Molecular electrostatic potential of the nucleic acids

Solution structure of a guanine-N7-linked complex of the mitomycin C metabolite 2,7-diaminomitosene and DNA. Basis of sequence selectivity

2,7-Diaminomitosene (2,7-DAM), the major metabolite of the antitumor antibiotic mitomycin C, forms DNA adducts in tumor cells. 2,7-DAM was reacted with the deoxyoligonucleotide d(GTGGTATACCAC) under reductive alkylation conditions. The resulting DNA adduct was characterized as d(G-T-G-[M]G-T-A-T-A-C-C-A-C) (5), where [M]G stands for a covalently modified guanine, linked at its N7-position to C10 of the mitosene. The adducted oligonucleotide complements with itself, retaining 2-fold symmetry in the 2:1 drug-duplex complex, and provides well-resolved NMR spectra, amenable for structure determination. Adduction at the N7-position of G4 ([M]G, 4) is characterized by a downfield shift of the G4(H8) proton and separate resonances for G4(NH(2)) protons. We assigned the exchangeable and nonexchangeable proton resonances of the mitosene and the deoxyoligonucleotide in adduct duplex 5 and identified intermolecular proton-proton NOEs necessary for structural characterization. Molecular dynamics computations guided by 126 intramolecular and 48 intermolecular distance restraints were performed to define the solution structure of the 2,7-DAM-DNA complex 5. A total of 12 structures were computed which exhibited pairwise rmsd values in the 0.54-1.42 A range. The 2,7-DAM molecule is anchored in the major groove of DNA by its C10 covalently linked to G4(N7) and is oriented 3' to the adducted guanine. The presence of 2,7-DAM in the major groove does not alter the overall B-DNA helical structure. Alignment in the major groove is a novel feature of the complexation of 2,7-DAM with DNA; other known major groove alkylators such as aflatoxin, possessing aromatic structural elements, form intercalated complexes. Thermal stability properties of the 2,7-DAM-DNA complex 5 were characteristic of nonintercalating guanine-N7 alkylating agents. Marked sequence selectivity of the alkylation by 2,7-DAM was observed, using a series of oligonucleotides incorporating variations of the 5'-TGGN sequence as substrates. The selectivity correlated with the sequence specificity of the negative molecular electrostatic potential of the major groove, suggesting that the alkylation selectivity of 2,7-DAM is determined by sequence-specific variation of the reactivity of the DNA. The unusual, major groove-aligned structure of the adduct 5 may account for the low cytotoxicity of 2,7-DAM.

2'-Deoxyguanosine reacts with a model quinone methide at multiple sites

Quinone methides and related intermediates have been implicated in a range of beneficial and detrimental processes in biology and effectively alkylate a variety of cellular components despite the ubiquitous presence of water. As a prerequisite to understanding the origins of their specificity, the major products generated by DNA and its components with an unsubstituted ortho quinone methide under aqueous conditions were recently characterized [Pande, P., Shearer, J., Yang, J., Greenberg, W. A., and Rokita, S. E. (1999) J. Am. Chem. Soc. 121, 6773-6779]. Investigations currently focus on the complete range of derivatives formed by deoxyguanosine (dG) and guanine residues in duplex DNA through product isolation and structure determination using reversed-phase chromatography and a range of one and two-dimensional NMR techniques. Previous construction of a synthetic standard for dG alkylation is now shown to have yielded the N1-linked adduct rather than the N(2)-linked adduct. This later adduct has also now been characterized and confirmed to be the major product of reaction between the quinone methide and both duplex DNA and dG under neutral conditions. An N7 adduct of guanine has additionally been identified under these conditions and appears to result from spontaneous deglycosylation of the corresponding N7 adduct of dG. A combination of steric and electronic properties of duplex DNA likely contribute to the enhanced selectivity of the quinone methide for its guanine N(2) position (7.8:3.2:1.0 for adducts of N(2):N7:N1) relative to that of dG (4.7:3.5:1.0 for adducts of N(2):N7:N1).

Development of distamycin-related DNA binding anticancer drugs

The relatively low therapeutic index of the clinically used alkylating agents is probably related to the fact that these compounds cause DNA damage in a relatively unspecific manner, mainly involving guanine-cytosine rich stretches of DNA present in virtually all genes, therefore inducing unselective growth inhibition and death, both in neoplastic and in highly proliferative normal tissues. These considerations explain why in the last twenty years there has been an increasing interest in the identification of compounds which can target DNA with a much higher degree of sequence specificity than that of conventional alkylators. Minor groove binders (MGBs) are one of the most widely studied class of alkylating agents characterised by a high level of sequence specificity. The prototype of this class of drugs is distamycin A which is an antiviral compound able to interact, non-covalently, in theminor groove of DNA in A-T rich regions. It is not cytotoxic against tumour cells and thus has been used as a carrier for targeting cytotoxic alkylating moieties in theminor groove of DNA. The benzoyl mustard derivative of distamycin A, tallimustine, was found to be able to alkylate the N(3) of adenine in theminor groove of DNA only in the target hexamer 5'-TTTTGA or 5'-TTTTAA. Tallimustine was investigated in the clinic and was not successful because it causes severe bone marrow toxicity. The screening of other distamycin derivatives, which maintain antitumour activity and exhibit much lower toxicity against human bone marrow cells than tallimustine led to the identification of brostallicin (PNU-166196) which is currently under early clinical investigation. Although MGBs which bind DNA in A-T rich regions have not fulfilled the expectations, it is too early to draw definitive conclusions on this class of compounds. The peculiar bone-marrow toxicity observed in the clinic both with tallimustine or with CC-1065 derivatives is not necessarily a feature of all MGBs, as indicated by recent evidence obtained with brostallicin and other structurally unrelated MGBs (e.g., ET-743).

Chemical reagents for investigating the major groove of DNA

Chemical modification provides an inexpensive and rapid method for characterizing the structure of DNA and its association with drugs and proteins. Numerous conformation-specific probes are available, but most investigations rely on only the most common and readily available of these. The major groove of DNA is typically characterized by reaction with dimethyl sulfate, diethyl pyrocarbonate, potassium permanganate, osmium tetroxide, and, quite recently, bromide with monoperoxysulfate. This commentary discusses the specificity of these reagents and their applications in protection, interference, and missing contact experiments.

