B-form Duplex Research Articles

Crystal structure of d(GCGAAAGCT) containing parallel-stranded duplex with homo base pairs and anti-parallel duplex with Watson-Crick base pairs

A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized under a slightly acidic condition, and its crystal structure has been determined at 2.5A resolution. In the first half of the oligomer, the sequence CGAA forms a parallel duplex with another symmetry-related half through the homo base pairs, C2:C2+ (semi-protonated between the Watson-Crick sites), G3:G3 (between the minor groove sites), A4:A4 (between the major groove sites) and A5:A5 (between the Watson-Crick sites). The second halves of the parallel duplex are split away in the different direction, and extended to form an anti-parallel B-form duplex with another second half.

2-Aminopurine: a probe of structural dynamics and charge transfer in DNA and DNA:RNA hybrids.

Spectroscopic techniques are employed to probe relationships between structural dynamics and charge transfer (CT) efficiency in DNA duplexes and DNA:RNA hybrids containing photoexcited 2-aminopurine (Ap). To better understand the variety of interactions and reactions, including CT, between Ap and DNA, the fluorescence behavior of Ap is investigated in a full series of redox-inactive as well as redox-active assemblies. Thus, Ap is developed as a dual reporter of structural dynamics and base-base CT reactions in nucleic acid duplexes. CD, NMR, and thermal denaturation profiles are consistent with the family of DNA duplexes adopting a distinct conformation versus the DNA:RNA hybrids. Fluorescence measurements establish that the d(A)-r(U) tract of the DNA:RNA hybrid exhibits enhanced structural flexibility relative to that of the d(A)-d(T) tract of the DNA duplexes. The yield of CT from either G or 7-deazaguanine (Z) to Ap in the assemblies was determined by comparing Ap emission in redox-active G- or Z-containing duplexes to otherwise identical duplexes in which the G or Z is replaced by inosine (I), the redox-inactive nucleoside analogue. Investigations of CT not only demonstrate efficient intrastrand base-base CT in the DNA:RNA hybrids but also reveal a distance dependence of CT yield that is more shallow through the d(A)-r(U) bridge of the A-form DNA:RNA hybrids than through the d(A)-d(T) bridge of the B-form DNA duplexes. The shallow distance dependence of intrastrand CT in DNA:RNA hybrids correlates with the increased conformational flexibility of bases within the hybrid duplexes. Measurements of interstrand base-base CT provide another means to distinguish between the A- and B-form helices. Significantly, in the A-form DNA:RNA hybrids, a similar distance dependence is obtained for inter- and intrastrand reactions, while, in B-DNA, a more shallow distance dependence is evident with interstrand CT reactions. These observations are consistent with evaluations of intra- and interstrand base overlap in A- versus B-form duplexes. Overall, these data underscore the sensitivity of CT chemistry to nucleic acid structure and structural dynamics.

Thermally Stable Sites for Electron Capture in Directly Ionized DNA: Free Radicals Produced by the Net Gain of Hydrogen at C5/C6 of Cytosine and Thymine in Crystalline Oligodeoxynucleotides

