Molecular electrostatic potentials and Mulliken charge populations of DNA mini-sequences

Transcription

1 Ž. Chemical Physics Molecular electrostatic potentials and Mulliken charge populations of DNA mini-sequences R. Santamaria ), G. Cocho, L. Corona, E. Gonzalez Instituto de Fısica, UNAM, Apdo. Post , Mexico D.F , Mexico Received 14 March 1997 Abstract Molecular electrostatic potentials Ž MEPs. are used to investigate the biochemical reactivity of DNA nucleic acid bases Ž NABs.. As a complementary scheme, a Mulliken population analysis is performed to determine internal charge distribution changes when nucleic acids take part in pair complexes and DNA mini-sequences. From the fact that MEPs are capable enough for predicting the formation of different hydrogen bonded pairs among NABs, it is inferred that for these compounds the electrostatic force plays a dominant role. Particular attention is paid to Watson Crick dimers as they exhibit different preferred sites for an electrophilic attack to these of single nucleic acids. Finally, from the mini-sequences studied here, it is concluded that recognition of DNA segments proceeds at relatively short distances as a result of a poor influence of NABs on sugar and phosphate fragments. All quantum mechanical computations are performed within the density functional formulation. q 1998 Elsevier Science B.V. PACS: Kg; By; Ew Keywords: Molecular electrostatic potentials; Mulliken populations; Reactivity; Nucleic acids; Density functional theory 1. The molecular electrostatic potential The determination of the deoxyribonucleic acid Ž DNA. chemical active sites becomes of great interest for understanding a variety of specific reactions between DNA and other molecular fragments. In turn, knowledge of the shape and relative locations of chemical active sites allows for DNA chemistry modeling. A large number of studies indicate that molecular electrostatic potentials represent a suitable quantum mechanical tool for elucidating reactive centers w1 3 x. ) Corresponding author. rso@fenix.ifisicacu.unam.mx The molecular electrostatic potential Ž MEP. is dewx fined as 4 Ý a < < 3 a 1 1 < 1 < a V Ž r. s Z r R yr yhd r r Ž r. r r yr, Ž 1. where Za and Ra denote the charge and position of nucleus a, respectively. Eq. Ž. 1 renders the electrostatic interaction between the unperturbed charge distribution of the molecule and a positive unit charge located at point r. Shortcomings from the application of the MEP to studying reactivity, at the early stage of the recognition process, are preponderantly due to the inability of a point charge to indicate orientation r98r$19.00 q 1998 Elsevier Science B.V. All rights reserved. Ž. PII S

2 318 ( ) R. Santamaria et al.rchemical Physics of an incoming partner molecule wx 5, and to the approximation resorted to for computing the electron density r. Because of the long-range nature of the forces involved in Eq. Ž. 1, interaction at far distances between a partner molecule and DNA is mostly dominated by the electrostatic force. However, as the separation between both fragments decreases other well-known relaxation forces must be taken into account, such as those coming from mutual polarization, exchange of electrons, charge transfer, disperw6,7 x. Encouraged by the simplicity and general good sion, etc. performance of the electrostatic potential scheme, and within the accuracy limits of Eq. Ž. 1, we use the MEP approach as a tool to explore the reactive field of B-DNA nucleotides in a single strand configuration. It is important to note that expression Ž. 1 is not the only identity that relates the potential V with the electron density r. In fact, the Poisson expression: = 2 V Ž r. s4pr Ž r. Ž 2. leads to an alternative way to compute V from r. Nevertheless, in this work, electrostatic potential computations are done according to Eq. Ž. 1. As a matter of further insight of DNA reactivity, we consider of interest to also carry out a Mulliken population wx 8 analysis on nucleotide sequences. Although such analysis may be arguable, for instance net atomic charges are incapable of reproducing the exact dipole moment wx 9, it is clear that Mulliken populations yield one of the simplest pictures of charge distribution. On the other hand, while Mulliken charges render net atomic populations in the molecule, electrostatic potentials yield the electric field out of the molecule produced by the internal charge distribution. Therefore, Mulliken populations appear as a complementary tool to the MEP approximation for studying reactivity, and correlation between results from both schemes is expected. In order to apply a MEP