Energetics of nucleic acid stability: the effect of DeltaCP

We report high-resolution differential scanning calorimetric data on the poly(dAdT)poly(dAdT), poly(dA)poly(dT), poly(dIdC)poly(dIdC), poly(dGdC)poly(dGdC), poly(rA)poly(rU), and poly(rI)poly(rC) nucleic acid duplexes. We use these data to evaluate the melting temperatures, TM, enthalpy changes, DeltaHM, and heat capacity changes, DeltaCP, accompanying helix-to-coil transitions of each polymeric duplex studied in this work at different NaCl concentrations. In agreement with previous reports, we have found that DeltaCP exhibits a positive, nonzero value, which, on average, equals 268 +/- 33 J mol(-1) K(-1). With DeltaCP, we have calculated the transition free energies, DeltaG, enthalpies, DeltaH, and entropies, DeltaS, for the duplexes as a function of temperature. Since, DeltaG, DeltaH, and DeltaS all strongly depend on temperature, the thermodynamic comparison between DNA and/or RNA duplexes (that may differ from one another with respect to sequence, composition, conformation, etc.) is physically meaningful only if extrapolated to a common temperature. We have performed such comparative analyses to derive differential thermodynamic parameters of formation of GC versus AT, AU, and IC base pairs as well as B' versus A and B helix conformations. We have proposed some general microscopic interpretations for the observed sequence-specific and conformation-specific thermodynamic differences between the duplexes.     

ACTION SPECTRA AND CHROMOPHORES FOR LETHAL PHOTOSENSITIZATION OF Candida albicans BY DNA MONOADDUCTS FORMED BY 8-METHOXYPSORALEN AND MONOFUNCTIONAL FUROCOUMARINS

The red-shift of furocoumarin action spectra, compared with their absorption spectra, has been investigated. An action spectrum for 8-methoxypsoralen (8-MOP) monoadduct formation in the yeast Candida albicans has been determined. The yeast cells were initially exposed to sublethal doses of monochromatic UVA at different wavelengths. Monoadduct formation was monitored by growth inhibition induced, after washing out any unbound 8-MOP, by re-irradiation with a constant second (non-lethal) dose of 330 nm radiation. A comparison between this action spectrum and the absorption spectrum of the dark complex of 8-MOP and DNA was made. In addition, the action spectra of monoadduct formation of five monofunctional compounds including a coumarin derivative have been determined. These action spectra were compared with their respective DNA dark complex absorption spectra. In general, the peaks of the furocoumarin DNA dark complexes show a red-shift when compared with the free furocoumarin molecule and the action spectra show peaks which correspond with the peaks of the dark complexes. Such data indicate that the DNA dark complex is the chromophore for growth inhibition in yeast rather than the free furocoumarin. The similarity of the 8-MOP monoadduct formation action spectrum and 8-MOP action spectra suggests that spectral dependence for the photobiological effects (including the red-shift) is dependent on monoadduct formation rather than, as previously suggested by several authors, crosslink formation. The action spectrum for the coumarin derivative 4-methyl N-ethylpyrrolo (3,2-g) coumarin (PCNEt) correlated well with the free molecule absorption spectrum rather than DNA dark complex indicating that the free molecule is the chromophore.(ABSTRACT TRUNCATED AT 250 WORDS)     

MONOADDITION OF DICTAMNINE TO SYNTHETIC DOUBLE-STRANDED POLYDEOXYRIBONUCLEOTIDES IN UVA AND THE EFFECT OF PHOTOMODIFIED DNA ON TEMPLATE ACTIVITY

Abstract— The photoreactivity of dictamnine, a furoquinoline alkaloid, towards different synthetic DNAs has been studied. The ratio of the photobinding of [₃H]-dictamnine to poly(dA-dT) poly(dA-dT): poly(dG-dC) poly(dG-dC): poly(dA-dU) poly(dA-dU): poly(dA) poly(dT), in relation to that of calf thymus DNA, is 18:1:0.5:0.3. Prior treatment of calf thymus DNA with dictamnine in light inhibits the subsequent incorporation of 8-methoxypsoralen (8-MOP). These results suggest that the sites in DNA for the photobinding of dictamnine are probably identical with those for monoad-ducts of 8-MOP. Furthermore, the template activity of photomodified DNA in the RNA polymerase reaction is considerably inhibited for poly(dA-dT)poly(dA-dT), to a lesser extent for calf thymus DNA, but almost not affected for the linear copolymer, poly(dA)-poly(dT).     