Selective intercalation of charge neutral intercalators into GG and CG steps: implication of HOMO-LUMO interaction for sequence-selective drug intercalation into DNA

We have synthesized naphthopyranone epoxide 4 from D-isoascorbic acid together with its three diastereoisomers. DNA alkylation of ODNs containing 5'XGT3' and 5'TGY3' by 4 (11R, 13R), where X and Y are any nucleotide bases, occurred at all G residues except at G of the 5'TGC3' sequence. In contrast, the three other diastereoisomers of 4 showed only weak G alkylation activity. Differential (1)H NMR NOE of the 4-G adduct confirmed the G-N7 alkylation at the epoxide carbon of 4 with concomitant S(N)2 ring opening of the epoxide. Quantitative HPLC analysis of G alkylation efficiency for 4 showed the order of G alkylation susceptibility as TGGT approximately CGT >> TGA > AGT > TGT >> TGC. The order was fully consistent with those reported for aflatoxin B(1) oxide and kapurimycin A(3), suggesting that the sequence selectivity observed for these DNA alkylating agents is not structure dependent but most likely due to the intrinsic property of DNA sequences. We found that the order of G alkylation susceptibility obtained for 4 completely matched the calculated HOMO energy level of G-containing sequences. These results underscore that 4 is a unique molecular probe for ranking the HOMO level of G-containing sequences by well-known G alkylation chemistry and suggests that the intercalation of charge neutral intercalators is a HOMO-controlled process.

Fluorescent DNA: the development of 7-deazapurine nucleoside triphosphates applicable for sequencing at the single molecule level

7-Deaza-2'-deoxyadenosine and -guanosine phosphoramidite building blocks as well as corresponding 5'-triphosphate derivatives are described carrying in position 7 substituents such as iodo, hexyn-1-yl or 5-aminopentyn-1-yl residues. The phosphoramidites were used to synthesize a series of modified oligodeoxynucleotides. A systematic study of the thermal stabilities of these oligonucleotide duplexes demonstrated that the 7-substituents are well accommodated in the major groove of B-DNA. The 7-(aminoalkyn-1-yl)-7-deazapurine 2'-deoxynucleoside triphosphates were labeled with bulky fluorophores such as Rhodamine Green(R) or tetramethylrhodamine.

Electrospray ionization mass spectrometry of oligonucleotide complexes with drugs, metals, and proteins

I. Introduction 61 II. Binding of Small Molecules to DNA 62 A. Covalent Binding 62 B. Reversible (Noncovalent) DNA-Binding Agents 65 III. DNA-Metal Ion Complexes 67 A. Platinum Complexes 70 B. Other Metal Ions 73 IV. DNA-Protein Complexes 74 A. Introduction 74 B. ESI-MS of DNA-Protein Complexes 76 C. ESI-MS Analysis of Proteolytic Products of DNA-Protein Complexes 79 D. ESI-MS of Ternary DNA-Protein-Ligand Complexes 80 V. Conclusions 80 Abbreviations 81 References 81 --Interactions of DNA with drugs, metal ions, and proteins are important in a wide variety of biological processes. With the advent of electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI), mass spectrometry (MS) is now a well-established tool for the characterization of the primary structures of biopolymers. The gentle nature of the ESI process, however, means that ESI-MS is also finding application for the study of noncovalent and other fragile biomolecular complexes. We outline here the progress, to date, in the use of ESI-MS for the study of noncovalent drug-DNA and protein-DNA complexes together with strategies that can be employed to examine the binding of small molecules and metal complexes to DNA. In the case of covalent complexes with DNA, sequence information can be derived from ESI-MS used in conjunction with tandem mass spectrometry (MS/MS) and/or enzymatic digestion. MS/MS can also be used to probe the relative binding affinities of drugs that bind to DNA via noncovalent interactions. Overall, the work in this area, to date has demonstrated that ESI-MS and MS/MS will prove to be valuable complements to other structural methods, offering advantages in terms of speed, specificity, and sensitivity. (c) 2001 John Wiley & Sons, Inc.

Semi-empirical, ab initio and molecular modeling studies on the DNA binding of a calicheamicinone-polyamide conjugate

AM1 semi-empirical and ab initio calculations were performed on certain synthetic polyamide conjugates of the aglycone of the minor groove binding antibiotic calicheamicin. Geometry optimized conformations and heats of formation were obtained. The binding of the optimized conformations of the drug to both alternating and non-alternating (AT)n and to (G)n x (C)n sequences were studied and the energies of binding were compared to each other. The results can be utilized in the design of novel enediyne-based drugs.

Replacement of an NH(3) by an iminoether in transplatin makes an antitumor drug from an inactive compound

To investigate the modifications of antitumor activity and DNA binding mode of transplatin after replacement of one nonleaving group NH(3) by an iminoether group, trans-[PtCl(2)(Z-HN=C(OMe)Me)(NH(3)] and trans-[PtCl(2)(E-HN=C(OMe)Me)(NH(3)] complexes (differing in the Z or E configuration of iminoether, and abbreviated mixed Z and mixed E, respectively), have been synthesized. In a panel of human tumor cell lines, both mixed Z and mixed E show a cytotoxic potency higher than that of transplatin, the mean IC(50) values being 103, 37, and 215 microM, respectively. In vivo mixed Z is more active and less toxic than mixed E in murine P388 leukemia and retains its efficacy against SK-OV-3 human cancer cell xenograft in nude mice. In the reaction with naked DNA, mixed Z forms monofunctional adducts that do not evolve into intrastrand cross-links but close slowly into interstrand cross-links between complementary guanine and cytosine residues. The monofunctional mixed Z adducts are removed by thiourea and glutathione. The interstrand cross-links behave as hinge joints, increasing the flexibility of DNA double helix. The mixed Z, transplatin, and cisplatin interstrand cross-links, as well as mixed Z monofunctional adducts are not specifically recognized by HMG1 protein, which was confirmed to be able to specifically recognize cisplatin d(GpG) intrastrand cross-links. These data demonstrate that the DNA interaction properties of the antitumor-active mixed Z are very similar to those of transplatin, thus suggesting that clinical inactivity of transplatin could not depend upon its peculiar DNA binding mode.

