DNA bases

We are presenting the electronic photo fragment spectra of the protonated pyrimidine DNA bases homo-dimers. Only the thymine dimer exhibits a well structured vibrational progression, while protonated monomer shows broad vibrational bands. This shows that proton bonding can block some non radiative processes present in the monomer.

2+ and deprotonated cytosine (C(-H)) were studied in [C(-H)Ba] + and [C(-H)BaC] + mono-charged complexes by means of IRMPD spectroscopy in the 1200 -1800 cm -1 region coupled to tandem mass-spectrometry in combination with DFT calculations. On one side, for the [C(-H)BaC] + complex only one [C(-H)KAN1O-Ba-Canti] + isomer was found, although the presence of another structure cannot be neglected. This isomer feature a central tetracoordinated Ba 2+ cation that simultaneously interacts with keto-amino [C(-H)] -deprotonated on N1 and neutral canonical keto-amino C. Both moieties are in different planes as a consequence of an additional NH ••• O=C hydrogen bond between the NH2 group of C and the C=O group of [C(-H)] -. An interesting sequential IRMPD dynamics is observed in this complex. On the other side, two isomers ([C(-H)KAN1OBa] + and [C(-H)KAN3OBa] + ) were identified for the [C(-H)Ba] + complex produced in the electrospray-ionization source, in which Ba 2+ interacts simultaneously with the C=O group and the N1 or N3 atom of the keto-amino [C(-H)] -, respectively. A comparison with the closely related [C(-H)Pb] + , previously studied by other authors(REF) is also presented.

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Recently, DNA molecules have received great attention because of their potential applications in material science. One interesting example is the production of highly fluorescent and tunable DNA-Ag n clusters with cytosine (C)-rich DNA strands. Here, we report the UV photofragmentation spectra of gas-phase cytosine complexes together with theoretical calculations. In both cases, the excitation energy does not differ significantly from that of isolated cytosine or protonated cytosine, indicating that the excitation takes place on the DNA base. However, the excited-state lifetime of the C 2 H + (τ = 85 fs), estimated from the bandwidth of the spectrum, is at least 2 orders of magnitude shorter than that of the C 2 Ag + (τ > 5000 fs). The increased excited-state lifetime upon silver complexation is quite unexpected, and it clearly opens the question about what factors are controlling the nonradiative decay in pyrimidine DNA bases. This is an important result for the expanding field of metal-mediated base pairing and may also be important to the photophysical properties of DNA-templated fluorescent silver clusters.

Gas-phase interactions between Ba 2+ and deprotonated cytosine (C(-H)) were studied in [C(-H)Ba] + and [C(-H)BaC] + complexes by IRMPD spectroscopy coupled to tandem mass-spectrometry in combination with DFT calculations. For the [C(-H)BaC] + complex only one [C(-H)KAN1O-Ba-Canti] + isomer was found, although the presence of another structure cannot be neglected. This isomer features a central tetracoordinated Ba 2+ that simultaneously interacts with keto-amino [C(-H)] -deprotonated on N1 and neutral keto-amino C. Both moieties are in different planes as a consequence of an additional NH ••• O=C hydrogen bond between C and [C(-H)] -. A sequential IRMPD dynamics is observed in this complex. For the [C(-H)Ba] + complex produced by electrospray ionization two isomers ([C(-H)KAN1OBa] + and [C(-H)KAN3OBa] + ) were identified, in which Ba 2+ interacts simultaneously with the C=O group and the N1 or N3 atom of the keto-amino [C(-H)] -, respectively. A comparison with the related [C(-H)Pb] + complex (

We are presenting the electronic photo fragment spectra of the protonated pyrimidine DNA bases homo-dimers. Only the thymine dimer exhibits a well structured vibrational progression, while protonated monomer shows broad vibrational bands. This shows that proton bonding can block some non radiative processes present in the monomer.