Electron paramagnetic resonance (EPR) spectroscopy is used to study radical trapping in crystalline oligodeoxynucleotides exposed to 70 keV x-irradiation at 4 K and annealed to 240 K. The four oligomers studied were the Z form d(CGCACG:GCGTGC), two A forms, d(CCCTAGGG) 2 and d(GTGCGCAC)2, and the B form d(CGCGAATTCGCG) 2. In each of these oligomers, evidence was found for trapping of a cytosine radical formed by the net gain of a hydrogen at C6 and a proton at N3 (the Cyt(C6+H, N3+H + ) +¥ radical). The data are consistent with the trapping of another cytosine radical formed by the net gain of hydrogen at C5 (the Cyt(C5+H, N3+H) +¥ or Cyt(C5+H) ¥ radical). The well-known thymine radical formed by the net gain of hydrogen at C5 (Thy(C6+H) ¥ radical) was observed in the Z- and B-form duplexes but not in the A-form duplexes. The relative yields of these three reduction species indicate that cytosine is comparable to, or better than, thymine as a stable trapping site for reductive damage. These three radicals, Cyt(C 6+H, N3+H + ) +¥ , Cyt(C5+H, N3+H) +¥ , and Thy(C6+H) ¥ , account for 85% of the total irreversibly trapped electrons in samples irradiated at 4 K and annealed to 240 K. Extrapolation of these results to B-form DNA hydrated to 9 waters per nucleotide, x-irradiated at 4 K, and warmed to room temperature predicts end product yields of 0.04-0.06 Imol/J for 5,6-dihydrouracil and 0.03-0.05 Imol/J for 5,6-dihydrothymine.

Synthesis and characterization of phenothiazine labeled oligodeoxynucleotides: novel 2'-deoxyadenosine and thymidine probes for labeling DNA.

A facile procedure for the incorporation of phenothiazine at the terminus of oligodeoxynucleotides is reported. Phenothiazine is covalently linked to the 5'-position of 2'-deoxyadenosine and thymidine. Next, the corresponding phosphoramidites are prepared, and then the labeled nucleosides are incorporated in DNA using an automated DNA solid-phase synthesizer. Phenothiazine labeled oligodeoxynucleotides form stable B-form duplexes with similar melting temperatures, CD spectra, and DSC traces compared to unlabeled DNA duplexes. The favorable photophysical properties of phenothiazine are also retained after covalent attachment to the oligodeoxynucleotide.

X-Ray analysis of d(CGCGAATTXGCG) 2 containing a 2′-deoxy- N4-methoxycytosine residue at X: a characteristic pattern of sugar puckers in the crystalline state of the Dickerson–Drew type DNA dodecamers

In a series of structural studies on damaged DNA, a modified Dickerson–Drew dodecamer with the sequence d(CGCGAATTmo 4CGCG), where mo 4C is 2′-deoxy- N 4-methoxycytidine, was synthesized and its structure in a new crystal form has been determined by the X-ray diffraction method. The two dodecamers form a B-form duplex, in which the two mo 4C residues, respectively, form a wobble pair and a Watson–Crick type pair with the guanine residues of the opposite strand. A comparison of the sugar conformations with those of the other related Dickerson–Drew dodecamers indicates a common feature of their puckering patterns. The sugar pucker of the third residue always adopts an intermediate state (C4′-exo∼O4′-endo) between the A-form and B-form. This deviation is ascribed to the stacking interaction of the ribose ring at the third residue with the guanine base at the 12th residue, which is brought about by an extra G12:G2 interaction between two duplexes related by a crystallographic 2 1 symmetry.

Crystallographic studies on damaged DNAs: III. N(4)-methoxycytosine can form both Watson-Crick type and wobbled base pairs in a B-form duplex.

To investigate the mutation mechanism of purine transition in DNA damaged with methoxyamine, a DNA dodecamer with the sequence d(CGCGAATTmo(4)CGCG), where mo(4)C is 2'-deoxy-N(4)-methoxycytidine, has been synthesized and its crystal structure determined. Two dodecamers form a B-form duplex. Electron density maps clearly show that one of the two mo(4)C residues forms a pair with a guanine residue of the opposite strand, the geometry being the canonical Watson-Crick type, and that the other mo(4)C residue forms a wobble pair with the opposite guanine residue. These two pairings are ascribed to the tautomerization of the methoxylated cytosine moieties between the amino and imino forms.

NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: implications for RNase H specificity toward DNA/RNA hybrid duplexes.