1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium

The 1 A resolution X-ray crystal structures of Mg(2+) and Ca(2+) salts of the B-DNA decamers CCAACGTTGG and CCAGCGCTGG reveal sequence-specific binding of Mg(2+) and Ca(2+) to the major and minor grooves of DNA, as well as non-specific binding to backbone phosphate oxygen atoms. Minor groove binding involves H-bond interactions between cross-strand DNA base atoms of adjacent base-pairs and the cations' water ligands. In the major groove the cations' water ligands can interact through H-bonds with O and N atoms from either one base or adjacent bases, and in addition the softer Ca(2+) can form polar covalent bonds bridging adjacent N7 and O6 atoms at GG bases. For reasons outlined earlier, localized monovalent cations are neither expected nor found.Ultra-high atomic resolution gives an unprecedented view of hydration in both grooves of DNA, permits an analysis of individual anisotropic displacement parameters, and reveals up to 22 divalent cations per DNA duplex. Each DNA helix is quite anisotropic, and alternate conformations, with motion in the direction of opening and closing the minor groove, are observed for the sugar-phosphate backbone. Taking into consideration the variability of experimental parameters and crystal packing environments among these four helices, and 24 other Mg(2+) and Ca(2+) bound B-DNA structures, we conclude that sequence-specific and strand-specific binding of Mg(2+) and Ca(2+) to the major groove causes DNA bending by base-roll compression towards the major groove, while sequence-specific binding of Mg(2+) and Ca(2+) in the minor groove has a negligible effect on helix curvature. The minor groove opens and closes to accommodate Mg(2+) and Ca(2+) without the necessity for significant bending of the overall helix. The program Shelxdna was written to facilitate refinement and analysis of X-ray crystal structures by Shelxl-97 and to plot and analyze one or more Curves and Freehelix output files.

Determination by electrospray mass spectrometry of the outersphere association constants of DNA/platinum complexes using 20-mer oligonucleotides and ([Pt(NH(3))(4)](2+), 2Cl(-)) or ([Pt(py)(4)](2+), 2Cl(-))

The cytotoxic effects of cisplatin, cis-diamminedichloroplatinum(II), are generally ascribed to the formation of DNA adducts. Several in vitro as well as in vivo studies showed that cisplatin binds preferentially to guanines belonging to (G)(n) sequences (n > or = 2). After mono- or diaquation of cisplatin, giving the cationic complexes cis-[PtCl(NH(3))(2)(H(2)O)](+) and cis-[Pt(NH(3))(2)(H(2)O)(2)](2+), DNA platination occurs in two steps: the cationic complex gives an outersphere association with DNA and the actual coordination then occurs by substitution of one aqua ligand by guanine-N7. For a better understanding of the (G)(n) selectivity of cisplatin giving the biologically active adducts, also necessary for the conception of new platinum drugs, the respective contribution of the outersphere association and actual guanine platination must be investigated. To check the role of outersphere association in the overall platination process, we used electrospray mass spectrometry (ESMS) to detect and quantify outersphere association between 20-mer oligonucleotides and platinum complexes. The 20-mer oligonucleotides were single- or double-stranded, with the same number of guanines either isolated or adjacent to each other. To deal only with outersphere association and check the influence of platinum ligands, the [Pt(NH(3))(4)](2+) and [Pt(py)(4)](2+) complexes were used. We characterized by ESMS all the different outersphere association species formed during titration of each oligonucleotide with the various platinum complexes and evaluated their affinity constants. The ESMS results demonstrate that the outersphere association depends on electrostatic interactions and on the ability of the platinum ligands to participate to hydrogen bonding, particularly within the duplex form.

DNA structure control by polycationic species: polyamine, cobalt ammines, and di-metallo transition metal chelates

Many polycationic species bind to DNA and induce structural changes. The work reported here is the first phase of a program whose long-term aim is to create a class of simple and inexpensive sequence-selective compounds that will enable enhanced DNA structure control for a wide range of applications. Three classes of molecule have been included in this work: the polyamine spermine (charge: 4(+)) and spermidine (charge: 3(+)) (which are known to induce a wide range of DNA conformational changes but whose binding modes are still not well understood); cobalt (III) amine transition metal complexes as potential polyamine mimics and [Fe(H(2)O)(6)](3+); and the first member of a new class of di-metallo tris-chelated cylinders of helical structure (charge 4(+)). Temperature-dependent absorption, circular dichroism, linear dichroism, gel electrophoresis, and molecular modeling data are presented. The cobalt amines prove to be effective polyamine mimics, although their binding appears to be restricted to backbone and major groove. All the ligands stabilize the DNA, but the 4(+) di-iron tris-chelate does so comparatively weakly and seems to have a preference for single-stranded DNA. All the molecules studied bend the DNA, with the di-iron tris-chelate having a particularly dramatic effect even at very low drug load.

Medium Effects on Reactivity Profiles for Platination of Phosphorothioate-Containing Oligonucleotides

Reactions of cis-[Pt(NH(3))(NH(2)C(6)H(11))Cl(OH(2))](+) with d(Tp(S)T) and d(T(n)()p(S)T(16)(-)(n)()), n = 1, 4, 8, 12, and 15, were investigated by use of HPLC in an aqueous medium with pH 4.1 +/- 0.1 and sodium and magnesium ion concentrations varying between 1.5 mM and 0.50 M. Platination of the oligonucleotide fragments is favored over platination of d(Tp(S)T) in the whole salt concentration interval studied. The maximum rate enhancement after incorporation of the p(S)-site into the polymeric DNA environment is observed for d(T(8)p(S)T(8)), which reacts up to ca. 500 times faster than d(Tp(S)T), after suitable changes of the cation concentrations in the reaction medium. The platination rates of the oligonucleotide fragments d(T(n)()p(S)T(16)(-)(n)()) decrease with increasing salt concentration. For a given phosphorothioate position, the rate also decreases when the cations in the medium are changed from Na(+) or K(+) to Mg(2+), even at constant ionic strength. The reactions with embedded p(S)-sites in d(T(n)()p(S)T(16)(-)(n)()), n = 4, 8, and 12, were found to be kinetically favored over reactions with the 5'- and 3'-end positions. In a reaction medium containing monovalent cations there is a strong preference for platination of d(T(8)p(S)T(8)), whereas d(T(4)p(S)T(12)) and d(T(12)p(S)T(4)) show intermediate reactivity compared with fragments with n = 1 and 15. In contrast, no kinetic discrimination is found between the p(S)-sites in d(T(n)()p(S)T(16)(-)(n)()), n = 4, 8, and 12, in the presence of Mg(2+). The results are interpreted in terms of a general mechanism where preaccumulation of the cationic Pt(II) complex on the oligomers is required for product formation. The kinetics are consistent with a reaction model that includes release of cations from the DNA surface during the adduct formation process.

