Preopening of the DNA base pairs

Preopening of the DNA Base Pairs

EUGENE S. KRYACHKO,∗ SERGEY N. VOLKOVBogoliubov Institute for Theoretical Physics, Kiev, Ukraine 03143

Received 1 August 2000; revised 15 January 2001; accepted 30 January 2001

ABSTRACT: The lower-energy stable structures of the A·T base pair are revealed undera search of its potential energy surface in the vicinity of its Watson–Crick configurationperformed at the PM3 computational level. Their properties and the mutual position of thenucleic acid bases A and T in these structures allow to partition them into three classes:partially preopened, stretched, and fully preopened. The preferable monohydration sitesof the preopened, stretched, and fully preopened pairs are also determined. It isdemonstrated, first, that the monohydration of the A·T pair at particular sites favors a basepair preopeness and, second, that a binding of the water molecule to the preopened A·Tbase pair on the major groove side enhances its stabilization. It is also shown that watermolecule placing in the vicinity of the central H bond of the A·T pair significantlyfacilitates its preopening. c© 2001 John Wiley & Sons, Inc. Int J Quantum Chem 82: 193–204, 2001

Key words: DNA base pair; hydrogen bonding; PM3 calculation; preopened state;interaction with water

Introduction

I n the DNA macromolecule, the adenine,thymine, guanine, and cytosine nucleic acid

bases form the Watson–Crick (WC) complementarybase pairs. These pairs link the polynucleotidestrands into the double helix by means of theplanar hydrogen (H) bonds. The H bonding of theadenine A to the thymine T via their amino andimino groups results in the A·T pair. Similarly, theguanine binds the cytosine via their H bonds andthey together form the G·C pair [1].

Correspondence to: E. S. Kryachko; e-mail: [email protected].∗Present address: Department of Chemistry, University of

Leuven, Celestijnenlaan 200 F, B-3001 Leuven, Belgium.

The geometries of the complementary base pairsare known from crystallographic experiments [2].At physiological conditions, the mutual dispositionof the nucleic acid bases in these pairs often under-goes some structural fluctuations so that the DNAbase pairs in the double helix may occupy a va-riety of conformational structures, particularly theclosed, WC, and opened states [3, 4]. For instance,transcription, replication, and recombination on thegenome cause sometimes significant deviations ofthe conventional DNA structure [4]. In the otherwords, the total potential energy surface (PES) of theDNA double helix has an extremely rich landscapewhere it likely behaves as a breathing structure.Its WC configuration completes the H bonding be-tween the nucleic acid bases and, for this reason,it refers to the closed one which attains one of thelowest energy minima on the PES [5]. For instance,

International Journal of Quantum Chemistry, Vol. 82, 193–204 (2001)c© 2001 John Wiley & Sons, Inc.

KRYACHKO AND VOLKOV

the WC configuration of the A·T pair shown inFigure 1 possesses two relatively strong H bonds,N6(A)—H· · ·O4(T) and N1(A)· · ·H—N3(T), and arather weak one C2(A)—H· · ·O2(T). The other typesof base pairing such as Hoogsteen, reverse Watson–Crick, and reverse Hoogsteen [1c – e, 6] will be notconsidered in the present work.

Structures of the opened states of the DNA dou-ble helix have not been clearly identified so far. Onthe one hand, there exists the complete opening ofthe base pair when all H bonds are ruptured. Thiscauses a complete unstacking of the bases in thepolynucleotide strands [3]. The occurrence of suchcomplete opening has been verified in experimentson the interaction of the base imino groups withformaldehyde and on the imino proton exchange[3, 7]. On the other hand, there also exist partiallyopened or preopened configurations of the base pairthat precede their complete opening. In the lattercase, the corresponding structural changes are lessfrustrated and disfavor the complete breakdownof the H-bonding pattern and the base unstacking[3, 8]. The appearance of such preopened configu-rations has been manifested in experiments on theinteraction of the base amino groups with formalde-hyde and on the exchange of the amino protons withthe protons of the solvent [8] as well. Preopenedconfigurations may be also considered as a prereq-uisite of the “base flipping” [1e, 4a]. The flipped-outbases have been observed in duplex DNA in a crys-tal structure [4b] and in nuclear magnetic resonance(NMR) experiments of B form DNA containing un-paired bases [4c, 4d]. Altogether, this implies thatthe study of preopened base pairs is of importancefor understanding the protein–nucleic acid recogni-tion processes and the mechanism of interaction ofDNA with drugs and small molecules. Therefore,some working definition of the preopened states ishighly demanded for these purposes and, primar-ily, for understanding of the very phenomenon ofbase pair opening. It is obvious that a preopeningstarts in vicinity of the WC configuration, and thusthe preopened configurations located there presum-ably determine the possible pathways of the basepair opening in DNA.