The first structure of a 2'-deoxy-2'-fluoro-D-arabinose nucleic acid (2'F-ANA)/RNA duplex is presented. We report the structural characterization by NMR spectroscopy of a small hybrid hairpin, r(GGAC)d(TTCG)2'F-a(GTCC), containing a 2'F-ANA/RNA stem and a four-residue DNA loop. Complete (1)H, (13)C, (19)F, and (31)P resonance assignments, scalar coupling constants, and NOE constraints were obtained from homonuclear and heteronuclear 2D spectra. In the chimeric duplex, the RNA strand adopts a classic A-form structure having C3' endo sugar puckers. The 2'F-ANA strand is neither A-form nor B-form and contains O4' endo sugar puckers. This contrasts strongly with the dynamic sugar conformations previously observed in the DNA strands of DNA/RNA hybrid duplexes. Structural parameters for the duplex, such as minor groove width, x-displacement, and inclination, were intermediate between those of A-form and B-form duplexes and similar to those of DNA/RNA duplexes. These results rationalize the enhanced stability of 2'F-ANA/RNA duplexes and their ability to elicit RNase H activity. The results are relevant for the design of new antisense drugs based on sugar-modified nucleic acids.

Conformations of nucleoside analogue 1-(2'-deoxy-beta-D-ribofuranosyl)-1,2,4-triazole-3-carboxamide in different DNA sequence contexts.

The concept of using a dynamic base-pairing nucleobase as a mode for degenerate recognition presents a unique challenge to analysis of DNA structure. Proton and phosphorus NMR studies are reported for two nine-residue DNA oligodeoxyribonucleotides, d(CATGGGTAC).d(GTACNCATG) (1) and d(CATGTGTAC).(GTACNCATG) (2), which contained 1-(2'-deoxy-beta-D-ribofuranosyl)-1,2,4-triazole-3-carboxamide (N) in the center of the helix at position 14. The duplexes were compared to the canonical Watson-Crick duplexes, d(CATGGGTAC).d(GTACCCATG) (3) and d(CATGTGTAC).d(GTACACATG) (4). Two-dimensional NOESY spectra of 1-4 in H(2)O and D(2)O solutions collected at 5 degrees C allowed assignment of the exchangeable and nonexchangeable protons for all four oligodeoxyribonucleotides. Thermodynamic and circular dichroism data indicated that 1-4 formed stable, B-form duplexes at 5 degrees C. Two-dimensional (1)H-(31)P correlation spectra indicated that there were minor perturbations in the backbone only near the site of the triazole base. Strong NOESY cross-peaks were observed between the H5 and H1' of N14 in 1 and, unexpectedly, 2, which indicated that, in both duplexes, N14 was in the syn(chi)() conformation about the glycosidic bond. NOESY spectra of 1 and 2 recorded in 95% H(2)O, 5% D(2)O indicated that the imino proton of the base opposite N14, G5, or T5, formed a weak hydrogen bond with N14. These conformations place the polar carboxamide functional group in the major groove with motional averaging on the intermediate time scale.

Synthesis and stability of oligodeoxynucleotides containing C8-labeled 2'-deoxyadenosine: novel redox nucleobase probes for DNA-mediated charge-transfer studies.

[reaction: see text] An efficient and convenient synthetic strategy to redox-labeled C8-derivatives of 2'-deoxyadenosine is described. The Pd(0) cross-coupling chemistry is amenable to both oxidative and reductive redox probes. The corresponding phosphoramidites of phenothiazine and anthraquinone nucleosides are amenable to automated DNA synthesis. The resulting labeled oligodeoxynucleotide strands form stable B-form duplexes with melting temperatures and CD spectra similar to those of the unlabeled analogues.

Control of electron transfer in DNA by peptide nucleic acids (PNA).

The one-electron oxidation of PNA-DNA hybrid containing G-triplet sequence was examined. In DNA duplex G-triplet was selectively cleaved by oxidation, whereas in PNA-DNA hybrid cleavage efficiency was extremely lowered. These result suggested that cleavage efficiency of PNA-DNA hybrid was different from that of B-form DNA duplex.