Nickel and cobalt reagents promote selective oxidation of Z-DNA

The structural characteristics of Z-DNA were used to challenge the selectivity of guanine oxidation promoted by nickel and cobalt reagents. Base pairing and stacking within all helical structures studied previously had hindered access to guanine and limited its reaction. However, the Z-helix uniquely retains high exposure of guanine N7. This exposure was sufficient to direct oxidation specifically to a plasmid insert -(CG)(13)AATT(CG)(13)- that adopted a Z-conformation under native supercoiling. An alternative insert -(CG)(7)- retained its B-conformation and demonstrated the expected lack of reactivity. For a nickel salen complex made from a particularly bulky ligand, preferential reaction shifted to the junctions within the Z-DNA insert as is common for large reagents. Inactivation of the nickel reagents by high-salt concentrations prevented parallel investigations of Z-DNA, formed by oligonucleotides. However, the activity of Co(2+) was minimally affected by salt and consequently confirmed the high reactivity of 5'-p(CG)(4) in its Z-conformation. These reagents may now be applied to a broad array of targets, since their structural specificity remains predictable for both complex and helical assemblies of nucleic acids.

Activity and DNA binding of new organoamidoplatinum (II) complexes

Two series of organoamidoplatinum (II) complexes were synthesized [Class 1, Pt(NRCH2)2L2 and Class 2, Pt(NRCH2CH2NR2')L(X)] and their antitumour activity examined by a range of in vitro, cellular and animal studies. All Class 1 compounds exhibited activity comparable to cisplatin in mouse leukemia L1210 cells, but were at least 8-fold more active against the cisplatin-resistant L1210/R line. The lead compound 1a (R=p-HC6F4) caused nearly complete tumour regression in the ADJ/PC6 mouse tumour model. Compound 1a exhibited similar DNA reactivity to cisplatin, resulting in virtually identical DNA sequence specificity as cisplatin, and had similar time and concentration dependency of interstrand crosslinks. Compared with cisplatin, la showed 3-fold greater cellular uptake into human ovarian carcinoma 2008 cells, and this was dramatically enhanced to 17-fold in the cisplatin-resistant 2008/R line. The activity of 1a, therefore, appears to be due at least in part to a greater cellular uptake into tumour cells, particularly cisplatin-resistant cells, and once in the cell it reacts with DNA in a similar manner to that of cisplatin. The enhanced uptake and enhanced cytotoxicity of Class 1 compounds, and 1a in particular, may be due to a greater hydrophobicity compared with cisplatin. The activity of the Class 2 compounds, especially in the cisplatin-resistant cell lines, is unusual because they have trans amine ligands, and further study of both classes of compounds is warranted.

How NF-kappaB can be attracted by its cognate DNA

NF-kappaB is involved in the transcriptional regulation of a large number of genes, in particular those of human immunodeficiency virus (HIV). Recently, we used NMR spectroscopy and molecular modelling to study the solution structure of a native duplex related to the HIV-1 kappaB site, together with a mutated duplex for which a three base-pair change abolishes NF-kappaB binding. The native duplex shows unusual dynamics of the four steps surrounding the kappaB site. Here, we explore the intrinsic properties of the NMR-refined structures of both duplexes in order to understand why the native sequence is recognised by NF-kappaB among other DNA sequences. We establish that only the native kappaB site can adopt a conformation where its structure (curvature and base displacement), the accessibility and the electrostatic potentials of key atoms become very favourable for binding the large loops of NF-kappaB, in contrast to the mutated duplex. Finally, we show that the neutralisation of phosphate groups contacted by NF-kappaB favours a more canonical DNA structure. These findings lead to a new hypothesis for specific recognition through the phosphodiester backbone dynamics of the sequences flanking a binding site. Such unusual behaviour confers upon the overall duplex properties that can be used by NF-kappaB to select its binding site. Thus, the selectivity determinants for NF-kappaB binding appear to depend on deformability of an "extended" consensus sequence.

A survey of the sequence-specific interaction of damaging agents with DNA: emphasis on antitumor agents

This article reviews the literature concerning the sequence specificity of DNA-damaging agents. DNA-damaging agents are widely used in cancer chemotherapy. It is important to understand fully the determinants of DNA sequence specificity so that more effective DNA-damaging agents can be developed as antitumor drugs. There are five main methods of DNA sequence specificity analysis: cleavage of end-labeled fragments, linear amplification with Taq DNA polymerase, ligation-mediated polymerase chain reaction (PCR), single-strand ligation PCR, and footprinting. The DNA sequence specificity in purified DNA and in intact mammalian cells is reviewed for several classes of DNA-damaging agent. These include agents that form covalent adducts with DNA, free radical generators, topoisomerase inhibitors, intercalators and minor groove binders, enzymes, and electromagnetic radiation. The main sites of adduct formation are at the N-7 of guanine in the major groove of DNA and the N-3 of adenine in the minor groove, whereas free radical generators abstract hydrogen from the deoxyribose sugar and topoisomerase inhibitors cause enzyme-DNA cross-links to form. Several issues involved in the determination of the DNA sequence specificity are discussed. The future directions of the field, with respect to cancer chemotherapy, are also examined.

DNA Binding by 4-Methoxypyrrolic Natural Products. Preference for Intercalation at AT Sites by Tambjamine E and Prodigiosin

The 4-methoxypyrrolic natural products contain a common 4-methoxy-2,2'-bipyrrole chromophore and exhibit promising anticancer, antimicrobial, and immunosuppressive activities. Herein, the ability of two representative members, tambjamine E (1) and prodigiosin (2), to bind calf thymus DNA (CT-DNA), polyd[G-C](2), and polyd[A-T](2) has been characterized using absorption and fluorescence spectroscopy. Scatchard plots showed that 1 occupies a site size (n) of ca. three base pairs and possesses affinity constants (K) ranging from 1 to 0.1 x 10(5) M(-)(1). Prodigiosin (2) binds DNA by mixed modes, as isobestic points were not evident in titration experiments. The neutral aldehyde precursor 4 was found to possess no measurable DNA binding affinity, indicating that the enamine structure of 1 and the pyrromethene of 2 are essential elements for DNA binding affinity. The enamine of 1 was found to undergo hydrolysis to 4 with a half-life (t(1/2)) of 14.5 h at pH 7.4 and 37.5 degrees C. For the B-ring nitrogen atom of 1, a pK(a) value of 10.06 was also established. From fluorescence spectroscopy it was found that 1, 2, and 4 possess weak emission spectra in water that is increased in nonaqueous solvents. For 1 and 2, DNA binding also increased the emission yield. Energy-transfer measurements suggested an intercalative binding mode, with preference for AT sites. The ability of distamycin to displace 1 and 2 from the helix also suggested that they intercalate from the minor-groove. This specificity differs from other unfused aromatic cations that bind by a minor-groove mode at AT sequences and intercalate at GC sites. Reasons for the specificity displayed by 1 and 2, as well as the implications of our findings to their biological properties are discussed.

