 0.51
32 H-rise 3.06 2.99 2.15 2.86 2.54 3.37
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Slide -1.01 -1.41 -1.88 -1.81 -1.38 0.47
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52 Figure 2: (A) The comparison between the 1ZEX structure (red) and the DNA overall averaged façade structure about X+
53 (cyan), Mg2+ (gray) and Z3+ (lime) three systems; (B) the RMSDs of the DNA trajectories with respect to the starting
54 DNA structures.
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57 3.2. Temperature and A-DNA structural conformation
58 In previous part, we discussed the relationship between ionic valency and A-DNA structure stability. Whether the
59 other external factors can affect the change of A-DNA structure?[34, 35, 36] Whether temperature as external factors
60 will affect the A-DNA structure stability in salt solution is also the content of our study. Mg2+ system was still chosen
61 as a reference system to contrast the effect of different temperatures. The three temperatures are 280K, 300K and
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23 Figure 3: (A) The comparison between the 1ZEX structure (red) and the DNA overall averaged façade structure about X+
24 (cyan); Mg2+ (gray) and Z3+ (lime) three systems; (B) the RMSDs of the DNA trajectories with respect to the starting
25 DNA structures.
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28 Table 4
29 The contrasts of DNA structure details
30 Sugar Pucker
31 1ZEX 280K 300K 330K
32 Strand I Strand II Strand I Strand II Strand I Strand II Strand I Strand II
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C3’-endo C3’-endo
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35 C3’-endo C3’-endo C2’-endo C2’-endo C1’-exo C1’-exo C2’-endo C1’-exo
36 C3’-endo C3’-endo O4’-endo O4’-endo C1’-exo C2’-endo C1’-exo C1’-exo
37 C3’-endo C3’-endo C3’-exo C2’-endo O4’-endo C2’-endo C1’-exo C2’-endo
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C3’-endo C3’-endo C2’-endo C3’-endo C4’-exo C4’-exo C3’-endo C1’-exo
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40 C3’-endo C3’-endo C3’-endo C1’-exo C3’-endo O4’-endo C2’-endo O4’-endo

41 C3’-endo C3’-endo C4’-exo C1’-exo C3’-endo C3’-exo C1’-exo C1’-exo

42 C3’-endo C3’-endo C4’-exo O4’-endo C3’-endo C1’-exo C1’-exo O4’-endo
43 C3’-endo C3’-endo C3’-endo C2’-endo C2’-endo C1’-exo C4’-exo C1’-exo
44
C3’-endo C3’-endo C3’-exo O4’-endoo C1’-exo C2’-endo
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46 Groove Width (Å)
47 280K 300K 330K 1ZEX
48 Minor Groove 17.33 15.25 12.98 17.52
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Major Groove 19.90 20.74 22.53 17.62
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53 330K.[37] At the temperature of 280K, the RMSDs are about 0.18nm and is really stable and is clearly smaller than
54 the other temperatures (from the figure 3(B)). And with the decrease of temperature, it is obvious final DNA structure is
55 more similar with 1ZEX (shown in figure 3(A)). At the temperature of 280K, the DNA final structure is almost exactly
56 the same as 1ZEX. Table 4 presents the comparison between the 1ZEX structure and the DNA structures of three
57 different temperatures. The DNA structure of 330K has the fewest number of C3’-endo, just one. And in the aspect
58 of groove width, compared with other tempratures, the DNA structure data of 280K is the most cloest with 1ZEX
59 structure, espacially minor groove. According to all the analyses, we suggested that, the A-DNA stability in system is
60 gradually improved with the temperature drops lower. That may be a result of atoms thermal motion in system. The
61 higher the system temperature, the quicker the motion of molecules, the more beneficial to the conformational change
62 of DNA.
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7 3.3. The interaction between metal ions and A-DNA in ionic solution
8 In solution, the presence of high concentration of metal ions favors the stability of A-DNA structure because of
9 the interaction between positively metal ions and negatively A-DNA. In aqueous solutions, DNA chains will hydrate
10 with waters and the first hydration shell can be formed around the phosphate groups of DNA. The DNA phosphate
11 groups will be protected by molecules of solvent. In high concentration metal ions solution, electropositive metal
12 ions will scatter around the DNA chains, metal ions can invade the hydration shell around the phosphate groups and
13 replace the some water molecules to reside in the first hydration shell.[38] Radial distribution function analyses were
14
conducted on the metal ions around electronegative oxygen atoms of phosphate groups (shown in figure 4(C)), metal
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ions are primarily in the first hydration shell. And the higer ionic valency is, more closely metal ions intergrate with
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17 phosphate groups. In Al3+ and Mg2+ system, the combination between metal ions and phosphate groups is clearly
18 stronger compared with Na+ system. This is the reason why the exsit of Al3+ and Mg2+ is favourable to the stability
19 of A-DNA structure in solution.