X-ray analyses of two DNA dodecamers containing N4-methoxy-cytosine paired with adenine or guanine.

To investigate mismatch of base-pairings in relation to mutagenesis by oxyamines, crystal structures of two DNA dodecamers with the sequence d(CGCZAA TTmo4CGCG) (Z = A or G), containing N4-methoxy-cytosine (mo4C), have been determined by X-ray analysis. These dodecamers essentially form right-handed B-form duplexes, respectively. In the dodecamer with Z = A, the two mo4C residues are adapted in imino form with the anti methoxyl group to form pairs with A on the opposite strand in a manner of Watson-Crick fashion. While in the dodecamer with Z = G, one mo4C in amino form with the anti methoxyl group forms a normal Watson-Crick pair with G, but the other one in imino form with syn methoxyl conformation wobbles with G. Based on these results, possible mutation mechanism has been proposed.

Structural basis of cleavage by RNase H of hybrids of arabinonucleic acids and RNA.

The origins of the substrate specificity of Escherichia coli RNase H1 (termed RNase H here), an enzyme that hydrolyzes the RNA strand of DNA-RNA hybrids, are not understood at present. Although the enzyme binds double-stranded RNA, no cleavage occurs with such duplexes [Lima, W. F., and Crooke, S. T. (1997) Biochemistry 36, 390]. Therefore, the hybrid substrates may not adopt a canonical A-form geometry. Furthermore, RNase H is exquisitely sensitive to chemical modification of the DNA strands in hybrid duplexes. This is particularly relevant to the RNase H-dependent pathway of antisense action. Thus, only very few of the modifications currently being evaluated as antisense therapeutics are tolerated by the enzyme, among them phosphorothioate DNA (PS-DNA). Recently, hybrids of RNA and arabinonucleic acid (ANA) as well as the 2'F-ANA analogue were shown to be substrates of RNase H [Damha, M. J., et al. (1998) J. Am. Chem. Soc. 120, 12976]. Using X-ray crystallography, we demonstrate here that ANA analogues, such as 2'F-ANA [Berger, I., et al. (1998) Nucleic Acids Res. 26, 2473] and [3.3.0]bicyclo-ANA (bc-ANA), may not be able to adopt sugar puckers that are compatible with pure A- or a B-form duplex geometries, but rather prefer the intermediate O4'-endo conformation. On the basis of the observed conformations of these ANA analogues in a DNA dodecamer duplex, we have modeled a duplex of an all-C3'-endo RNA strand and an all-O4'-endo 2'F-ANA strand. This duplex exhibits a minor groove width that is intermediate between that of A-form RNA and B-form DNA, a feature that may be exploited by the enzyme in differentiating between RNA duplexes and DNA-RNA hybrids. Therefore, the combination of the established structural and functional properties of ANA analogues helps settle existing controversies concerning the discrimination of substrates by RNase H. Knowlegde of the structure of an analogue that exhibits enhanced RNA affinity while not interfering with RNase H activity may prove helpful in the design of future antisense modifications.

Crystallographic studies on damaged DNAs. II. N6-methoxyadenine can present two alternate faces for Watson-Crick base-pairing, leading to pyrimidine transition mutagenesis

In a previous paper, 2′-deoxy- N 6-methoxyadenosine (mo 6A) was shown to form a mismatch base-pair with 2′-deoxycytidine with a Watson-Crick-type geometry. To fully understand the structural basis of genetic mutations with damaged DNA, it is necessary to examine whether the methoxylated adenine residue still has the ability to form the regular Watson-Crick pairing with a thymine residue. Therefore, a DNA dodecamer with the sequence d(CGCGmo 6AATTCGCG) has been synthesized and its crystal structure determined. The methoxylation has no significant effect on the overall DNA conformation, which is that of a standard B-form duplex. The methoxylated adenine moieties adopt the amino tautomer with an anti conformation around the C 6-N 6 bond to the N 1 atom, and they form a Watson-Crick base-pair with thymine residues on the opposite strand, similar to an unmodified adenine residue. It is concluded that methoxylated adenine can present two alternate faces for base-pairing, thanks to the amino↔imino tautomerism allowed by methoxylation. Based on this property, two gene transition routes are proposed.