Treatment of human cells with N-Nitroso(acetoxymethyl)methylamine: distribution patterns of piperidine-sensitive DNA damage at the nucleotide level of resolution are related to the sequence context

The nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) present in tobacco smoke is a major carcinogen involved in tobacco-induced lung cancer. Its complex bioactivation along two pathways, which leads to methylation and pyridyloxobutylation of DNA, makes the study of NNK-induced DNA damage difficult. We selected two nitroso compounds, N-methyl-N-nitrosourea (MNU) and N-nitroso(acetoxymethyl)methylamine (NDMAOAc), with which to map NNK-induced DNA methylation frequency at every nucleotide position. We address the issue of how sequence context and complex chromatin structures, present in living cells, regulate the formation of modified purines through methylation generated by MNU and NDMAOAc. For comparison purposes, purified DNA was treated with dimethyl sulfate (DMS). We used ligation-mediated polymerase chain reaction to map and conduct a high-resolution footprinting analysis of the DNA damage along the p53 gene (exons 5-8), the ras gene family (exons 1 and 2 of H-, K-, and N-ras genes), and the c-jun promoter in living cells. The distribution of piperidine-sensitive DNA damage induced in cellular DNA and purified DNA by MNU or NDMAOAc was identical. MNU and NDMAOAc methylate more frequently the central guanines in a run of guanines, suggesting a regioselective mechanism for DNA methylation. In contrast, DMS methylates more frequently guanines at the 5'-end of a guanine run; this frequency decreased from the 5'- to the 3'-end. While the presence of adenines in a guanine run does not affect the distribution pattern, the presence of pyrimidines does change said pattern. Our data lead us to suggest that NNK would also methylate DNA sequences in a way similar to that of MNU or NDMAOAc. Footprinted areas of DNA methylated with MNU or NDMAOAc correspond to a consensus sequence for transcription factors AP-1, NF-Jun, CCAAT box, SP-1, and RSRF, as observed in c-jun promoters. Our results are in line with the fact that NNK metabolites, generated through the alpha-hydroxylation pathways, could potentially be mutagenic, since these activated metabolites can methylate guanines. In p53 and ras genes, the frequency of methylation of guanines parallels the frequency of mutations of those same guanines in lung cancer.

Synthesis and structure determination of the adducts formed by electrochemical oxidation of Dibenzo[a,l]pyrene in the presence of adenine

Because the radical cations of polycyclic aromatic hydrocarbons (PAH) are involved in tumor initiation, determination of the structures of biologically formed PAH-DNA adducts is important and relies on comparison of their properties with those of synthesized adducts. One of the possible sites of adduct formation is the N-3 position of Ade, but this depurinating adduct is not obtained by one-electron oxidation of dibenzo[a,l]pyrene (DB[a,l]P) in the presence of deoxyadenosine. Therefore, we turned to electrochemical oxidation of DB[a,l]P in the presence of Ade in dimethylformamide and produced the following adducts: DB[a,l]P-10-N1Ade (47%), DB[a, l]P-10-N3Ade (5%), DB[a,l]P-10-N7Ade (2%), and DB[a,l]P-10-N(6)Ade (6%). In Me(2)SO, this reaction afforded the same four adducts, but in slightly different yields: DB[a,l]P-10-N1Ade (44%), DB[a, l]P-10-N3Ade (9%), DB[a,l]P-10-N7Ade (1%), and DB[a,l]P-10-N(6)Ade (3%). These adducts were purified by reverse-phase HPLC, and the subtle differences between the isomers were revealed by NMR, tandem mass spectrometry, and fluorescence line-narrowing spectroscopy. The relative yields of the N1Ade, N3Ade, and N7Ade adducts reflect the nucleophilicity and steric accessibility of these three nitrogen atoms in Ade.

Crystal structure of the topoisomerase II poison 9-amino-[N-(2-dimethylamino)ethyl]acridine-4-carboxamide bound to the DNA hexanucleotide d(CGTACG)2

The structure of the complex formed between d(CGTACG)(2) and the antitumor agent 9-amino-[N-(2-dimethylamino)ethyl]acridine-4-carboxamide has been solved to a resolution of 1.6 A using X-ray crystallography. The complex crystallized in space group P6(4) with unit cell dimensions a = b = 30.2 A and c = 39.7 A, alpha = beta = 90 degrees, gamma = 120 degrees. The asymmetric unit contains a single strand of DNA, 1. 5 drug molecules, and 29 water molecules. The final structure has an overall R factor of 19.3%. A drug molecule intercalates between each of the CpG dinucleotide steps with its side chain lying in the major groove, and the protonated dimethylamino group partially occupies positions close to ( approximately 3.0 A) the N7 and O6 atoms of guanine G2. A water molecule forms bridging hydrogen bonds between the 4-carboxamide NH and the phosphate group of the same guanine. Sugar rings adopt the C2'-endo conformation except for cytosine C1 which moves to C3'-endo, thereby preventing steric collision between its C2' methylene group and the intercalated acridine ring. The intercalation cavity is opened by rotations of the main chain torsion angles alpha and gamma at guanines G2 and G6. Intercalation perturbs helix winding throughout the hexanucleotide compared to B-DNA, steps 1 and 2 being unwound by 8 degrees and 12 degrees, respectively, whereas the central TpA step is overwound by 17 degrees. An additional drug molecule, lying with the 2-fold axis in the plane of the acridine ring, is located at the end of each DNA helix, linking it to the next duplex to form a continuously stacked structure. The protonated N,N-dimethylamino group of this "end-stacked" drug hydrogen bonds to the N7 atom of guanine G6. In both drug molecules, the 4-carboxamide group is internally hydrogen bonded to the protonated N-10 atom of the acridine ring. The structure of the intercalated complex enables a rationalization of the known structure-activity relationships for inhibition of topoisomerase II activity, cytotoxicity, and DNA-binding kinetics for 9-aminoacridine-4-carboxamides.