A variety of models describing the preopenedconfigurations of the DNA base pairing have beendeveloped in the past to interpret the aforemen-tioned experiments on the amino proton exchangeand on the interaction of the base amino groupswith formaldehyde. For example, the structure ofthe preopened pair where one of the bases is flippedout of the double helix has been considered in

Ref. [8c] (see also Refs. [4a – d]). Another model ofthe base pair preopeness with the sheared bases hasbeen studied in Ref. [9a]. In Ref. [9b], the authorssuggest that the base pair preopening can be a resultof intruding of water molecule between the bases.Based on a possible occurrence of tautomeric transi-tions in the bases, the preopened configuration hasbeen modeled by the sheared bases in different tau-tomeric forms [9c]. Base pairs with two nucleobaseslinked by a single or bifurcated H bond have beenrecently studied in Ref. [10].

The location of the preopened base pair configu-rations as stationary points on the DNA PES charac-terized by a certain H-bonded pattern is actually anunfeasable task due to the enormous number of thedegrees of freedom of the DNA double helix. It isusually solved via the divide-and-conquer method-ology, namely, by means of selecting out the specificpathways of a particular conformational rearrange-ment [11]. Some pathways leading to the base pairopening have been determined with the usage of theempirical force field models [11, 12]. These studieshave shown the absence of any local minima in theneighborhood of the WC configuration. In particu-lar, these pathways have been recently examined byLavery et al. [11b, 12d – f] using the AMBER poten-tial energy function. The A·T and G·C base pairssurrounded by water molecules have been sepa-rated along their principal H-bond axis. It has beendemonstrated that the PESs of these base pairs alongthe chosen reaction coordinate possess two minima.One of them corresponds to the WC configurationwhile the other one, at ca. 5.6 Å, describes actuallythe water-bridged configuration A·water·T [11b]. Inthis case, the angle of base pair opening varies in therange of 34◦–50◦ depending on a chosen pathwayand DNA bending as well. It is interesting to noticethat without water, such PESs have shown only thepresence of the single WC minimum [6b]. A veryclose vicinity of the WC configuration has been thesubject of numerous quantum chemical studies (seeRef. [13] and references therein) although they havefocused so far only on determining the global WCminimum.

The present work aims to perform a rather ex-haustive search of the PES of the base pair in orderto locate lower-energy local minima in the vicin-ity of the WC configuration. For our purpose, weuse the semiempirical PM3 method [14], whichrather accurately describes the geometries of the H-bonded bases [15, 16]. The following two key goalsare undertaken in the present work. One of them isto classify possible preopened states of the base pair

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PREOPENING OF THE DNA BASE PAIRS

and to study their properties while the other oneis to understand how does a water environment,which is a well-known factor of the DNA archi-tecture [17], influence a base pair preopening. Thepresent study is restricted to study a preopening ofthe A·T pair due to the fact that, first, it is less stablecomparing with the G·C one, and, thus, the occur-rence of its preopening would be more probableand, second, its preopening is more experimentallyelaborated (see Ref. [8]).

The remainder of the present work is organizedin the following manner. The following sectionbriefly describes its computational methodology.For the purpose of completeness, the global mini-mum of the PES of the A·T pair corresponding to theWC configuration is discussed in the third section.Then we introduce the preopened configurations ofthe A·T base pair, analyze their properties, and offertheir classification. The preopeness motif is furtherpursued in the fifth section, which studies the effectof hydration on a base pair preopening. Finally, weconclude and summarize the present work.

Sketch of Computational Methodology

Present calculations were performed within PM3self-consistent field molecular orbital (SCF MO)semiempirical method based on the approximationof neglecting the diatomic differential overlap usingthe MOPAC 6.0 package of programs [18]. The PM3method was employed with the keywords PRE-CISE and NOMM. All calculated structures werefurther verified on stationary points using keywordFORCE and THERMO. The PRECISE option was al-ways used in input data files in order to increasethe convergence criteria by default by a factor of100. The keyword GNORM=0.01 was also used toobtain the lowest possible gradient residue. In allcomputations, no constraints were imposed on thegeometry of the A·T base pair. Full geometrical op-timization was performed for each lower-energystructure. Harmonic frequencies were retained un-scaled.

Base Pairing in Watson–CrickConfiguration

The closed WC configuration is the global min-imum of the PES of the A·T base pair at the PM3computational level. It is shown in Figure 1. Thecalculated value of parameter R, which determines

FIGURE 1. Watson–Crick (WC) A·T base pairconfiguration. Dashed line indicates a hydrogen bond.Bond lengths in Å.

the distance between the carbon atoms of the sugarrings linked by glycosidic bond to the nucleic basesat the N9(A) and N1(T) positions and replaced bythe hydrogen atoms in the present study (see Fig. 1),is equal to 10.35 Å. It is in a rather good agreementwith its experimental value of 10.44 Å for the A·Upair [1c, 2c]. The angles α1 and α2, measuring theinclination of the glycosidic links to the R line anddefined in Figure 1 are equal to 52.6◦ (57.4◦) and50.9◦ (56.2◦), also match rather well the experimen-tal values [1c, 2c] given in the parentheses.