Cross-strand purine-pyrimidine stack and sheared purine·pyrimidine pairing in the human HIV-1 reverse transcriptase inhibitors

Cross-strand homo purine-purine (G-G or A-A) stacks and sheared purine·purine pairing have been found to be important motifs in nucleic acid duplex structures. We now report novel cross-strand purine-pyrimidine (A-C) and hetero purine-purine (G-A) stacks that are established from a sheared purine·pyrimidine (A·C) pair adjacent to a sheared G·A pair in the 5′-AA/GC-3′ sequence. This “internal loop” sequence is conserved in two families of single-stranded DNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus. The distorted backbone of these inhibitors, resulting from the unique helical twists and kinks in the 5′-AA/GC-3′ sequence, may be responsible for the increased affinities of these single-stranded DNA inhibitors as compared with other regular B-form duplex substrates. Two simple rules have been generalized to account for all reported cross-strand stacks.

NMR solution structure of a DNA dodecamer containing single G.T mismatches.

The three-dimensional solution structure of the self-complementary DNA dodecamer (CGT_GACGT_TACG above GCAT_TGCAG_TGC] which contains the thermodynamically destabilizing [TG_A above AT_T] motif was determined using two-dimensional NMR spectroscopy and simulated annealing protocols. Relaxation matrix analysis methods were used to yield accurate NOE derived distance restraints. Scalar coupling constants for the sugar protons were determined by quantitative simulations of DQF-COSY cross-peaks and used to determine sugar pucker populations. Twenty refined structures starting from random geometries converged to an average pairwise root mean square deviation of 0.49 A. Back calculated NOEs give Rc and Rx factors of 0.38 and 0.088, respectively. The final structure shows that each of the single G@T mismatches form a wobble pair with two hydrogen bonds where the guanine projects into the minor groove and the thymine projects into the major groove. The incorporation of the destabilizing [TG_A above AT_T] motif has little effect on the backbone torsion angles and helical parameters compared to standard B-form duplexes, which may explain why G.T mismatches are among the most commonly observed in DNA. The structure shows that perturbations caused by a G.T mismatch extend only to its neighboring Watson-Crick base pair, thus providing a structural basis for the applicability of the nearest-neighbor model to the thermodynamics of internal G.T mismatches.

Selective and Stable DNA Base Pairing without Hydrogen Bonds.

Selective and Stable DNA Base Pairing without Hydrogen Bonds.

Studies of the Base-Dependent Binding of Cu(T4) to DNA Hairpins (H2T4 = meso-Tetrakis(4-(N-methylpyridiumyl))porphyrin)

Water-soluble, cationic metalloporphyrins that bind to DNA show promise as artificial nucleases and as sensitizers for photodynamic therapy, but fundamental questions remain about the binding motifs and sequence specificities. To address these issues, we have studied the interactions of Cu(T4) with a series of oligonucleotides that form hairpin structures (H2T4 = meso-tetrakis(4-(N-methylpyridiniumyl))porphyrin). Each oligonucleotide is a 16-mer with a central run of four thymine (T) bases and complementary ends that can combine to form a specific sequence of six adenine−thymine (AT) and guanine−cytosine (G⋮C) base pairs. The techniques employed include thermal melting as well as circular dichroism (CD), absorbance, and emission spectroscopies. The number of G⋮C base pairs in the stem is the most important factor that determines the melting temperature of the hairpin, and in every case investigated, the uptake of Cu(T4) stabilizes the hairpin. Depending on the nature of the adduct that forms, Δε varies from −22 to +17 M-1 cm-1 in the Soret region of the CD spectrum, and the emission intensity from Cu(T4) changes by an order of magnitude. The results yield several useful insights regarding the binding interactions. One is that robust hydrogen bonding within a B-form duplex promotes intercalative binding of Cu(T4). Thus, if the composition is at least 50% G⋮C base pairs, intercalation will occur even in the absense of a G⋮C step. On the other hand, a run of four AT base pairs defines a groove-binding site with an affinity comparable to that for intercalation at a G⋮C step. Finally, at least in solutions containing excess oligonucleotide, there is no sign that either loop binding or hemiintercalation is a prevalent mode of interaction between Cu(T4) and hairpin hosts.