and Mulliken population analysis, the use of accurate geometries is required. Thus, in Section 2, we briefly describe the way in which we generate DNA nucleotide sequences and the quantum mechanical method to compute the electron density r. In Section 3, population charges and MEPs of nucleic acid bases and their pair complexes in the gas phase are estimated, with the aim of elucidating charge distribution changes of these compounds when they are incorporated into the DNA helix. At the second part of Section 3, we discuss the same features for the case of single mini-strands of B-DNA. Finally, Section 4 gives the main conclusions derived from a MEP and Mulliken population analysis on the different DNA fragments, and the corresponding expectations for the whole DNA system. 2. Geometries of the B-DNA nucleotide sequences The large size of DNA prevents the application of any accurate quantum mechanical method to determine its structure and electronic properties. However, it is important to recall that only four different nucleotides constitute the basic building blocks of DNA. Then, we have recourse to accurate nucleotide structures as a departure point to create arbitrary DNA sequences. In a previous investigation, the geometries of nucleic acid bases and these of their pair complexes were determined w10 x. The method under use was a density functional approach which in particular has shown to give reliable results for these kind of compounds w11 x. Hence, by making use of the same scheme the structures of the B-DNA nucleotides: adenine Ž A., guanine Ž G., cytosine Ž C. and thymine Ž T., were obtained w12 x. From such structures, we now face the possibility of building single and even double strand sequences of B-DNA. The process to create the chain from its basic components essentially follows the next steps. We first proceed to overlap the sugar rings of all nucleotides. This is a process that becomes possible as the sugar ring represents a common structure to all monomeric units. Next, we locate nucleotide structures in such a way that nucleic acids lie in the Zs0 plane, without loosing the previous overlap among sugar rings. This is also an event that becomes possible since nucleic acids are to great extent planar. In order to find the position of the helix origin, we put in a stacking configuration a couple of nucleotides. The position of the origin is found out by matching the location of the phosphate oxygen with

3 ( ) R. Santamaria et al.rchemical Physics largest Z-component of the first nucleotide, with the oxygen that links the sugar ring of the second one. The matching process requires of the fact that ten B-DNA bases yield a complete helix turn, and therew13 x. From this step we obtain an average helix rise per fore the twist angle between bases is ; 368 base of 3.0 A. We note that such a value falls inside the experimental range of 3.36"0.42 A w13 x. Once the rise per base along the Z-direction and the twist angle around the helix axis are known, the desired sequence of nucleotides in a single strand conformation can be built up by repeating the above steps 1. Complementary nucleotides to these which appear in the single strand, in order to form a double helix, may be produced by transforming the Cartesian coordinates Ž x, y, z. of the partner nucleotide to the coordinates Ž x, yy, yz.. With the use of the nucleic acid pair complexes w10x as coupling molecules, it is possible to build the entire complementary strand, thereby forming the required double helix of B-DNA nucleotides. Local variations in the helix geometry are possible by allowing subtle changes on parameters, as for example; the rise per base, twist angle between nucleotides, propeller twist angle between bases, etc. w14 x. Also, it is important to note that, since the helix chain was not allowed for an energetic relaxation, the resulting structure represents a first approximation to the true helix in the gas phase. Nevertheless, the DNA molecule is a dynamic entity which preserves its identity under certain limits and, as a result, our approximate B-DNA structure should to good extent retain the important electronic features of the true system. To our best knowledge, this is the first B-DNA structure whose monomeric species are obtained from all-electron self-consistent-field calculations. Finally, in this work we focus attention on nucleotides in a single strand configuration and in the usual direction recognized as 5 X 3 X. In fact, we limit our analysis to doublets, considered as the shortest sequences, since we are interested on charge 1 w x In addition to the nucleotide coordinates of Ref. 