The intermolecular bond lengths and angles forthe WC configuration are collected in Table I, which,for comparison, includes also their experimentaland previous theoretical values. It is seen that PM3provides a rather accurate geometry of the WC con-figuration, although, in comparison with the exper-imental data [2c], it slightly underestimates the in-termolecular bond length of the N6(A)—H· · ·O4(T)hydrogen bond. The present bond lengths and an-gles are also consistent with the semiempirical, abinitio, and density functional theory (DFT) results[6a, 6b, 13c – e, 15c, 15d, 19, 20]. In particular, the re-ported values of bond angles are very close to thecalculated ones in Refs. [15c, 15d, 19b, 19d].

The PM3 binding energy, EHB, of the WC config-uration is equal to 5.7 kcal/mol (see Table II). In thepresent work, the binding energy is defined in theusual manner as the difference between the energyof the optimized pair and the sum of the energies ofthe isolated bases. The zero-point vibrational energy(ZPVE) correction is not taken into account. Suchvalue of the binding energy is in good accordancewith the previous PM3 calculations of the energy ofbase pair formation equal to 5.6 kcal/mol [15c] and

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TABLE IHydrogen bond distances (Å) and angles (degree) of the A·T Watson–Crick pair.

Intermolecular bond lengths and angles

N6(A)—H· · ·O4(T) N1(A)· · ·H—N3(T) C2(A)—H· · ·O2(T)

Experiment [1c, 2c]a 2.95 2.82 —Present work 2.83 176.4 2.81 176.0 3.81 128.8PM3 [15c] 2.83 175.4 2.82 175.8 —PM3 [15d]b 2.83 177.6 2.82 177.0 —AM1 [19a] 2.82 2.91 —AM1 [15c] 3.10 179.9 3.46 170.4 —AMBER [15c] 2.89 168.8 2.90 175.2 —HF/3-21G [20a] 2.96 2.78 —HF/MINI-1 [19b] 2.80 177.31 2.74 178.41 —HF/MINI-1 [6a] 2.97 177.0 2.91 180.0 —HF/6-31G(d) [13c] 3.08 3.01 —HF/6-31G(d,p) [19c] 3.09 2.99 2.96c

HF/cc-pVTZ(-f) [6b] 3.06 2.92 —B3LYP/6-31+G(d,p) [19d]a 2.941 173.8 2.872 179.0 3.688 132.4

a A·U pair.b Calculations were performed for nucleotides pA·pT.c H(C2)· · ·O2 distance. In the present work, it is equal to 3.02 Å.

the energy of the association of the bases in pair of6.72 kcal/mol [15d], although it is nearly half of theexperimental energy of the formation of the A·T WCpair. This is a well-known discrepancy already dis-cussed in the literature [6a, 6b, 13c – e].

To this end, it is worth noticing that the presentWC configuration of the A·T pair is planar. Thisresult is consistent with the originally proposedWC structure of nucleobase pairs [1a, 1b], althoughit has been known that in the native DNA, thecomplementary pair may be nonplanar, propeller

twisted, and buckled [1c – e] as well. The nonpla-narity of WC pairs has been also pointed out insemiempirical calculations [21]. For instance, anearly coplanar configuration for A·T pair has beenobtained at the PM3 level in Ref. [15c]. Nevertheless,AM1 and AMBER calculations have shown smalldeviations from coplanarity. On the contrary, abinitio studies (see, e.g., Ref. [13c] and referencestherein) and the vibrational analysis of the A·T paircarried out in Ref. [20] have demonstrated that it isin fact intrinsically planar.

TABLE IIBinding energy EHB, total dipole moment, and geometrical parameters of base pairs of the preopenedconfigurations of the A·T pair.a

Pair Binding DipoleIntermolecular bond lengths and angles Mutual base positionconfigu- energy moment

ration (kcal/mol) (D) N6(A)—H· · ·O4(T) N1(A)· · ·H—N3(T) C2(A)—H· · ·O2(T) R α1 α2

WC 5.70 1.3 2.83 176.4 2.81 176.0 3.81 128.8 10.35 52.6 50.9PP 4.58 0.6 3.39 166.0 2.84 175.2 3.45 135.2 10.05 57.3 56.7ST 2.60 2.7 3.49 163.8 3.39 167.6 4.30 129.4 10.73 54.2 56.2FP 1.64 3.0 5.22 146.7 3.43 154.6 2.93 163.9 9.17 72.1 79.7FPb 3.07 5.184 149.1 3.433 154.6 3.024 159.0 8.685 71.9 79.5

a Bond lengths in Å, bond angles in degrees.b Present HF/3-21G calculations.

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Preopened Configurations of A·T Pair

A rather exhaustive search of the PM3 PES of theA·T pair consisting in varying the N6(A)—O4(T),N1(A)—N3(T), and C2(A)—O2(T) distances overrather large intervals and the corresponding an-gles 6 N6(A)—H(A)· · ·O4(T), 6 N1(A)· · ·H(T)—N3(T),and 6 C2(A)—H(A)· · ·O2(T) in the neighborhood ofthe WC configuration reveals three lower-energynon-WC structures. They are displayed in Figure 2.Their binding energies and H-bonded geometriesare gathered in Table II, together with the corre-sponding values of the parameters R, α1, and α2.Analyzing these data, particularly, the binding en-ergy and the latter three parameters, we partitionthese configurations into three structural classes,viz., partly preopened (PP), stretched (ST), and fullypreopened (FP). It is worth noticing that the PPand ST configurations are nonplanar. As shown inFigure 2, the PP base pair are slightly twisted by 11◦whereas the ST one is buckled by only 9◦. The FPone is perfectly planar.