20 Electropositive cations can suppress the electrostatic repulsion between electronegative DNA strands and benefits
21 the folding of A-DNA which has shorter and compacter double helix. As shown in figure 4(A) and 4(B), the electro-
22 static interaction dominates the interaction between metal ions and A-DNA. By contrast, the highest ionic valency Al3+
23 ions and Z3+ ions have the strongest interaction with DNA. By the increase of valenc,the interactio between metal ions
24 and DNA is becoming stonger and stronger which is in favour of the inhibition of the extension of DNA structure. This
25 means high valenc metal ions have stronger bonding trend with phosphate groups in comparison to low valence metal
26 ions, so high valenc ions have more benefits for the stability of A-DNA structure. We also simulated and analysed
27 the A-DNA in 1.5M MgCl2 and 1.5M NaCl salt solution under 300K. The competition of the combination between
28 different metal ions and phosphate groups happened. By comparing with Na+ system and Mg2+ system,the stability
29 of A-DNA structures are: Mg2+ > Na+ & Mg2+ > Na+ . Figure 4(D) shows the distribution of metal ions around DNA.
30 Compared with Na+ , it is obvious that more Mg2+ ions are around the DNA especially the major groove and phosphate
31 groups part of DNA . This means Mg2+ ions have stronger bonding trend with the DNA chains bond compared with
32 Na+ ions which is consistent with previous discussion.
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58 Figure 4: The electrostatic energies and total interaction energies of DNA chains-metal ions about (A) Na+ , Mg2+ , Al3+ ,
59 and (B) X+ , Mg2+ , Z3+ ; (C) the RDFs of metal ions around electronegative oxygen atoms of phosphate groups about
60 Na+ , Mg2+ , Al3+ ; (D) the spatial distribution of Na+ ions (red) and Mg2+ ions (blue) around DNA.
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5 Short Title of the Article
6
7 4. Conclusion
8
9 Deep A-DNA structure transition studies have important implications for DNA packaging, new DNA drugs de-
10 signing and so on.[39] At present, about DNA structure, most researchers focus on the B-form DNA.[40, 41, 42] Most
11 studies of A-DNA structure are being focused on univalent cations. The point of our studies focused more on the mul-
12 tivalent ions and transformation of A-form DNA structure. Different external conditions all will affect the change of
13 A-DNA structure in salt solution. We exploited molecular dynamics (MD) simulation method to analysis the function
14 of Ionic valency and temperature on the A-DNA structure transformation.
15 In the present work, a series of MDs about the A-DNA in salt solution was run to figure out the function of ionic
16 valency and temperature on the A-DNA structure. In salt solution, the strength of A-DNA structure stability is: Al3+
17 > Mg2+ > Na+ . Based on this conclusion, by using of two kinds of virtual ions (monovalent X+ and divalent Z3+ ),
18 we identified the relationship between ionic valency and A-DNA sturcture stability. We found that in metal ions salt
19 solution the higher ionic valency is, the better stability the A-DNA is with. And low temperature environment is also
20 in favour of the stability of A-DNA structure in solutions.
21 In salt solution, most electropositive metal ions will closely coupled with the electronegative phosphate groups of
22
DNA which can suppress the electrostatic repulsion between electronegative DNA strands.This contributes to benifits
23
the inhibition of the extension of DNA structure and the folding of shorter and compacter A-DNA structure. The
24
25 electrostatic interaction dominates the interaction between metal ions and DNA. The electrostatic interaction is major
26 force in the interaction force between metal ions. And multivalent metal ions have stronger bonding trend with the DNA
27 bond. The rule of interaction force coincided with the distribution situation of metal ions around phosphate groups.
28 The interaction between metal ions and DNA chains is not only connected with ions properties but also associated
29 with ions distribution. Next, our research direction will extend to the specifics process of interaction between metal
30 ions and DNA and the ions distribution.[43]
31
32
33
Acknowledgement
34 This work was supported by the National Natural Science Foundation of China (Grant No. 11564015), the Research
35 Fund for the Doctoral Program of China (Grant No. 3000990110) and the Fund for Distinguished Young Scholars of
36 Jiangxi Science & Technology Normal University (Grant No. 2015QN-BJRC002).
37
38
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