12, bonds of terminal oxygens, linked to the deoxyribose ring, were saturated with hydrogen in order to simulate continuation of the helix chain. In Fig. 3 such a hydrogen appears under notation H15. distribution changes of nucleic bases when these are incorporated into nucleotides in a stacking geometry. We resort to density functional theory Ž DFT. to perform all computations. It is understood that DFT is one of the most flexible and reliable quantum mechanical techniques, appropriate for the relative large size compounds studied here, since simpler methods unfortunately fail on accuracy, while higher accurate schemes demand for time-consuming comw15 x. Hence DFT seems to be the suitable putations approach to study reactivity. In particular the method is based on the use of the wave function as traditional quantum mechanical methods do, and on the electron density. Both variables play a major role for solving self-consistently Schrodinger-type monoelectronic equations that emerge in the theory, and represent key ingredients for evaluating relevant quantities, among which MEPs and Mulliken population charges are of our concern. Further details about the application of the DFT approximation to DNA fragw10 12 x, and details about the method itself from literature ments are available from previous works w16 18 x. 3. Mulliken charge populations and molecular electrostatic potentials 3.1. The case of the nucleic acid bases and their pair complexes We show Mulliken populations of the nucleic acid bases in Fig. 1. It is found that all nitrogens and oxygens accumulate negative charge as a result of molecular relaxation. The excess is taken from nearby hydrogens and carbons which appear with positive sign. Negative populations around those nitrogens and oxygens with no hydrogen link promote the formation of deep electrostatic potential wells in the neighborhood, thus pointing out chemical active sites Ž also depicted at Fig. 1.. For the case of purine Ž A and G. molecules we find 3 electrostatic potentials wells, while for the case of pyrimidine Ž T and C. species only 2 are located. Their minima are reported in Table 1. Cytosine and guanine yield the deepest minima in comparison with their counterparts thymine and adenine.

4 320 ( ) R. Santamaria et al.rchemical Physics Fig. 1. Mulliken charge populations and molecular electrostatic potentials of DNA nucleic acid bases. Small rings identify minima in the electrostatic potential surfaces. Therefore, the G and C fragments yield the highest probabilities for interaction with alkylating agents or for an electrophilic attack. Our results are in good agreement with those of Ref. wx 3, except for cytosine. According to that reference, nitrogen N3 of cytosine renders a value of y93.5 kcalrmol, apparently more negative than O8 of the same molecule by just 6.8 kcalrmol. A result that, under the own words of its authors, is rather remarkable. The number, location and shape of reactive sites associated to nucleic acids represent important electronic features, in addition to geometric factors, that

5 ( ) R. Santamaria et al.rchemical Physics Table 1 Ž. a, b Minima of molecular electrostatic potentials MEPs for the case of DNA nucleic acids Center MEP Ž base. MEP Ž baserpair. MEP Ž baserdinucletide Ž C. 39 Ž CrCG " 8.5 Ž CrAC, CG, CT, CC, CC. N7 66 Ž G. 72 Ž GrCG. 163" 2 Ž GrAG, CG. O10 61 Ž G. 63 Ž GrCG. 144" 2 Ž GrAG, CG. N3 60 Ž C "6.5Ž CrAC, CG, CT, CC, CC. N3 52 Ž A. 51 Ž ArAT " 5.5 Ž ArAT, AG, AC. N1 51 Ž A. 140" 4 Ž ArAT, AG, AC. N7 49 Ž A. 44 Ž ArAT " 3.5 Ž ArAT, AG, AC. O8 47 Ž T. 40 Ž TrAT. 134" 1 Ž TrAT, CT. O7 42 Ž T. 45 Ž TrAT. 149" 0 Ž TrAT, CT. N3 37 Ž G. 48 Ž GrGC " 0.5 Ž GrAG, CG. a All minima, in ykcalrmol, are found at the planes of nucleic acid bases. b Abbreviations: Asadenine; Cscytosine; Gsguanine; Tsthymine. For pairs ArAT, for example, denotes adenine in the Watson Crick pair AT, while for dinucleotides, it denotes adenine in the dinucleotide AT with T above A as depicted in Fig. 3. must be taken into account in order to infer the kind of compounds that NABs may interact with wx 7. As an example, let us consider the case of guanine and cytosine. Both molecules contain the type of nitrogens and oxygens responsible for the presence of potential wells, then we can visualize such atoms as acceptor-like elements. On the other hand, hydrogens are recognized as donor-type entities with opposite sign. Hence, formation of different hydrogen bridges between G and C becomes possible due to the presence of donor and acceptor species in both fragments. As a result, different dimer residues are expected to appear, among which the