The partly preopened configuration is the mostenergetically favorable among the three non-WCstructures reported in the present work. It lies

FIGURE 2. Preopened A·T base pairs: partlypreopened, stretched, and fully preopened. Dashed lineindicates a hydrogen bond. Bond lengths in Å.

higher compared to the WC configuration by1.11 kcal/mol without ZPVE and 0.77 kcal/mol af-ter ZPVE. Its total dipole moment is equal to 0.6 D.Structurally, PP is characterized by the elongationof the N6(A)—H· · ·O4(T) bond by ∼0.6 Å and itsbending by ∼13◦ compared to the WC A·T basepair. Therefore, the N6(A)—H· · ·O4(T) bond can betreated as partially broken H bond (see Table II). Thecorresponding redshift of the ν(N6(A)H) stretchingvibration with respect to that in adenine is foundequal to 101 cm−1. This is smaller by 65 cm−1

compared to the analogous redshift in the WC con-figuration. The central H bond N3(T)—H· · ·N1(A)remains nearly unchanged. It is also indicated spec-troscopically in that the frequency of the stretchingvibration ν(N3(T)H) is smaller by only 3 cm−1 thanthe similar one in the WC base pair. We also observethat the weak one C2(A)—H· · ·O2(T) is shortened by0.3 Å. Thus, comparing with the closed WC config-uration, the PP one is viewed as being preopenedon the major groove side and partly shrinked on theminor groove side.

The ST configuration of the A·T base pair withrather large total dipole moment of 2.7 D isplaced above the WC one by 3.10 kcal/mol. Thisenergy difference lowers to 2.33 kcal/mol afterZPVE. Its H bonds become elongated by approx-imately 0.7, 0.6, and 0.5 Å for N6(A)—H· · ·O4(T),N3(T)—H· · ·N1(A), and C2(A)—H· · ·O2(T), respec-tively. This causes, on the one hand, an increaseof the parameter R by ∼0.4 Å and, on the otherone, smaller redshifts of the H-bonded stretchingvibrations ν(N6(A)H) and ν(N1(T)H), viz., by 100and 98 cm−1, respectively, compared to the WC basepair. By the analogy with the partly preopened con-figuration, the H bonds in the stretched one aresomewhat bent.

The fully preopened configuration lies above thestretched one by 0.95 kcal/mol without the ZPVEand by 1.36 kcal/mol with the ZPVE correction. Itpossesses the largest total dipole moment of 3.0 Damong the revealed lower-energy non-WC config-urations of the A·T pair. It is also characterized bythe very short and substantially less bent C2(A)—H· · ·O2(T) H bond of 1.84 Å. The total C2(A)—O2(T)separation comprises of 2.93 Å, which is extremelyshort for this type of bonding in DNA and RNA(cf. Ref. [22]). This is likely due to a rather poordescription of such bonding by semiempirical meth-ods because the additionally performed HF/3-21Goptimization increases this bond length to 3.02 Å(the other HF/3-21G geometrical parameters arelisted in Table II). On the contrary, its N6(A)—


KRYACHKO AND VOLKOV

H· · ·O4(T) bond becomes significantly elongated by2.4 Å compared with the WC base pair and by 1.8 Åcompared with the PP one, and it is actually broken.This is also indicated by the frequency of the stretch-ing vibration ν(N6(A)H) equal to 3438 cm−1, whichis nearly the same as that in adenine (3441 cm−1).The elongation of the N3(T)—H· · ·N1(A) bond by0.52 Å is also predicted in the present study. Thus,summarizing, the FP configuration opens the A·Tpair on the major groove side, locks it on the minorgroove side, and thus, possesses the smallest valueof R = 9.17 Å among all reported configurations.

In the PP, ST, and FP configurations, the N6(A)—H· · ·O4(T) bond length exceeds the limit of 3.07 Åknown for this bond in the base pairs [2d] andfor this reason, should be considered as a brokenone. Under physiological conditions, some solventmolecule(s) may enter the base pair interior andmediate their intermolecular bonds as has beenshown particularly by Lavery et al. [11]. The centralN1(A)· · ·H—N3(T) bond in the preopened config-uration becomes longer by 0.6 Å. As noticed byDonohue [23a], the N—H· · ·N bond length variesfrom 2.7 to 3.4 Å in organic crystals, while in the nu-cleobase pairs, it reaches the maximum value equalto 3.15 Å [2d, 23b], though evidently, these dataare crystallographic and actually valid for thoseconfigurations of the base pairs that reside at theglobal minima. We may therefore conclude that theN1(A)· · ·H—N3(T) bond in the PP and ST configu-rations of the A·T pair is preserved to certain extent.