SENSITIVITY OF DNA REPAIR-DEFICIENT STRAINS OF ESCHERICHIA COLI K-12 TO VARIOUS FUROCOUMARINS AND NEAR-ULTRAVIOLET RADIATION

Abstract— Survival curves were obtained for DNA repair-deficient strains of Escherichia coli K-12 ( polA1, uvrB5 , and recA56 ) exposed to near-ultraviolet radiation [black light (BL)] in the presence of the DNA cross-linking agent 8-methoxypsoralen (8-MOP) or in the presence of photosensitizers forming primarily monoadducts with DNA [angelicin; 3-carbethoxypsoralen (3-CPs); 5,7-dimethoxycoumarin (DMC)], and after exposure to blue light (BluL) in the presence of 8-MOP or 3-CPs. An interpretation of these data suggests that DNA polymerase I is required for the major pathway of monoadduct repair, but appears to play little or no role in the repair of 8-MOP cross-links. The uvrB and recA strains were very sensitive, both to the cross-linking agent and to the monoadduct formers. The markedly different results for BL plus DMC or 3-CPs compared to angelicin suggests that the DMC and 3-CPs monoadducts are repaired by a different mechanism than are the angelicin monoadducts, or else DMC and 3-CPs undergo photochemical side reactions that produce DNA lesions other than the expected monoadducts. From photochemical evidence, we predicted that fewer 8-MOP monoadducts should be converted to cross-links by BluL vs BL; this appears to be the case. 3-CPs showed dramatically different biological results when irradiated with BL vs BluL, suggesting that 3-CPs may form more types of photoproducts than the expected monoadducts; BluL, however, appears to favor monoadduct formation.     

Highly emissive,nine-coordinate enantiopure lanthanide complexes incorporating tetraazatriphenylenes as probes for DNA

The interaction of q = 0 delta- and lambda-Tb and Eu complexes with poly(dAdT), poly(dGdC) and calf-thymus DNA has been examined by absorption, emission and chiroptical spectroscopy and is sensitive to complex helicity, base-pair type and the nature of the lanthanide excited state.     

Surface-enhanced Raman study of the interactions between tripodal cationic polyamines and polynucleotides

Raman and surface-enhanced Raman spectra of new DNA/RNA-binding compounds consisting of three imidazole (Im) and three pyridine (Py) rings connected by tripodal polyaminomethylene linkages were obtained by the near-infrared excitation at 1064 nm. Study of interactions of Im and Py polyamines with single-stranded RNA polynucleotides (poly?A, poly?G, poly?C, poly?U), double-stranded DNA polynucleotides (poly?dAdT-poly?dAdT, poly?dGdC-poly?dGdC) and calf thymus DNA (ct-DNA) by surface-enhanced Raman spectroscopy (SERS) reveals unambiguous enhancement of the Raman scattering from the small molecules as well as appearance of new bands in spectra associated mainly with nucleobases. The SERS experiments point toward comparable interactions of Im and Py polyamines with single-stranded purine and pyrimidine polynucleotides. Furthermore, SERS experiments with double stranded polynucleotides reveal the base-pair dependent selectivity of Im and Py, whereby interactions within both, major and minor groove are indicated for poly?dAdT-poly?dAdT, at variance to preferred binding of Im and Py to only major groove of poly?dGdC-poly?dGdC. SERS spectra of Im and Py with ct-DNA imply that protonated amino groups of these compounds preferentially interact with N7 atoms (adenine, guanine) while nitrogen in aromatic rings of polyamines might be attracted to C6-NH(2) (adenine), all sites being located at the major groove of the DNA helix. Wavenumber downshift of the imidazole (Im) and pyridine (Py) ring vibrations supports aromatic stacking interactions of imidazole and pyridine aromatic moieties with DNA base-pairs.     

Hydration changes accompanying nucleic acid intercalation reactions:volumetric characterizations

We use high precision ultrasonic velocimetric and densimetric techniques to determine at 25 degrees C the changes in volume, deltaV, and adiabatic compressibility, deltaK(S), that accompany the binding of ethidium to the poly(rA)poly(rU), poly(dAdT)poly(dAdT), poly(dGdC)poly(dGdC), and poly(dIdC)poly(dIdC) duplexes, as well as to the poly(rU)poly(rA)poly(rU) triplex. The binding of ethidium to each of the duplexes and the triplex is accompanied by negative changes in volume, deltaV, and adiabatic compressibility, deltaK(S). We discuss the basis for relating macroscopic and microscopic properties, particularly, emphasizing how measured changes in volume and compressibility can be quantitatively interpreted in terms of the differential hydration properties of DNA and RNA structures in their ligand-free and ligand-bound states. We also estimate the entropic cost of intercalation-induced changes in hydration of each of the nucleic acid structures and the drug. In general, our results emphasize the vital role of hydration in modulating the energetics of drug-DNA binding, while also underscoring the fact that hydration must be carefully taken into account in analysis and prediction of the energetics of nucleic acid recognition.     