Watson Crick pair Ž Fig. 2. represents a particular situation. Table 2 gives all feasible forms of H-bonded pairs among the NABs. The different conformers are described according to the donor and acceptor atoms taking part in the binding. In all these structures at least two hydrogen links appear 2, and in most cases donor atoms from one fragment fall deep inside the potential wells created by the acceptor atoms of the partner molecule. Experimental evidence about the occurrence of these H-bonded pairs in vacuo has so far been missing. However, in solution, pair formation of nucleic acid bases can be indirectly inferred. Nucleic 2 In general, pairs with only one hydrogen bridge are energetically less stable than those which contain two or more bridges. Thus, in this work, a H-bonded complex should be understood as containing two or more H-links. residues immersed in a non-aqueous medium tend to pair with higher rate than these in an aqueous solution. In the latter case water molecules come into competition to produce H-bonded compounds, leading to lower association constants among NABs that show on enthalpy changes. Nevertheless, problems arise when one tries to elucidate the kind of microscopic conformation adopted by dimers. A direct way to obtain structural information is by forming crystalline complexes among the different derivatives of the NABs, and performing the corresponding X-ray diffraction analysis. Henceforth, when one compares results from experiment with these predicted from Table 2, it is found that most of them indeed crystallize in a diversity of arrangements w19 x. Observations under this scheme show that nucleic acid bases are capable of linking with themselves producing homologous pairs, or with other bases resulting in mixed complexes where two, three or more NAB derivatives coexist in the H-bonded infinite network. Water molecules, and either tautomeric species of NABs, may also engage in the binding to give rise to alternative crystallographic forms. Interestingly enough is the fact that contrary to NABs immersed in solution, in crystals, Watson Crick linkages among the different nucleic acid derivatives seem to be energetically less stable than other types of H-bonding. Differences in their stability are attributed to different environments. For the particular case of Watson Crick pair complexes in vacuo, we have also carried out a

6 322 ( ) R. Santamaria et al.rchemical Physics

7 ( ) R. Santamaria et al.rchemical Physics Table 2 Different pairs of acceptor and donor atoms for each nucleic acid a, b, c base Adenine Guanine Thymine Cytosine N1, H12 N3, H13 O7, H13 N3, H9 N1, H13 N3, H16 O7, H14 O8, H13 N3, H13 N7, H15 O8, H10 N3, H15 O10, H14 O8, H14 N7, H11 a As a matter of example, adenine is capable of producing two hydrogen bridges with cytosine if atoms N1 and H12 of A link with atoms H9 and N3 of C, respectively. b In particular, the AT Watson Crick pair corresponds to the binding of the set N1, H12 of adenine with the set O8, H14 of thymine. For the GC Watson Crick pair, the corresponding sets are O10, H14 of guanine and N3, H9 of cytosine. The extra hydrogen bridge in the GC pair is implicitly contemplated in this binding since two links are enough to determine the kind of pair conformation. c Take note that, in addition to mixed dimers, homologous pairs should be also contemplated from the table. Mulliken analysis. Similar charge population results to these reported for single residues are found, refer to Fig. 2. No Mulliken charge transfer is noted from one molecule to the other since each fragment that builds the complex essentially retains its zero initial charge. However, substantial electronic reorganization occurs within each nucleic acid at the interaction region. If we compare Mulliken charges of those atoms taking part in the binding, before and after the formation of the complex, it is observed that hydrogens increase their positive charge while nitrogens and oxygens increase their negative charge. The new electron distribution induces local charge polarization between the partner molecules forming the dimer. It calls our attention that carbons 2, 5 and 6 of adenine, 4 of thymine, 5 and 6 of guanine, and 2 and 4 of cytosine also exhibit considerable charge readjustment, even when they are located relatively far away from the binding region. MEPs for the Watson Crick nucleic complexes are likewise depicted in Fig. 2. In pair complexes some of the original electrostatic potential wells attached to single NABs disappear. For instance, a total of 3 wells are found for single adenine before forming the complex, and only 2 of them are left