Crystal structures of B-DNA with incorporated 2'-deoxy-2'-fluoro-arabino-furanosyl thymines: implications of conformational preorganization for duplex stability.

The fundamental conformational states of right-handed double helical DNA, the A- and B-forms, are associated with distinct puckers of the sugar moieties. The furanose conformation itself is affected by the steric and electronic nature of the ring substituents. For example, a strongly electronegative substituent at the C2' position, such as in the 2'-deoxy-2'-fluoro ribo furanosyl analogue, will drive the conformational equilibrium towards the C3'- endo type (north). Conversely, the 2'-deoxy-2'-fluoro arabino furanosyl modification with opposite stereochemistry at C2' appears to have a preference for a C2'- endo type pucker (south). Incorporation of 2'-fluoroarabinofuranosyl thymines was previously shown to enhance the thermodynamic stability of B-DNA duplexes. We have determined the crystal structures of the B-DNA dodecamer duplexes [d(CGCGAASSCGCG)]2and [d(CGCGAASTCGCG)]2with incorporated 2'-deoxy-2'-fluoroarabinofuranosyl thymines S (south) at 1.55 A resolution. In the crystal structures, all S residues adopt an O4'- endo conformation (east), well compatible with an overall B-form duplex geometry. In addition to the increased rigidity of S nucleosides, a clathrate-like ordered water structure around the 2'-fluorines may account for the observed larger thermodynamic stability of DNA duplexes containing 2'-deoxy-2'-fluoroarabino thymidines.

Consequences of Replacing the DNA 3‘-Oxygen by an Amino Group: High-Resolution Crystal Structure of a Fully Modified N3‘ → P5‘ Phosphoramidate DNA Dodecamer Duplex

As part of the quest for antisense compounds with relative to DNA and RNA improved nuclease-resistance and favorable RNA hybridization properties, a large variety of oligonucleotide analogues has been generated in recent years. Among these, the oligonucleotide N3‘ → P5‘ phosphoramidate DNA (3‘-NP DNA), an analogue with the 3‘-oxygen in the nucleic acid sugar−phosphodiester backbone replaced by an amino group, displays several unique features. Self-pairing of 3‘-NP DNA single strands is significantly favored thermodynamically over self-pairing of both DNA and RNA (Gryaznov, S. M.; et al. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 5798−5802). CD measurements in solution have shown that the duplex conformation of 3‘-NP DNA is very similar to the RNA A-form. Moreover, 3‘-NP DNA can form stable triplexes with double-stranded DNA under conditions where native DNA fails to do so. Recently, it was shown that all-phosphoramidate DNA analogues of HIV-1 RRE and TAR RNA specifically bind to the RNA-binding Rev- and Tat-related peptides (Rigl, C. T.; et al. Biochemistry 1997, 36, 650−659). We have determined the X-ray crystal structure of the all-modified 3‘-NP DNA duplex [5‘-d(CnpGnpCnpGnpAnpAnpTnpTnpCnpGnpCnpG)]2 at 2-Å resolution. Whereas the Dickerson−Drew type phosphodiester DNA 5‘-d(CGCGAATTCGCG) adopts a B-form duplex in the crystal as well as in solution, the 3‘-NP DNA duplex with identical sequence displays an A-RNA conformation in the crystal. Combined with the earlier CD results in solution, our observation provides convincing evidence that the A-conformation with 3‘-NP DNA is modification- and not sequence-induced. The crystal structure reveals a dramatically improved hydration of the phosphoramidate DNA relative to DNA due to the presence of the amino group in its sugar−phosphate backbone. Compared with A-DNA and A-RNA, the 3‘-NP DNA duplex geometry appears more uniform, with backbone torsion angles of individual nucleotides displaying only minor variations. This is consistent with an observed repetitive pattern of coordination by either chloride anions or water molecules to the 3‘-amino groups in the crystal, suggesting a strong anomeric effect between the 3‘-nitrogen lone electron pair and the σ* orbital of the P−O5‘ bond. Our crystal structure can qualitatively explain the exceptional thermodynamic stability of 3‘-NP DNA, and helps to rationalize previously ill understood findings, such as the surprising fact that DNA with NH substituted for O5‘ fails to pair with either DNA or RNA. The crystal structure also establishes 3‘-NP DNA as the quintessential RNA mimetic, in terms of overall duplex structure, rigidity, and level of hydration.