THE EXCITATION OF 8-METHOXYPSORALEN WITH VISIBLE LIGHT: REVERSED PHASE HPLC QUANTITATION OF MONOADDUCTS and CROSS-LINKS

Abstract— The formation of 8-methoxypsoralen-DNA monoadducts and cross-links is presumed to be responsible for the efficacy of photochemotherapies that employ 8-methoxypsoralen activated with long-wavelength ultraviolet radiation (UVA,320–400 nm). In this report it is shown that 8-methoxypsoralen can also be activated with visible light (419 nm). Bovine aorta smooth muscle cells were treated with 8-methoxypsoralen (1000 ng/mL) and 419 nm light (up to 12 J/cm²). Cellular DNA was isolated, hydrolyzed using nucleolytic enzymes and then analyzed by reversed-phase high-performance liquid chromatography. The primary effect of using visible light instead of long-wavelength ultraviolet radiation is a more than 10-fold reduction in the extent of cross-link formation. Because the extent of monoadduct and cross-link formation has not been routinely measured in experiments in which cellular assays have been performed, it is difficult to correlate cell response to the presence of a particular type of 8-methoxypsoralen photoadduct (monoadduct or cross-link). Thus, the use of visible light allows the study of cells containing nearly 100% monoadducts. In addition, the reduction in cross-link formation when visible light is used to activate the compound may also reduce the mutagenicity of 8-methoxypsoralen and hence enhance its therapeutic efficacy.     

PHOTOADDUCTS OF 8-METHOXYPSORALEN TO CYTOSINE IN DNA

Abstract— The isolation and partial characterization of several photoadducts formed between 8-methoxypsoralen (8-MOP) and cytosine is described. The formation of these adducts was analysed in E. coli DNA containing ³H-labeled cytosine and/or ¹⁴C-labeled thymine, and in oligonucleotides of defined sequence. The major initial adduct has been identified as an 8-MOP cytosine monoadduct, most likely forming at the pyrone end of the 8-MOP molecule. Further irradiation converts this adduct to several other species, including both cytosine:cytosine and cytosine:thymine diadducts, as well as a number of derivative monoadducts. One isomer of the C:T diadduct appears to undergo a reversible isomerization under the conditions normally used to analyse adduct mixtures by HPLC. The isomerization can cause this adduct to exhibit a retention time on reversed-phase HPLC closely resembling either that of a thymine-thymine crosslink or a thymine monoadduct.     

THIOPYRONINE- AND 8-METHOXYPSORALEN-SENSITIZED PHOTODYNAMIC EFFECT ON CELL GROWTH, COLONY FORMING ABILITY and RNA SYNTHESIS IN Saccharomyces MUTANTS DEFICIENT IN DNA REPAIR

Abstract –We compared the photodynamic effects of thiopyronine (TP) and visible light, and 8-methoxypsoralen (8-MOP) and ultraviolet A (UV-A) light, on growth, colony forming ability and RNA synthesis in a repair-proficient Saccharomyces strain and three mutants deficient in DNA repair mechanisms (DNA repair assays). With 8-MOP and UV-A repair-deficient mutants were significantly more sensitive than the repair-proficient strain indicating that the system is sensitive for the detection of DNA damage. With TP and visible light, the photodynamic effects were comparable in the mutants and the control, indicating no DNA damage. These results support previous work showing that the main target of TP photosensitization in eukaryotes is not nuclear DNA.     

Fluorescence of the DNA double helices (dAdT)n.(dAdT)n studied by femtosecond spectroscopy

Polymeric and oligomeric DNA helices, poly(dAdT).poly(dAdT) and (dAdT)(10).(dAdT)(10), composed of 200-400 and 20 adenine-thymine base pairs, respectively, are studied by fluorescence upconversion. Fluorescence decays, anisotropy decays and time-resolved spectra, obtained for this alternating base sequence, are compared with those determined previously for the homopolymeric sequence (dA)(n).(dT)(n). It is shown that identical fluorescence decays may correspond to quite different anisotropy decays and vice versa, both varying with the emission wavelength, the base sequence and the duplex size. Our observations cannot be explained in terms of monomer and excimer emission exclusively, as concluded in the past on the basis of steady-state measurements. Excitons also contribute to the fluorescence. These are rapidly trapped by excimers, characterized by long-lived weak emission.     