once the formation of the AT dimer has taken place. The main reason is the near presence of atom H14 of thymine which produces a hydrogen bridge with N1 of adenine. Equivalent results about the lost of binding sites are observed for complex GC, where the formation of hydrogen bridges N3 H14 and O8 H12 essentially eliminates two potential wells initially attached to atoms N3 and O8 of cytosine. On the other hand, electrostatic potential wells that survive in the process of dimer formation largely preserve their original shape, and only some of them are cut or confined within a shorter region. Such potential wells in turn become the characteristic reactive centers of the Watson Crick pair complexes. The lowest values of the electrostatic potential surfaces corresponding to the AT and GC compounds are shown in Table 1. In comparison with single nucleic acids, the relative order among minima is greatly modified by pair formation. For example, the most drastic change is recorded for site O8 of cytosine. In the case of pairs, active site O8 shows the shallowest minimum, contrary to the case of single nucleic acids where it represents the deepest one. For other pair conformations among NABs, with equal demand of time-consuming computations, similar results are expected. In fact, Watson Crick dimers represent just an example where chemical active centers of single nucleic acids are potentially capable of linking a molecular partner in different conformations. Still, the question remains about possible changes of MEPs and population charges of NABs when other DNA constituents remain in their vicinity, a topic to be investigated next The case of the B-DNA single strand In this section we analyze charge populations and electrostatic potentials when nucleotides Žnucleic acid bases in conjunction with sugar and phosphate subunits. appear in a stacking configuration, or equiva- Fig. 2. Mulliken charge populations and molecular electrostatic potentials of DNA pair complexes. Small rings identify minima in the electrostatic potential surfaces. For comparison, charge populations of nucleic acids before pairing are also included.

8 324 ( ) R. Santamaria et al.rchemical Physics lently in a single strand conformation. This analysis represents a more general study than previous studies performed on single nucleic acids by other authors as we now take into account the additional contributions of phosphate groups and sugar compounds. Such contributions can not be neglected due to the long range nature of the forces that participate in the electrostatic potential expression. On the other hand, because of the large size of the DNA chain, we concentrate our study on the shortest complexes, this is doublets of nucleotides. Sixteen possible structures is the total number of compounds; however, we only need analyze the four combinations between purines and pyrimidines to determine electron distribution changes. Hence, we choose pairs AT, AG, CT and CG as examples. Figs. 3 and 4 illustrate the AT and AG doublets and establish atom numbering. We first pay attention to sugar and phosphate subunits and later on to the nucleic acids themselves. Careful comparisons of Mulliken populations among corresponding atoms, taking part in sugars and phosphates of the above mini-strands, indicate small differences. In Fig. 5, plots of Mulliken net charges versus atom label are shown. Only three curves are depicted there since all remaining data fall on one of such curves. It is not difficult to see that the largest discrepancies in sugar compounds are recorded for atoms C3, C4, O6 and H9, while for phosphate fragments differences appear at oxygens O3, O4 and O5. The deviations are indeed small and, in most instances, curves follow a similar trend. Changes computed on atoms C3, C4 and H9 of sugar molecules are attributed to a poor influence of the adjacent nucleic bases that participate in the doublet, while these changes recalled on oxygens are mainly due to the location of the phosphate molecule. The phosphate may stay in between or at the end of the strand, leading to different kinds of binding which in turn originate different atomic charges because of the finite size of the chain. In spite of that, atomic population discrepancies in sugar compounds and Fig. 3. Molecular electrostatic potentials, at the planes of nucleic acids, for the DNA sequence AT. Dark and transparent surfaces belong to A and T, respectively. Small rings identify relative minima and strips gaps of 10 kcalrmol, starting from 120 downwards, in the electrostatic potential surfaces. Refer to Fig. 1 for atom numbering in the nucleic acid bases.