Site-specific DNA methylation and apoptosis: induction by diabetogenic streptozotocin

Streptozotocin (STZ) is known to induce insulin-dependent diabetes mellitus via DNA damage in experimental animals. The mechanism of induction of DNA damage by STZ was investigated in vitro, using a human cell line and 32P-labeled DNA fragments isolated from human genes. STZ induced cellular DNA damage and apoptosis, and frequently initiated DNA modification at guanines, especially at the middle guanine in runs of three and at the guanine at the 3'-end of runs of two guanines, similar to N-methyl-N-nitrosourea, a typical methylating agent. Scavengers for reactive oxygen species or nitric oxide did not inhibit the induction of DNA damage by STZ. On the other hand, damage induction was inhibited by sodium acetate and sodium chloride, which can reduce the reactivity of methylating agents to DNA via the sodium cation. These results suggest that STZ induces DNA damage by methylation of guanines via methyl cations. This alkylation may be responsible for triggering apoptosis, and subsequently diabetes.

Major versus minor groove DNA binding of a bisarginylporphyrin hybrid molecule: a molecular mechanics investigation

On the basis of theoretical computations, we have recently synthesised [Perrée-Fauvet, M. and Gresh, N., Tetrahedron Lett., 36 (1995) 4227] a bisarginyl conjugate of a tricationic porphyrin (BAP), designed to target, in the major groove of DNA, the d(GGC GCC)2 sequence which is part of the primary binding site of the HIV-1 retrovirus site [Wain-Hobson, S. et al., Cell, 40 (1985) 9]. In the theoretical model, the chromophore intercalates at the central d(CpG)2 step and each of the arginyl arms targets O6/N7 belonging to guanine bases flanking the intercalation site. Recent IR and UV-visible spectroscopic studies have confirmed the essential features of these theoretical predictions [Mohammadi, S. et al., Biochemistry, 37 (1998) 6165]. In the present study, we compare the energies of competing intercalation modes of BAP to several double-stranded oligonucleotides, according to whether one, two or three N-methylpyridinium rings project into the major groove. Correspondingly, three minor groove binding modes were considered, the arginyl arms now targeting N3, O2 sites belonging to the purine or pyrimidine bases flanking the intercalation site. This investigation has shown that: (i) in both the major and minor grooves, the best-bound complexes have the three N-methylpyridinium rings in the groove opposite to that of the phenyl group bearing the arginyl arms; (ii) major groove binding is preferred over minor groove binding by a significant energy (29 kcal/mol); and (iii) the best-bound sequence in the major groove is d(GGC GCC)2 with two successive guanines upstream from the intercalation. On the other hand, due to the flexibility of the arginyl arms, other GC-rich sequences have close binding energies, two of them being less stable than it by less than 8 kcal/mol. These results serve as the basis for the design of derivatives of BAP with enhanced sequence selectivities in the major groove.

Sequence-specific DNA cleavage by Fe2+-mediated fenton reactions has possible biological implications

Preferential cleavage sites have been determined for Fe2+/H2O2-mediated oxidations of DNA. In 50 mM H2O2, preferential cleavages occurred at the nucleoside 5' to each of the dG moieties in the sequence RGGG, a sequence found in a majority of telomere repeats. Within a plasmid containing a (TTAGGG)81 human telomere insert, 7-fold more strand breakage occurred in the restriction fragment with the insert than in a similar-sized control fragment. This result implies that telomeric DNA could protect coding DNA from oxidative damage and might also link oxidative damage and iron load to telomere shortening and aging. In micromolar H2O2, preferential cleavage occurred at the thymidine within the sequence RTGR, a sequence frequently found to be required in promoters for normal responses of many procaryotic and eucaryotic genes to iron or oxygen stress. Computer modeling of the interaction of Fe2+ with RTGR in B-DNA suggests that due to steric hindrance with the thymine methyl, Fe2+ associates in a specific manner with the thymine flipped out from the base stack so as to allow an octahedrally-oriented coordination of the Fe2+ with the three purine N7 residues. Fe2+-dependent changes in NMR spectra of duplex oligonucleotides containing ATGA versus those containing AUGA or A5mCGA were consistent with this model.

Sequence-dependent binding of metal ion to DNA oligomeres. A comparison of molecular electrostatic potentials with NMR data

Experimentally observed sequence-selective binding of metal ion to DNA oligonucleotides have been compared with variations of electrostatic potential (EP) along the helix. Calculations of EP have been performed for three atomic models of the oligonucleotide duplex [d(CGCGAATTCGCG)2] using several variants of EP calculations, including a solution of non-linear Poisson-Boltzmann equation (NPBE). N7 atom of guanine adjacent to adenine base was identified as a region with the most negative electrostatic potential in the major groove. The EP value for the Me ion binding site surpasses the value for N7 of other guanines by 10-26% depending on particular duplex conformation. Qualitatively, the sequence dependent variations of EP near guanine N7 atoms are in agreement with the sequence-selective behavior of Mn(II) and Zn(II) ions as revealed by NMR experiments. But the difference in EP between the two most negative regions near guanine N7 atoms does not exceed 1.25 kT/e. Simple model suggests that metal ions are capable to form ion-hydrate complexes with G-Pu steps of DNA duplex. These complexes are formed via one Me...G and five Me...water coordination bonds with water molecules hydrogen bonded to two adjacent purine bases in the same chain. We suppose that such a stereospecific structural possibility is the main factor which control the sequence-selectivity in the metal ion binding. A combination of both mechanisms allows to explain sequence specific Mn(II) and Zn(II) binding to a set of oligonucleotides.

Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results

Molecular dynamic (MD) simulations using the BMS nucleic acid force field produce environment and sequence dependent DNA conformations that closely mimic experimentally derived structures. The parameters were initially developed to reproduce the potential energy surface, as defined by quantum mechanics, for a set of small molecules that can be used as the building blocks for nucleic acid macromolecules (dimethyl phosphate, cyclopentane, tetrahydrofuran, etc.). Then the dihedral parameters were fine tuned using a series of condensed phase MD simulations of DNA and RNA (in zero added salt, 4M NaCl, and 75% ethanol solutions). In the tuning process the free energy surface for each dihedral was derived from the MD ensemble and fitted to the conformational distributions and populations observed in 87 A- and B-DNA x-ray and 17 B-DNA NMR structures. Over 41 nanoseconds of MD simulations are presented which demonstrate that the force field is capable of producing stable trajectories, in the correct environments, of A-DNA, double stranded A-form RNA, B-DNA, Z-DNA, and a netropsin-DNA complex that closely reproduce the experimentally determined and/or canonical DNA conformations. Frequently the MD averaged structure is closer to the experimentally determined structure than to the canonical DNA conformation. MD simulations of A- to B- and B- to A-DNA transitions are also shown. A-DNA simulations in a low salt environment cleanly convert into the B-DNA conformation and converge into the RMS space sampled by a low salt simulation of the same sequence starting from B-DNA. In MD simulations using the BMS force field the B-form of d(GGGCCC)2 in a 75% ethanol solution converts into the A-form. Using the same methodology, parameters, and conditions the A-form of d(AAATTT)2 correctly converts into the B-DNA conformation. These studies demonstrate that the force field is capable of reproducing both environment and sequence dependent DNA structures. The 41 nanoseconds (nsec) of MD simulations presented in this paper paint a global picture which suggests that the DNA structures observed in low salt solutions are largely due to the favorable internal energy brought about by the nearly uniform screening of the DNA electrostatics. While the conformations sampled in high salt or mixed solvent environments occur from selective and asymmetric screening of the phosphate groups and DNA grooves, respectively, brought about by sequence induced ion and solvent packing.

Electrostatic interaction between helical macromolecules in dense aggregates: an impetus for DNA poly- and meso-morphism

DNA exhibits a surprising multiplicity of structures when it is packed into dense aggregates. It undergoes various polymorphous transitions (e.g., from the B to A form) and mesomorphous transformations (from hexagonal to orthorhombic or monoclinic packing, changes in the mutual alignment of nearest neighbors, etc). In this report we show that such phenomena may have their origin in the specific helical symmetry of the charge distribution on DNA surface. Electrostatic interaction between neighboring DNA molecules exhibits strong dependence on the patterns of molecular surface groups and adsorbed counter-ions. As a result, it is affected by such structural parameters as the helical pitch, groove width, the number of base pairs per helical turn, etc. We derive expressions which relate the energy of electrostatic interaction with these parameters and with the packing variables characterizing the axial and azimuthal alignment between neighboring macromolecules. We show, in particular, that the structural changes upon the B-to-A transition reduce the electrostatic energy by approximately kcal/mol per base pair, at a random adsorption of counter ions. Ion binding into the narrow groove weakens or inverts this effect, stabilizing B-DNA, as it is presumably the case in Li+-DNA assemblies. The packing symmetry and molecular alignment in DNA aggregates are shown to be affected by the patterns of ion binding.

The interaction of zinc(II) ions with antiparallel-stranded d(GA)n DNA homoduplexes

In the presence of specific metal-ions (namely zinc but also cadmium, cobalt and manganese), d(GA x TC)n DNA sequences can form non-B-DNA conformations. At low metal-ion concentration they form [GA(GA x TC)] intramolecular triplexes but, upon increasing the metal concentration, the formation of (GA x GA) intramolecular hairpins is detected. In this paper we address the question of the specific effects of zinc on the structure of the d(GA x TC)n sequences. In the presence of zinc, the DMS-reactivity of the (GA x GA) hairpins is strongly reduced suggesting a direct interaction of the metal-ion with the N7-group of the guanines. This effect is specific for antiparallel-stranded d(GA)n homoduplexes. No such strong decrease in DMS-reactivity is observed in B-DNA duplexes or in d(GGA)n and d(GGGA)n homoduplexes. In addition, the thermal stability of antiparallel-stranded d(GA)n homoduplexes increases in the presence of zinc. On the contrary, the melting temperature of similar B-DNA molecules decreases upon increasing the zinc concentration. Altogether, these result indicate that zinc plays an specific role on the stabilization of the (GA x GA) intramolecular hairpins.

Theoretical studies employing an ab initio and molecular modeling combination method on the DNA binding of bis-benzimidazoles designed for bioreductive activation

Ab initio calculations (Hartree-Fock) using the 3-21G and the STO-3G Gaussian basis sets were performed on synthetic analogues of the minor groove binding bis-benzimidazole Hoechst 33258 designed to be subject to bioreductive activation. Such compounds have been shown experimentally to react with DNA to exhibit sequence dependent inhibition of human placental helicase and display significant anticancer properties. Geometry optimized conformations and energies were derived. The binding of the optimized conformations of the drugs to both alternating and non-alternating (AT)n and to (G)n-(C)n sequences were studied. The energetics of reaction at alternative DNA base sites are calculated and compared.

GG versus AG Platination: A Kinetic Study on Hairpin-Stabilized Duplex Oligonucleotides

The kinetics of the reactions between the diaqua form of the antitumor drug cisplatin, cis-[Pt(NH(3))(2)(H(2)O)(2)](2+), and two hairpin-stabilized duplex oligonucleotides, d(TATGGTATTTTTATACCATA) (I) and d(TATAGTATTTTTATACTATA) (II), were investigated. Oligonucleotides I and II were used as models for GG and AG sequences within duplex DNA, which are known as the major sites of platinum binding. The two GG guanines of I are shown to react with similar rates (k(5)(') = 18 +/- 2 and k(3)(') = 15 +/- 1 M(-)(1) s(-)(1)), roughly twice as fast as the AG guanine of II (k(3)(') = 9 +/- 1 M(-)(1) s(-)(1)). Platination of the AG adenine of II was also observed to a minor extent (k(5)(') = 1.5 +/- 0.3 M(-)(1) s(-)(1)), whereas no other adenine of I or II was platinated to a detectable extent. The overall platination rate of I is approximately three times larger than that of II. The 3'-monoadduct of I undergoes chelation to the GG intrastrand adduct with a rate 10.5 times larger than the 5'-monoadduct (k(3)(')(c) = (1.9 +/- 0.1) x 10(-)(3) s(-)(1) and k(5)(')(c) = (0.18 +/- 0.05) x 10(-)(3) s(-)(1)). For II, the chelation rate constants of the guanine- and adenine-bound monoadducts are k(5)(')(c) = 0.3 +/- 0.1 and k(3)(')(c) = 0.08 +/- 0.01 s(-)(1), respectively. These results are discussed in relation to the platination kinetics determined for other model systems.