Concluding this section, it is worth mentioningthat an occurrence of preopened pairs in the DNAdouble helix strongly depends on their geometri-cal parameters. It has been already demonstrated bySpencer [2a] that slight distortions of the intermole-cular bond lengths and angles of the nucleobasepair cause a change of geometrical parameters. Ac-cording to Spencer’s estimations for the A·T pair,the parameter R varies from 10.5 to 12.1 Å, whilethe angles α1 and α2 vary from 36◦ to 59◦. It isclear that such natural variability of the base posi-tions in the pair pointed out by Spencer does notsignificantly affect the double helix structure. Thistherefore implies that if values of R and α1 and α2 ofthe preopened configurations fall into the aforemen-tioned interval, such configurations of the base pairmay occur in the DNA without a significant distor-tion of its double helix motif. Comparing these datawith the values of R, α1, and α2 presented in Table II,we notice that only the ST configuration matchesthem satisfactorily. Nevertheless, as demonstratedby Chuprina and Poltev [24], an incorporation of

unusual base pair configurations such as the non-WC pairs studied in the present work into thedouble helix distort slightly the DNA structure.Summarizing, we conclude that all reported pre-opened configurations of the A·T pair may appearin the DNA double helix and might cause minorchanges in its duplex structure.

Water Effect on Base Pair Preopening

A realistic modeling of a base pair preopening inthe DNA demands to include water into considera-tion. This is done in the present work by restrictingthe treatment to a single water molecule w. The per-formed search of the lower-energy portion of thePES of such complex A·T–w reveals a number of theenergy minima, which are listed in Tables III–V andwhich are the subject of the present section.

COMPLEXES OF WC PAIR WITHWATER MOLECULE

Thirteen minimum energy structures are locatedon the PES of the WC A·T pair with water mole-cule. They are depicted in Figure 3 and some of theirproperties are collected in Table III. One may antic-ipate that these A·T–w structures can be naturallydivided into three groups where two of them mimicthe lower-energy minima of A–w and T–w com-plexes (see also Ref. [25a – d] and references therein),respectively, while the third group comprises of theWC–w complexes of the WC A·T pair with wa-ter molecule bonded to both nucleobases (see Ref.[25e – h] and references therein).

The global minimum WC–w1 is attained at thestructure where the water molecule forms theH bond with the N1—H group of thymine. Itsbinding energy is ∼10.0 kcal/mol. This is in goodagreement with the recent B3LYP/6-31++G(d,p) es-timation of the binding energy of ∼10.2 kcal/molof the thymine–water complex T–w1 of the typeN1—H· · ·Ow—H· · ·O2 [25c]. Nevertheless, on theone hand, in the WC–w1 complex, the N1—H· · ·Ow

H bond is stronger because it is found shorter by0.12 Å and less bent by 15◦ than that in the isolatedT–w complex. On the other hand, due to the pres-ence of the weak C2(A)—H· · ·O2(T) H bond in theWC A·T pair, the water molecule forms a relativelyweak H bond with the oxygen atom O2 of thymine.

The two other minima WC–w2 and WC–w3 cor-respond to the third group. The former one is placedabove the global minimum by only 0.3 kcal/mol.

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FIGURE 3. Energetically preferable sites of the watermolecule around the A·T base pair in the WC, PP, ST,and FP configurations. The oxygen atom Ow of watermolecule is shown by a shadow circle with the attachedsolid lines for the hydrogens. Dashed line indicates ahydrogen bond.

The water molecule resides between the A and Tnucleobases on the minor groove side, slightly outof the pair interior, and forms the strong H bond ofthe length of 1.82 Å and the bond angle of 157.6◦with the O2 atom of thymine. The formation of suchH bond is accompanied, as seen in Figure 3, by aslight twist of the A·T base pair. The insertion of thewater molecule from this side increases the C2(A)—H· · ·O2(T) distance by 0.07 Å and less, by 0.01 Åonly, the N1(A)· · ·H—N3(T) one. The WC–w3 struc-ture lying above the WC–w2 by 0.2 kcal/mol has awater molecule that approaches the base pair fromthe major groove side and forms the H bond withthe O4 oxygen atom of thymine. It slightly affects theinterbase H bonds and causes a small nonplanarityof the A·T pair (see Fig. 3). It is interesting to notice,first, that these two lower-energy structures, WC–w2 and WC–w3, are not certainly among the knownlower-energy of the complexes of thymine with wa-ter because their origins are due to the A·T basepairing. Second, WC–w1 resembles the structure ofthe quaruply hydrated A·T base pair optimized atthe HF/3-21G computational level in Ref. [25e] (seealso Ref. [25f]). Both of them are analogous to thewater sites revealed in Monte Carlo studies per-formed in Ref. [25a] (see also Ref. [25b] for review).