9 ( ) R. Santamaria et al.rchemical Physics Fig. 4. Molecular electrostatic potentials, at the planes of nucleic acids, for the DNA sequence AG. Dark and transparent surfaces belong to A and G, respectively. Small rings identify relative minima and strips gaps of 10 kcalrmol, starting from 120 au downwards, in the electrostatic potential surfaces. Refer to Figs. 1 and 3 for atom numbering in the nucleic acid bases, sugar and phosphate compounds. phosphate groups in general appear negligible enough that, it is our opinion, they are incapable of producing decisive changes on reactivity. Such an argument is based on the fact that DNA assumes a dynamical role in a variety of biochemical processes. Therefore, the flexibility of DNA is one of the main reasons that such a molecule is capable of preserving, even under different conformations, the important genetic code. However, take note that it may be equally valid the conclusion that the observed differences in population charges of sugar and phosphates are important enough that such subunits can be considered as the first recognition sites to discriminate among the attached nucleic acid bases w20 22 x. Nevertheless, we remark and insist on the molecular flexibility of DNA to preserve the genetic information under relatively wide structural and electronic limits. Consequently, we may say that sugar and phosphate molecular groups preserve their electronic identity within some margins and constitute not only a structural, but also a common electronic backbone of DNA according to a Mulliken population analysis. Mulliken population comparisons have been also carried out for nucleic acid bases in the four possible single strands. We find that charge populations of A in the sequence AG are almost identical to these of A in AT, see Fig. 6. The same situation is observed for G in AG and CG, for T in AT and CT, and for C in CG and CT. Then, within the doublet approximation, Mulliken charges of nucleic bases are indifferent to the contiguous base, whether this last one is situated above or under the reference nucleic acid. As a matter of fact, major charge population changes in nucleic bases are produced by the near presence of sugar and phosphate compounds. For instance, adenine alone and within the mini-strands shows substantially different charge populations, refer to Fig. 6. Equivalent results occur for the other bases. The new charge distribution of nucleic bases in the ministrands is mainly perceived at their junction with the

10 326 ( ) R. Santamaria et al.rchemical Physics Fig. 5. Mulliken populations of the eight sugar and phosphate subunits taking part in the mini-sequences AG, AT, CG and CT. Only three curves are shown since all data fall in one of such curves: sugar and phosphate of adenine in AG Ž v., of guanine in CG Ž B. and of thymine in AT Ž '.. Refer to Fig. 3 for atom numbering in sugar and phosphate groups. sugar molecule Ž see, e.g., N9 in Fig. 6. and in the case of purines, the redistribution includes the sixmembered rings. On the other hand, MEPs of A inside the sequences AT and AG are depicted at Figs. 3 and 4. In these figures, the two surfaces generated by the A nucleotide show similar not only in shape, but also in reference to the depth of potential wells. However, this is not the case when we compare the adenine surface with that generated by the G nucleotide. Guanine with its phosphate group yield an extended surface with just one isolated well Žin the vicinity of N3. that simulates an island, see Fig. 4. In contrast, adenine and its corresponding phosphate molecule exhibit a less extended surface and two isolated wells Ž one near to N1 and the other near to N3.. On the other hand, if we compare MEPs produced by purines against these of pyrimidines, clear differences emerge. Pyrimidines present surfaces separated from those of the phosphate group due to the interposition of H-bonds of either the amino group NH of cytosine or radical CH of thymine, refer for instance to Fig. 3. Hence, electrostatic potential wells of pyrimidines, because of their relative small size, become slightly more inaccessible within the DNA complex. Still note that the external part of the electrostatic potential surfaces produced by phosphate groups of purines and pyrimidines resemble each other. In fact, main differences in MEPs of dinucleotides are introduced by the nucleic acids themselves. For larger single strands we expect similar results. In Table 1, we consider the lowest values in the MEP surface associated to nucleic acid bases. Six different dinucleotide systems have been now contemplated there to carry out some statistics, namely; AG, AT, AC, CG, CT and CC. Values appear with deviations in order to summarize results in one central value and be able to establish relative order among minima. In particular, we observe that chemi-