Duck Hepatitis B Virus Inactivation and 8-Methoxypsoralen Photoadduct Formation in Human Platelet Concentrates*

Photochemical inactivation (PCI) of virus and bacteria in platelet concentrates (PC) has been demonstrated using 8-methoxypsoralen (8-MOP) and long-wavelength UV light (UVA). To study inactivation of blood-borne virus, we have employed duck hepatitis B virus (DHBV), a model for human hepatitis B virus. A specific hepatocyte culture infectivity assay, with PCR detection, could measure 5–6 log₁₀ virus kill. The DHBV inactivation in PC was dependent on UVA dose, was enhanced when plasma was reduced from 100% to 20% and was limited by 8-MOP solubility in the reduced-plasma medium. Optimum conditions for PCI were 100 μg/mL 8-MOP in 20% plasma and 80% synthetic platelet storage medium. A radiolabeling assay for 8-MOP photoadducts in hepatocytes seeded into PC confirmed that DHBV inactivation reflected DNA modification and indicated that adduct formation was insensitive to minor variations in conditions. Kinetic modeling indicated that optimum adduct formation was a compromise between 8-MOP dark binding and optical transmittance and that plasma proteins competed for 8-MOP binding. The PCI results in various media correlated with corresponding DNA modification densities and were compared to statistical models incorporating DHBV characteristics and predictions of 8-MOP crosslink formation between DNA strands. Behavior was consistent with one or a small number of lethal modifications per DNA strand, including monoadducts, but probably not crosslinks alone. A minor subpopulation of DHBV was found to be, somewhat more difficult to inactivate, consistent with three-fold lower modification, due possibly to single-stranded DNA character or host repair of photoadducts.     

One- and two-photon ionization of DNA single and double helices studied by laser flash photolysis at 266 nm

The ionization of the DNA single and double helices (dA)20, (dT)20, (dAdT)10(dAdT)10 and (dA)20(dT)20, induced by nanosecond pulses at 266 nm, is studied by time-resolved absorption spectroscopy. The variation of the hydrated electron concentration with the absorbed laser intensity shows that, in addition to two-photon ionization, one-photon ionization takes place for (dAdT)10(dAdT)10, (dA)20(dT)20 and (dA)20 but not for (dT)20. The spectra of all adenine-containing oligomers at the microsecond time-scale correspond to the adenine deprotonated radical formed in concentrations comparable to that of the hydrated electron. The quantum yield for one-photon ionization of the oligomers (ca. 10(-3)) is higher by at least 1 order of magnitude than that of dAMP, showing clearly that organization of the bases in single and double helices leads to an important lowering of the ionization potential. The propensity of (dAdT)10(dAdT)10, containing alternating adenine-thymine sequences, to undergo one-photon ionization is lower than that of (dA)20(dT)20 and (dA)20, containing adenine runs. Pairing of the (dA)20 with the complementary strand leads to a decrease of quantum yield for one photon ionization by about a factor of 2.     

RESEARCH NOTE: THIOPYRONINE-AND 8-METHOXYPSORALEN-SENSITIZED PHOTODYNAMIC EFFECT ON CELL GROWTH, COLONY FORMING ABILITY AND RNA SYNTHESIS IN Saccharomyces MUTANTS DEFICIENT IN DNA REPAIR

Abstract: We compared the photodynamic effects of thiopyronine (TP) and visible light, and 8-methoxypsoralen (8-MOP) and ultraviolet A (UV-A) light, on growth, colony forming ability and RNA synthesis in a repair-proficient Saccharomyces strain and three mutants deficient in DNA repair mechanisms (DNA repair assays). With 8-MOP and UV-A repair-deficient mutants were significantly more sensitive than the repair-proficient strain indicating that the system is sensitive for the detection of DNA damage. With TP and visible light, the photodynamic effects were comparable in the mutants and the control, indicating no DNA damage. These results support previous work showing that the main target of TP photosensitization in eukaryotes is not nuclear DNA.     