A terbenzimidazole that preferentially binds and conformationally alters structurally distinct DNA duplex domains: a potential mechanism for topoisomerase I poisoning.

The terbenzimidazoles are a class of synthetic ligands that poison the human topoisomerase I (TOP1) enzyme and promote cancer cell death. It has been proposed that drugs of this class act as TOP1 poisons by binding to the minor groove of the DNA substrate of TOP1 and altering its structure in a manner that results in enzyme-mediated DNA cleavage. To test this hypothesis, we characterize and compare the binding properties of a 5-phenylterbenzimidazole derivative (5PTB) to the d(GA4T4C)2 and d(GT4A4C)2 duplexes. The d(GA4T4C)2 duplex contains an uninterrupted 8-bp A.T domain, which, on the basis of x-ray crystallographic data, should induce a highly hydrated "A-tract" conformation. This duplex also exhibits anomalously slow migration in a polyacrylamide gel, a feature characteristic of a noncanonical global conformational state frequently described as "bent." By contrast, the d(GT4A4C)2 duplex contains two 4-bp A.T tracts separated by a TpA dinucleotide step, which should induce a less hydrated "B-like" conformation. This duplex also migrates normally in a polyacrylamide gel, a feature further characteristic of a global, canonical B-form duplex. Our data reveal that, at 20 degrees C, 5PTB exhibits an approximately 2. 3 kcal/mol greater affinity for the d(GA4T4C)2 duplex than for the d(GT4A4C)2 duplex. Significantly, we find this sequence/conformational binding specificity of 5PTB to be entropic in origin, an observation consistent with a greater degree of drug binding-induced dehydration of the more solvated d(GA4T4C)2 duplex. By contrast with the differential duplex affinity exhibited by 5PTB, netropsin and 4',6-diamidino-2-phenylindole (DAPI), two AT-specific minor groove binding ligands that are inactive as human TOP1 poisons, bind to both duplexes with similar affinities. The electrophoretic behaviors of the ligand-free and ligand-bound duplexes are consistent with 5PTB-induced bending and/or unwinding of both duplexes, which, for the d(GA4T4C)2 duplex, is synergistic with the endogenous sequence-directed electrophoretic properties of the ligand-free duplex state. By contrast, the binding to either duplex of netropsin or DAPI induces little or no change in the electrophoretic mobilities of the duplexes. Our results demonstrate that the TOP1 poison 5PTB binds differentially to and alters the structures of the two duplexes, in contrast to netropsin and DAPI, which bind with similar affinities to the two duplexes and do not significantly alter their structures. These results are consistent with a mechanism for TOP1 poisoning in which drugs such as 5PTB differentially target conformationally distinct DNA sites and induce structural changes that promote enzyme-mediated DNA cleavage.