11 ( ) R. Santamaria et al.rchemical Physics Fig. 6. Mulliken populations of adenine alone and in the mini-strands AG and AT. Refer to Fig. 1 for atom numbering. cal active center N7 of guanine and adenine leads to the deepest potential wells. They are closely followed by these produced by O8 and N3 of cytosine, and O7 of thymine. Note also that the relative order among minima in this last column differs from previous columns of Table 1. Therefore, preferred sites for electrophilic attack of nucleic bases participating in dinucleotides are different to these previously predicted for single nucleic acids and base pairs. However, as a common factor among values of Table 1, all minima are found at the planes of nucleic acid bases Žregardless the bases stay alone, forming pairs or building dinucleotides.. Other auwx 3 have found secondary minima out of the thors planes of nucleic acids A and C. Nevertheless, a careful DFT analysis indicates that it is due to the nonplanarity of amino hydrogens. When nucleic bases take part in base pairs, such hydrogens become planar and the secondary minima disappear. In dinucleotides, minima out of the molecular plane are observed for A in AG and AT, and for C in CG and CT. The minima of A and C are located in opposite direction to the other nucleotide building the dinucleotide, in this case G or T. For the interesting mini-sequence AC, which involves both A and C, we observe a minimum out of the plane of A but do not observe a minimum out of the plane of C. A similar situation occurs for C in C1C 2, where there is an out of plane minimum attributed to the first cytosine Ž C. but not found in the second one Ž C Hence, the stacking conformation of nucleotides becomes an important factor, in addition to the planarity of amino hydrogens, to make disappear such kind of secondary minima. Based on the above results of Mulliken charge populations and MEP for phosphates, sugars and nucleic acid bases, we conclude that recognition of specific DNA sequences proceeds at short distances. The assertion derives from the fact that Mulliken charges and MEPs associated to phosphate and sugar subunits keep to great part their own electronic identity as a result of a relative poor influence from adjacent nucleic acid bases. Therefore, a partner molecule approaching to DNA is expected to be first

12 328 ( ) R. Santamaria et al.rchemical Physics attracted by the strong field created by the phosphate group w23x and, as the partner gets closer, potential wells of nucleic acid bases come into play in the selective process favoring a close contact recognition. This result is experimentally evidenced in gene regulatory proteins w24 x. Finally, our results should be useful to understand processes related to genetic recognition, such as DNA transcription, where discrimination of nucleotides plays an important role. Also, they should be of help to build more realistic models about the dynamics of DNA replication. In this last case we call attention to the molecular machine approximation, where one might refer to a molecular machine as an assembly of polymeric molecules with one of them sliding over the other, in order to transport some energy or certain type of mass. Note that the transportation of mass may be also understood as the transportation of information w25 x. Of course, the sliding Ž or sticking. of molecules should depend on the potential wells that one molecule finds along the other one. 4. Conclusions In this work we have shown the simplicity and importance of molecular electrostatic potentials and Mulliken charge populations to elucidate reactive centers of DNA. The application of both schemes to the nucleic acid bases revealed the existence of a variety of H-bonded associates among NABs. Experiments based on their derivatives confirm the dominant role of the electrostatic force, that participates in the MEPs, for predicting the pairing of compounds of such nature. Particular attention given to Watson Crick dimers showed that, electronic charge is mainly reaccommodated at the interaction region between fragments, inducing local