Joint molecular modeling and spectroscopic studies of DNA complexes of a bis(arginyl) conjugate of a tricationic porphyrin designed to target the major groove

To target selectively the major groove of double-stranded B DNA, we have designed and synthesized a bis(arginyl) conjugate of a tricationic porphyrin (BAP). Its binding energies with a series of double-stranded dodecanucleotides, having in common a central d(CpG)2 intercalation site were compared. The theoretical results indicated a significant energy preference favoring major groove over minor groove binding and a preferential binding to a sequence encompassing the palindrome GGCGCC encountered in the Primary Binding Site of the HIV-1 retrovirus. Spectroscopic studies were carried out on the complexes of BAP with poly(dG-dC) and poly(dA-dT) and a series of oligonucleotide duplexes having either a GGCGCC, CCCGGG, or TACGTA sequence. The results of UV-visible and circular dichroism spectroscopies indicated that intercalation of the porphyrin takes place in poly(dG-dC) and all the oligonucleotides. Thermal denaturation studies showed that BAP increased significantly the melting temperature of the oligonucleotides having the GGCGCC sequence, whereas it produced only a negligible stabilization of sequences having CCCGGG or TACGTA in place of GGCGCC. This indicates a preferential binding of BAP to GGCGCC, fully consistent with the theoretical predictions. IR spectroscopy on d(GGCGCC)2 indicated that the guanine absorption bands, C6=O6 and N7-C8-H, were shifted by the binding of BAP, indicative of the interactions of the arginine arms in the major groove. Thus, the de novo designed compound BAP constitutes one of the very rare intercalators which, similar to the antitumor drugs mitoxantrone and ditercalinium, binds DNA in the major groove rather than in the minor groove.

Cadmium inhibits BPDE alkylation of DNA in the major groove but not in the minor groove

Cadmium, a constituent of tobacco, has the potential to act in synergy with other carcinogens in tobacco smoke. Working on the hypothesis that cadmium interactions with DNA enhances the mutagenic lesions induced by tobacco carcinogens, we investigated the site and sequence selectivity of DNA binding by cadmium using DNA reactive chemical probes. Our results show that this divalent cation binds to N7 guanines with a great preference for those occurring in runs of G's. Further, cadmium considerably diminishes N7 guanine alkylation by the tobacco carcinogen metabolite BPDE; however, the biologically relevant guanine alkylation in the minor groove by BPDE was not affected. The relevance of our findings to cadmium's role in the tobacco carcinogenesis is discussed.

Platination of a GG site on single-stranded and double-stranded forms of a 14-base oligonucleotide with diaqua cisplatin followed by NMR and HPLC -- influence of the platinum ligands and base sequence on 5'-G versus 3'-G platination selectivity

Detailed studies of the kinetics of platination of the single-stranded 14-base DNA oligonucleotide d(ATACATGGTACATA) and the corresponding duplex by cis-[Pt(NH3)2(H2O)2]2+ show that HPLC and NMR are complementary methods which provide similar results. The 5'-G and 3'-G monofunctional intermediates were trapped, separated and characterized by NMR (via 15NH3 labeling) and enzymatic digestion followed by mass spectrometry. The kinetic data are compared with those for the corresponding reactions of cis-[PtCl2(NH3)2] (cisplatin) and its monohydrolysed analogue. For both single and double strands of the oligonucleotide, the aqua complex shows little selectivity for the 5'-G or the 3'-G in the initial platination step, whereas the chloro-complex preferentially platinates the 3'-G. The base on the 3' side of the GG sequence appears to play an important role in controlling this selectivity; replacement of T by C increases the selectivity of duplex platination by the diaqua complex by a factor of about 6, and the selectivity of chelation of the 3'-G monofunctional adduct by a factor of about 3. In general the reactivity of the 5'-G in a GG sequence appears to be enhanced in a duplex compared with a single-strand. For both the aqua-monoadduct and chloro-monoadduct, cis-[Pt(NH3)2(N7G)(H2O or Cl)], the 5'-G monoadduct is much longer lived (t1/2 approximately 4 h at 288 K for aqua, 80 h at 298 K for chloro) than the 3'-G monoadduct (t1/2 < or = 45 min at 288 K for aqua, 6 h at 298 K for chloro). Inspection of molecular mechanics models of the end states of various monofunctional adducts provided insight into H-bonding and destacking interactions in these adducts and the sequence selectivity observed in their formation. Such adducts may play an important role in the mechanism of action of platinum anticancer drugs.

Structural modification changes the DNA binding mode of cation-substituted anthraquinone photonucleases: association by intercalation or minor groove binding determines the DNA cleavage efficiency

The mode of binding anthraquinone derivatives, bearing positively charged ammonium side chains, to duplex DNA was investigated by optical and NMR spectroscopy. Absorption, circular dichroism, emission, and one- and two-dimensional homonuclear NMR spectroscopy show that mono- and dication-substituted quinones, AQS and 27AQS, bind primarily by intercalation. In contrast, these experiments indicate that the tetracationic anthraquinone 27AQS2 is bound nonintercalatively to duplex DNA. In particular, analysis of the NMR spectrum of 27AQS2 bound to a specially designed synthetic self-complementary dodecanucleotide (5'-CGCGAATTCGCG-3') shows it to be associated primarily with the minor groove of the central AATT sequence. The change in the DNA binding mode greatly affects the photophysical and photochemical properties of these photonucleases with DNA.

Analytical Debye-Huckel model for electrostatic potentials around dissolved DNA

We present an analytical, Green-function-based model for the electric potential of DNA in solution, treating the surrounding solvent with the Debye-Huckel approximation. The partial charge of each atom is accounted for by modeling DNA as linear distributions of atoms on concentric cylindrical surfaces. The condensed ions of the solvent are treated with the Debye-Huckel approximation. The resultant leading term of the potential is that of a continuous shielded line charge, and the higher order terms account for the helical structure. Within several angstroms of the surface there is sufficient information in the electric potential to distinguish features and symmetries of DNA. Plots of the potential and equipotential surfaces, dominated by the phosphate charges, reflect the structural differences between the A, B, and Z conformations and, to a smaller extent, the difference between base sequences. As the distances from the helices increase, the magnitudes of the potentials decrease. However, the bases and sugars account for a larger fraction of the double helix potential with increasing distance. We have found that when the solvent is treated with the Debye-Huckel approximation, the potential decays more rapidly in every direction from the surface than it did in the concentric dielectric cylinder approximation.