Interaction of cyanine dyes with nucleic acids: XXVI. Intercalation of the trimethine cyanine dye cyan 2 into double-stranded DNA: study by spectral luminescence methods

The interaction between double-stranded (ds) DNA and the cyanine dye Cyan 2 has been studied with spectral luminescence methods. Binding constant values have been determined by fluorescence titration and dye distribution in the two-phase system ethyl acetate-water (3.6 x 10(4) and 1.5 x 10(4) M(-1), respectively). Cyan 2 exhibits a small specificity for guanine-cytosine (GC) sequences in total DNA and synthetic polydeoxynucleotides poly(dA/dT) and poly(dGdC/dGdC). The DNA complexes with Cyan 2 are stable at high-ionic strength solution when NaCl is added. The dye molecule complexed with DNA is apparently shielded from the anionic quencher--iodide ion. The negative linear dichroism of the visible absorption band of aligned Cyan 2-DNA complexes indicates that the bound dye lies almost perpendicularly to the DNA helix axis. The linear dichroism of the absorption band at 260 nm suggests a considerable change in the DNA B-form. The results are consistent with an intercalative binding interaction between Cyan 2 and ds DNA.     

DNA damage induced by 4,6,8,9-tetramethyl-2H-furo[2,3-h]quinolin-2-one, a new furocoumarin analog: photochemical mechanisms

Some photochemical and photobiological properties of 4,6,8,9-tetramethyl-2H-furo[2,3-h]quinolin-2-one (HFQ) were studied in comparison with its isomer 1,4,6,8-tetramethyl-2H-furo[2,3-h]quinolin-2-one (FQ) and 8-methoxypsoralen (8-MOP). The HFQ photobinds to DNA forming furan-side monoadducts (MAHFQ) that have molecular structure very similar to those of FQ (MAFQ). Unlike MA8-MOP and MAFQ, MAHFQ no longer photoreact. The HFQ, like FQ, produces moderate amounts of singlet oxygen but no superoxide anions. The HFQ and FQ induce numbers of DNA-protein cross-links (DPC), much more plentiful than those of 8-MOP (about two and seven times, respectively) but no interstrand cross-links. The mechanism of DPC formation was studied in vivo in mammalian cells by alkaline elution and in vitro using a new test mixing histones and DNA from calf thymus. The latter is a very useful technique for the double irradiation protocol. The DNA (or histones) are separately exposed to a first UVA dose in the presence of the sensitizer; then, after its unbound molecules have been removed, histones (or DNA) are added to assemble the chromatin-like complex that is irradiated again. According to in vitro and in vivo methods, DPC appear to be formed by FQ and 8-MOP by a biphotonic process that starts with monoadduct induction in DNA, followed by their conversion into DPC. In the resulting lesions, the sensitizer molecule forms a covalent bridge between the two macromolecules (DPC at length greater than zero). Instead, HFQ induces DPC by a monophotonic process; thus, HFQ is probably not a physical part of the bridge between DNA and proteins, which may be linked together directly, like DPC at zero length induced by UVC.     

CHARACTERIZATION OF THE PHOTOREACTION BETWEEN DNA AND AMINOMETHYL-TRIMETHYLPSORALEN USING ABSORPTION AND FLUORESCENCE SPECTROSCOPY

–The use of absorption and fluorescence spectroscopy for following the progress of the photo-reaction between DNA and 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT) has been investigated. Absorption at long wavelengths and fluorescence both decline upon intercalation of AMT into the DNA helix. The loss of fluorescence from AMT and the accompanying appearance of monoadduct fluorescence upon irradiation by UV light can be easily followed by using the excitation beam of a spectro-fluorometer as the source of irradiation and monitoring the changing emission spectrum. Where cross-link formation is possible, the subsequent decline of monoadduct fluorescence is seen as well. This suggests that the 4,5-tnonoadduct is a precursor of cross-links. Both monoaddition and cross-linking are more rapid with poly d(A·T) than with calf thymus DNA or poly d(A·T). Excitation spectra can be helpful in resolving the levels of AMT and 4',5'-monoadduct when both are contributing to the emission spectrum. Some changes are observed in the emission spectrum of AMT–poly d(A·T) monoadducts after prolonged irradiation which indicate further photoreaction.     