The fourth and sixth lower-energy minimumstructures placed above the global one by ∼0.6 and0.9 kcal/mol, respectively, belong to the secondgroup. The other WC–w5,7–13 structures referringto the first group resemble rather accurately thelower-energy adenine–water complexes. The low-est structure among them is similar to the complexA reported in Ref. [25d], although its binding en-ergy in the A·T base pair is higher by∼1.1 kcal/molthan that of complex A. The WC–w8 structure withthe binding energy of 8.5 kcal/mol is apparently thecomplex B found in Ref. [25d].

INTERACTION OF PREOPENED A·T BASEPAIRS WITH WATER

The present search of the PES of the interactionof preopened A·T base pair with water molecule re-sults in a large number of the PP, ST, and FP configu-rations with the binding energy EHB ≥ 5.1 kcal/mol.All these A·T–water structures shown in Figures 4and 5 fall into two categories. The first one com-poses the structures similar to the WC–wi (i = 1–13)ones. Their binding energies and H-bonded geome-tries are collected in Table IV. They are numberedmerely as PPi, STi, and FPi to distinguish them fromthe representatives of the second class. The latter


KRYACHKO AND VOLKOV

TABLE IIIThe WC A·T complexes with water molecule w.a

Donor H bond Acceptor H bond

Structure EHB X(Y) Rd rd αd X(Y) Ra ra αa Dipole

WC–w1 9.99 N1(T) 2.79 1.82 158.9 O2(T) 3.16 2.71 110.7 1.9WC–w2 9.70 O2(T) 2.73 1.82 157.6 — — — — 2.6WC–w3 9.50 O4(T) 2.75 1.81 164.6 — — — — 1.9WC–w4 9.37 Cm(T) 3.56 2.61 171.1 — — — — 2.6WC–w5 9.16 N3(A) 2.78 1.83 164.4 N9(A) 3.37 2.79 117.8 3.5WC–w6 9.06 C6(T) 2.91 1.82 163.7 — — — — 3.0WC–w7 8.80 N9(A) 2.81 1.81 170.2 — — — — 2.3WC–w8 8.50 N6(A) 2.83 1.83 177.7 N7(A) 3.22 2.55 127.7 1.4WC–w9 8.19 N6(A) 3.50 2.57 156.4 N7(A) 2.77 1.83 162.7 1.5WC–w10 8.11 C8(A) 2.92 1.81 179.6 — — — — 2.1WC–w11 7.81 N6(A) 3.50 2.56 156.8 N7(A) 2.78 1.82 171.7 1.8WC–w12 7.51 N9(A) 3.27 2.49 135.4 N3(A) 3.35 2.63 132.5 1.8WC–w13 6.92 C8(A) 3.50 3.05 105.5 — — — — 2.1

N9(A) 2.35 2.54 128.4 — — — — —

a Rd is the distance between the atom X (Y = A, T) and the water oxygen atom in the donating H bond X(Y)—H· · ·Ow and rd and αdare its bond length and bond angle, respectively. Similarly, Ra is the distance between the atom X(Y = A, T) and the water oxygenatom in the accepting H bond X(Y)· · ·Hw—Ow and ra and αa are its bond length and bond angle, respectively. Binding energy EHBin kcal/mol, distance in Å, angle in degrees, and total dipole moment in D.

one is the most remarkable and actually describesa preopeness of the A·T base pair due to interactionof its interior hydrogen bonds with the water mole-cule. Here, the water molecule intrudes the base pairinterior and recovers “loose” H bonds. The bindingenergies of these preopened P–water structures ofthis class and their H-bonded geometries are givenin Table V.

As shown in Table IV, the binding energy ofthe most stable PP–w complex PP1 is placed by1.51 kcal/mol (0.99 kcal/mol after ZPVE) above themost stable WC–w1 structure. The preferential po-sitions of the water molecule for the PP type ofthe A·T base pair lie in the vicinity of the N3 andN6 atoms of adenine and the O2 and C6 atoms ofthymine, and its methyl group as well (Fig. 3). Re-garding the ST type of the A·T base pair, waterfavors to reside closer to the N7 atom of adenine andthe C6 and O2 atoms of thymine (Fig. 3). The bind-ing energy of these ST–w complexes are lower, by2.5 kcal/mol, than that of the PP–w1 one. All ST–wcomplexes are buckled. There are also found twoplanar FP–w configurations with the water mole-cule locating near the N1 and O2 atoms of thyminecharacterized by nearly the same binding energiesEHB of ∼6.1 kcal/mol (Fig. 3).

Six P–w structures belonging to the second classshown in Figure 4 are reported in the present work.