polarization, with the consequent lost of some binding sites. Surviving electrostatic potential wells in the process of dimer formation remain essentially with the same shape, except at some instances where they show clipped sides. A study on nucleotides indicated that sugar molecules and phosphate groups represent not only a structural, but also an electronic backbone of DNA. Nucleic acid bases in dinucleotides do not show important charge readjustment for the presence of a contiguous base, weather this last one is positioned above or under the reference nucleic acid. Then, it is assumed that selective interactions between partner molecules with DNA may be characterized as close contact interactions since nucleic acids are uncapable of substantially altering the charge populations and molecular electrostatic potentials of sugar and phosphate subunits that could indicate the presence of one or another adjacent nucleic acid base. Nucleic acids taking part in dinucleotides yield different preferred sites for an electrophilic attack to these found in single nucleic acids and pair complexes. This is due to the additional contributions of phosphate and sugar compounds, which are not negligible because of the long range nature of the electrostatic forces that appear in the MEP expression. However, a common factor among all reactive centers is the fact that they appear with their lowest values at the planes of nucleic acids, with some secondary sites observed out of molecular planes under special circumstances. Finally, it is important to mention that, the set of hydrogen atoms that participate in the binding of nucleic acid bases not only ensures a weak linking between bases, but also help to preserve the identity of each base inside the DNA complex. This is due to the limited charge reorganization that hydrogen atoms can suffer in comparison with heavier elements that, otherwise, could appear at the interaction region. Features like weak bonding make possible the process of exact duplication, while electronic identity preservation of nucleic acids in DNA makes possible the saving and interpretation of the genetic information. References wx 1 P. Politzer, D.G. Truhlar Ž Eds.., Chemical Applications of Atomic and Molecular Electrostatic Potentials, Plenum, New York, wx 2 J.S. Murray, K. Sen Ž Eds.., Molecular Electrostatic Potentials: Concepts and Applications, Elsevier, New York, wx 3 R. Bonaccorsi, A. Pullman, E. Scrocco, J. Tomasi, Theor. Chim. Acta 24 Ž wx 4 J.J.M. Wiener, M.E. Grice, J.S. Murray, P. Politzer, J. Chem. Phys. 104 Ž wx 5 P.C. Mishra, R.D. Tewari, Int. J. Quantum Chem. 32 Ž

13 ( ) R. Santamaria et al.rchemical Physics wx 6 K. Morokuma, K. Kitauro, in: P. Politzer, D.G. Truhlar Ž Eds.., Chemical Applications of Atomic and Molecular Electrostatic Potentials, Plenum, New York, 1981, pp wx 7 I. Alkorta, J.J. Perez, Int. J. Quantum Chem. 57 Ž wx 8 R.S. Mulliken, J. Chem. Phys. 23 Ž wx 9 C.G. Mohan, A. Kumar, P.C. Mishra, Int. J. Quantum Chem. 60 Ž w10x R. Santamaria, A. Vazquez, J. Comput. Chem. 15 Ž w11x R. Santamaria, E. Charro, A. Zacarias, M. Castro Ž1997, submitted for publication.. w12x R. Santamaria, A. Quiroz-Gutierrez, C. Juarez, J. Mol. Struct. Ž Theochem. 357 Ž w13x R.E. Dickerson, Sci. Am. 249 Ž w14x C.R. Calladine, J. Mol. Biol. 161 Ž w15x G. Bakalarski, P. Grochowski, J.S. Kwiatkowski, B. Lesyng, J. Leszczynski, Chem. Phys. 204 Ž w16x R.G. Parr, W. Yang, Density Functional Theory of Atoms and Molecules, International Series of Monographs on Chemistry, 16, Oxford University Press, Oxford, w17x J.K. Labanowski, J.W. Andzelm Ž Eds.., Density Functional Methods in Chemistry, Springer, New York, w18x J.M. Seminario, P. Politzer Ž Eds.., Modern Density Functional Theory: A Tool for Chemistry, Theoretical and Computational Chemistry Series, vol. 2, Elsevier, Amsterdam, w19x D. Voet, A. Rich, Prog. Nucleic Acid Res. Mol. Biol. 10 Ž , and references therein. w20x T. Shinoda, N. Shima, M. Tsukada, J. Theor. Biol. 151 Ž w21x T. Shinoda, N. Shima, M. Tsukada, Int. J. Quantum Chem. 47 Ž w22x T. Shinoda, N. Shima, M. Tsukada, Int. J. Quantum Chem. 49 Ž w23x P.K. Weiner, R. Langridge, J.M. Blaney, R. Schaefer, P.A. Kollman, Proc. Natl. Acad. Sci. USA 79 Ž w24x A. Klug, in: D.A. Chambers Ž Ed.., DNA: The Double Helix, vol. 758, Ann. N.Y. Acad. Sci., New York, w25x R.M. Stroud, C.R. Cantor, T.D. Pollard Ž Eds.., Annual Review of Biophysics and Biomolecular Structure, vol. 23, Annual Reviews Inc., Palo Alto, CA, 1994.