Label-free emission assay of mercuric ions using DNA duplexes of poly(dT)

In this study, an assay to quantify the presence of mercuric ions and methyl mercury by double-stranded DNA containing a poly(dT) sequence was developed using a light switch compound, Ru(phen)(2)(dppz)(2+) (1), which is known to intercalate into double-stranded DNA. Upon treatment with mercuric ions, the metal-to-ligand charge transfer (MLCT) emission derived from the intercalation of 1 was reduced due to the formation of DNA duplexes containing T-Hg(2+)-T base pairs by the dehybridization of poly(dT)-poly(dA) duplexes at room temperature. As the concentration of Hg(2+) was increased, the emission of 1 gradually decreased. This label-free method had a detection limit of 5 nM. Other metal ions, such as K(+), Ag(+), Ca(2+), Mg(2+), Zn(2+), Mn(2+), Co(2+), Ni(2+), Cu(2+), Cd(2+), Cr(3+), Fe(3+), had no significant effect on reducing emission. This emission method can differentiate matched and mismatched poly(dT) sequences based on the dehybridization rate of dsDNA and the rate decreased in the order of T(10)C·A(11)～ T(10)A·A(11) > T(10)G·A(11) > T(11)·A(11).     

SINGLET OXYGEN FORMATION BY SENSITIZATION OF FUROCOUMARINS COMPLEXED WITH, OR BOUND COVALENTLY TO DNA

Abstract— The formation of singlet molecular oxygen (¹O₂) by sensitization of the furocoumarins 5-methoxypsoralen (5-MOP), 8-methoxypsoralen (8-MOP) and psoralen complexed with DNA was investigated. From the results it is concluded that 5-MOP complexed with native DNA is able to generate ¹O₂, even in a larger extent than 5-MOP free in solution. Also, with 8-MOP and especially with psoralen, ¹O₂ formation by the complexed compound could be observed. The ¹O₂ formation sensitized by covalently bound furocoumarin was demonstrated with psoralen as a model compound. 4',5'-Dihydropsoralen, a model compound for the UVA light absorbing 4',5'monoadducts of furocoumarins to DNA, is also able to generate ¹O₂.     

Neomycin-neomycin dimer: an all-carbohydrate scaffold with high affinity for AT-rich DNA duplexes

A dimeric neomycin-neomycin conjugate 3 with a flexible linker, 2,2'-(ethylenedioxy)bis(ethylamine), has been synthesized and characterized. Dimer 3 can selectively bind to AT-rich DNA duplexes with high affinity. Biophysical studies have been performed between 3 and different nucleic acids with varying base composition and conformation by using ITC (isothermal calorimetry), CD (circular dichroism), FID (fluorescent intercalator displacement), and UV (ultraviolet) thermal denaturation experiments. A few conclusions can be drawn from this study: (1) FID assay with 3 and polynucleotides demonstrates the preference of 3 toward AT-rich sequences over GC-rich sequences. (2) FID assay and UV thermal denaturation experiments show that 3 has a higher affinity for the poly(dA)·poly(dT) DNA duplex than for the poly(dA)·2poly(dT) DNA triplex. Contrary to neomycin, 3 destabilizes poly(dA)·2poly(dT) triplex but stabilizes poly(dA)·poly(dT) duplex, suggesting the major groove as the binding site. (3) UV thermal denaturation studies and ITC experiments show that 3 stabilizes continuous AT-tract DNA better than DNA duplexes with alternating AT bases. (4) CD and FID titration studies show a DNA binding site size of 10-12 base pairs/drug, depending upon the structure/sequence of the duplex for AT-rich DNA duplexes. (5) FID and ITC titration between 3 and an intramolecular DNA duplex [d(5'-A(12)-x-T(12)-3'), x = hexaethylene glycol linker] results in a binding stoichiometry of 1:1 with a binding constant ～10(8) M(-1) at 100 mM KCl. (6) FID assay using 3 and 512 hairpin DNA sequences that vary in their AT base content and placement also show a higher binding selectivity of 3 toward continuous AT-rich than toward DNA duplexes with alternate AT base pairs. (7) Salt-dependent studies indicate the formation of three ion pairs during binding of the DNA duplex d[5'-A(12)-x-T(12)-3'] and 3. (8) ITC-derived binding constants between 3 and DNA duplexes have the following order: AT continuous, d[5'-G(3)A(5)T(5)C(3)-3'] > AT alternate, d[5'-G(3)(AT)(5)C(3)-3'] > GC-rich d[5'-A(3)G(5)C(5)T(3)-3']. (9) 3 binds to the AT-tract-containing DNA duplex (B* DNA, d[5'-G(3)A(5)T(5)C(3)-3']) with 1 order of magnitude higher affinity than to a DNA duplex with alternating AT base pairs (B DNA, d[5'-G(3)(AT)(5)C(3)-3']) and with almost 3 orders of magnitude higher affinity than a GC-rich DNA (A-form, d[5'-A(3)G(5)C(5)T(3)-3']).