Two of them, P–w1 and P–w2, possess the bind-ing energies EHB, which are somewhat closer to thebinding energy EHB of the WC–w1 structure, viz. thedifference comprises of 0.70 (1.44 after ZPVE) and0.77 (1.39 after ZPVE) kcal/mol, respectively. Theother four P–w3–6 configurations are placed by 1.18(1.81), 2.13 (2.28), 2.21 (2.45), 3.58 (3.08), and 3.95(3.56) kcal/mol above the global minimum of theWC–w type (the ZPVE-corrected energy differencesare given in parentheses). As shown in Figure 4,they are structurally rather close to the FP–w config-urations, although here a water molecule penetratesin between the N6(A) and O4(T) atoms. Therefore,for their formation, it must be attached to the basepair on the side of the major groove of the doublehelix and form the corresponding hydrogen bonds.Their stretching vibrations, ν(N6(A)—H· · ·Ow) andν(Ow—H· · ·O4(T)) are redshifted by 19 and 29 cm−1,respectively, whereas the stretching vibration as-signed to the N3—H(T)· · ·N1(A) bond undergoes anenormous redshift of 558 cm−1. Analyzing the P–w3–6 configurations displayed in Figure 4, we con-clude that two hydrogen bonds, N3(T)—H· · ·N1(A)and C2(A)—H· · ·O2(T), for the latter being shortercompared to that in the WC base pair, play the keyrole in their stabilization. This conclusion is verifiedvia performing HF/3-21G and HF/3-21+G(d) cal-culations whose results are also collected in Table V.

200 VOL. 82, NO. 4


FIGURE 4. Preopened A·T pairs mediated by the watermolecule where the latter is placed on the major grooveside (P–w1–2 base pairs) and on the minor grooveside (P–w3–6 base pairs). Dashed line indicates ahydrogen bond.

As seen there, the lengths of the C2(A)—H· · ·O2(T)bond in the P–w3 and P–w6 configurations are stillrather short, viz. about 3.1 Å. Such shrinking ofthe C2(A)—H· · ·O2(T) bond prevents an intrusionof the water molecule into the pair on its minorgroove side. It is also worth mentioning that in

TABLE IVMost stable complexes of the preopened A·T basepair with water molecule.a

Dipole H-BondedStructure EHB moment base atom Distance

PP1 8.48 2.3 Cm(T) 3.54PP2 8.02 2.5 N3(A) 2.78PP3 7.69 1.6 O2(T) 3.02PP4 7.62 2.8 C6(T) 2.93PP5 7.59 2.1 C6(T) 3.62PP6 7.41 2.3 N6(A) 2.83PP7 7.25 1.6 O2(T) 3.20PP8 6.51 3.0 Cm(T) 3.60PP9 6.46 2.3 C6(T) 3.56FP1 6.14 4.0 O2(T) 2.79FP2 6.10 1.5 O2(T) 2.73ST1 5.99 3.6 C6(T) 2.91ST2 5.71 1.2 O2(T) 3.18ST3 5.12 3.6 N7(A) 2.77

a Binding energy EHB in kcal/mol, distance in Å, and totaldipole moment in D; m indicates the methyl group of thymine.

the P–w6 configuration with the binding energy of∼6.03 kcal/mol, T is flipped out from A with theN3(T)—H· · ·N1(A) equal 3.34 Å (Table V).

The P–w1 and P–w2 configurations are formedvia binding of the water molecule to the N1(A)and N3(T) atoms (see Fig. 4). The P–w1 structureis buckled with the buckling angle of 18.6◦. On thecontrary, the base pair in P–w2 is slightly twistedby 9◦. These pair configurations have a reverse angleof the pair opening than the P–w3–6 pairs. P–w1 isvery similar to the base pair configuration reportedby Poltev and Steinberg [26] and characterized bythe following geometrical parameters: R = 13.7 Å,α1 = 31◦, and α2 = 23◦, which are rather close tothe values reported in Table V. The formation of theP–w1 and P–w2 configurations is certainly a two-stage process. At the first stage, water moleculesattach to the double helix on the minor groove side.The elongation and further breaking of the C2(A)—H· · ·O2(T) bond takes place at the second stagewhen the water molecule intrudes on the interiorof this bond, moves further to the other N3(T)—H· · ·N1(A) bond, and then mediates it by donatingits H bond to the N1 atom of adenine and acceptingthe N3—H bond of thymine. Spectroscopically, theformation of the P–w1 configuration is manifestedin the redshifts of the stretching vibrational modesN6(A)—H· · ·O4(T) by 97 cm−1, Ow—Hw· · ·N1(A) by182 cm−1, and finally, N3(T)—H· · ·Ow by 330 cm−1.


KRYACHKO AND VOLKOV

TABLE VPreopened water-bridged A·T pairs.a

Structure EHB Dipole H Bonds Length R α1 α2

P–w1 9.29 3.2 N6(A)—H· · ·O4(T) 2.76 12.59 31.7 21.3N1(A)· · ·Hw—Ow 2.77Ow· · ·H—N3(T) 2.79

P–w2 9.21 3.2 N6(A)—H· · ·O4(T) 2.76 12.81 27.3 23.4N1(A)· · ·Hw—Ow 2.77Ow· · ·H—N3(T) 2.79

P–w3 8.81 2.9 N6(A)—H· · ·Ow 2.78 9.30 65.8 70.62.826∗ 9.431∗ 65.9∗ 66.4∗

Ow—Hw· · ·O4(T) 2.72 (2.667)∗N1(A)· · ·H—N3(T) 2.82 (3.073)∗C2(A)—H· · ·O2(T) 2.88 (3.134)∗

P–w4 7.86 3.8 N6(A)—H· · ·Ow 2.80 10.02 6.54 70.3Ow—Hw· · ·O4(T) 2.73N1(A)· · ·H—N3(T) 3.53C2(A)—H· · ·O2(T) 3.56

P–w5 6.41 3.6 N6(A)—H· · ·Ow 2.81 9.95 66.6 71.1Ow—Hw· · ·O4(T) 3.00N1(A)· · ·H—N3(T) 3.56C2(A)—H· · ·O2(T) 3.59

P–w6 6.03 4.5 N6(A)—H· · ·Ow 2.83 9.22 71.2 77.12.736† 8.585† 67.2† 70.4†

Ow—Hw· · ·O4(T) 3.06 (2.680)†

N1(A)· · ·H—N3(T) 3.34 (3.090)†

C2(A)—H· · ·O2(T) 2.94 (3.103)†

a Binding energy EHB in kcal/mol, distance in Å, angle in degrees, and total dipole moment in D.The P–w3 pair is reoptimized at the HF/3-21+G∗ level (indicated by the superscript ∗) and characterized by the energy of−986.690423 hartrees. The geometry of the other one, P–w6, is refined at the HF/3-21G as indicated by the superscript † andhas the energy equal to −986.530904 hartrees.

Nearly the same redshifts (95, 180, and 324 cm−1,respectively) of the corresponding stretching vibra-tions are predicted for the P–w2 configuration.

As mentioned above, the P–w1 and P–w2 con-figurations possess relatively large binding energiescomparable with the most stable complexes of theWC A·T base pair with water. However, comparingtheir geometrical parameters with those of the P–w3–6 pairs, which are closer to the regular WC basepair, we notice that their formation causes largerperturbations of the sugar–phosphate backbone. Wemay thus conclude that the appearance of such pre-opened configurations is less probable than that ofthe P–w3–6 pairs.

Summary and Conclusions

We have revealed three different structures onthe lower-energy portion of the PES of the A·T base

pair describing its preopeness. The most energeti-cally favorable local minimum refers to the partlypreopened configuration, which preopens the A·Tbase pair on the major groove side of the DNA dou-ble helix and shortens the A·T interbase distance onthe minor groove side. It is followed by the stretchedconfiguration, and further, by the fully preopenedconfiguration, which possesses two partially brokenH bonds and a rather short C—H· · ·O bond of 3.02 Åat the HF/3-21G level. In polar solvents, however,such order could be likely changed because the fullypreopened configuration possesses the largest to-tal dipole moment among the all studied A·T pairsin the gas phase including also the WC pair. Thestretched A·T pair has rather weak H bonds, and itsmutual position of the bases is close to the normalWC configuration. This implies that such configu-ration may rather likely occur in the double helixstructure.

202 VOL. 82, NO. 4


The evaluation of occurrence of the preopenedA·T base pair under physiological conditions highlydemands to include its interaction with water intothe consideration. We have shown that water mole-cule intrudes the base pair interior and mediatesone of its intermolecular H bonds forming in sucha way rather stable complexes. Among them, themost favorable structures are those where the wa-ter molecule attaches the A·T base pair on the majorgroove side of the double helix. These configura-tions refer to the partly or fully preopened ones withthe water molecule bridging the N6(A)—H· · ·O4(T)H bond. Their geometrical parameters resemblethose inherent for the WC configuration. It is alsoworth noticing that the binding energy of these pre-opened pairs with water are rather close to those ofthe WC base pair complex with water. Hence, theinsertion of water molecule into the A·T pair on themajor groove side is quite probable. Regarding that,it seems interesting that under formation of suchpreopened configurations with water, the latter onebinds the amino group of adenine and, as a whole,this group moves toward to the major groove ofthe double helix. Therefore, an appearance of sucha group can be tested in experiments on the interac-tion of probe molecules such as, e.g., formaldehyde,with the adenine amino group and on the aminoproton exchange as well.

On the other hand, the insertion of the wa-ter molecule to the place of the central H bondN1(A)· · ·H—N3(T) in the A·T pair leads to the for-mation of the structure with the reverse angle ofopening and with the broken C2(A)—H· · ·O2(T)bond. The geometrical parameters of these pairsmarkedly differ from the parameters of the WC con-figuration. In this case, the interaction of the basepair with water likely facilitates the pair opening.The formation of such preopened pairs with wateris the first stage of the base pair opening in DNA,which determines the pathways of this process inthe DNA double helix. One of them, mentioned inthe Introduction and associated with the “base flip-ping,” embarks likely on the P–w6 configuration.

ACKNOWLEDGMENTS

The authors acknowledge fruitful discussionswith Viktor Danilov, Maxim Frank-Kamenetskii,George Malenkov, and Valery Poltev. One of theauthors (E.S.K.) expresses his thanks to ThérèsaZeegers-Huyskens and Minh Tho Nguyen for use-ful discussion and warm hospitality. The authorsalso thank Pavel Hobza and Jerzy Leszczynski for

providing reprints of their publications and the ref-erees for valuable comments and suggestions.

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Preopening of the DNA base pairs