Recently, DNA molecules have received great attention because of their potential applications in material science. One interesting example is the production of highly fluorescent and tunable DNA-Agn clusters with cytosine (C)-rich DNA strands. Here, we report the UV photofragmentation spectra of gas-phase cytosine···Ag(+)···cytosine (C2Ag(+)) and cytosine···H(+)···cytosine (C2H(+)) complexes together with theoretical calculations. In both cases, the excitation energy does not differ significantly from that of isolated cytosine or protonated cytosine, indicating that the excitation takes place on the DNA base. However, the excited-state lifetime of the C2H(+) (τ = 85 fs), estimated from the bandwidth of the spectrum, is at least 2 orders of magnitude shorter than that of the C2Ag(+) (τ > 5000 fs). The increased excited-state lifetime upon silver complexation is quite unexpected, and it clearly opens the question about what factors are controlling the nonradiative decay in pyrimidi...

Gas-phase interactions between Ba 2+  and deprotonated cytosine (C (-H) ) were studied in [C (-H) Ba] +  and [C (-H) BaC] +  complexes by IRMPD spectroscopy coupled to tandem mass-spectrometry in combination with DFT calculations.  For the [C (-H) BaC] +  complex only one [C (-H) KAN1O-Ba-C anti ] +  isomer was found, although the presence of another structure cannot be neglected. This isomer features a central tetracoordinated Ba 2+  that simultaneously interacts with keto-amino [C (-H) ] -  deprotonated on N1 and neutral keto-amino C. Both moieties are in different planes as a consequence of an additional NH ●●● O=C hydrogen bond between C and [C (-H) ] - .  A sequential IRMPD dynamics is observed in this complex. For the [C (-H) Ba] +  complex produced by electrospray ionization two isomers ([C (-H) KAN1OBa] +  and [C (-H) KAN3OBa] + ) were identified, in which Ba 2+  interacts simultaneously with the C=O group and the N1 or N3 atom of the keto-amino [C (-H) ] - , respectively. A...

Carbohydrate-aromatic interactions are highly relevant for many biological processes. Nevertheless, experimental data in aqueous solution relating structure and energetics for sugararene stacking interactions are very scarce. Here, we evaluate how structural variations in a monosaccharide including carboxyl, N-acetyl, fluorine and methyl groups affect stacking interactions with aromatic DNA bases. We find small differences on stacking interaction among the natural carbohydrates examined. The presence of fluorine atoms within the pyranose ring slightly increases the interaction with the C-G DNA base pair. Carbohydrate hydrophobicity is the most determinant factor. However, gradual increase in hydrophobicity of the carbohydrate does not translate directly into a steady growth in stacking interaction. The energetics correlates better with the amount of apolar surface buried upon sugar stacking on top of the aromatic DNA base pair.

Carbohydrate-aromatic interactions are highly relevant for many biological processes. Nevertheless, experimental data in aqueous solution relating structure and energetics for sugararene stacking interactions are very scarce. Here, we evaluate how structural variations in a monosaccharide including carboxyl, N-acetyl, fluorine and methyl groups affect stacking interactions with aromatic DNA bases. We find small differences on stacking interaction among the natural carbohydrates examined. The presence of fluorine atoms within the pyranose ring slightly increases the interaction with the C-G DNA base pair. Carbohydrate hydrophobicity is the most determinant factor. However, gradual increase in hydrophobicity of the carbohydrate does not translate directly into a steady growth in stacking interaction. The energetics correlates better with the amount of apolar surface buried upon sugar stacking on top of the aromatic DNA base pair.

A theoretical (HF/6-31G** and DFT, B3LYP/6-31G**) study of the interactions between methyllithium and the DNA bases or several nucleosides is presented. Both the complexes following the binding of MeLi on these substrates and the structure of the entities resulting from the subsequent deprotonation reaction have been characterized.

A series of glycoconjugates, derivatives of genistein containing a C-glycosylated carbohydrate moiety, were synthesized and their anticancer activity was tested in vitro in the human cell lines HCT 116 and DU 145. The target compounds 15-17 were synthesized by treating ω-bromoalkyl C-glycosides derived from L-rhamnal (1) with a tetrabutylammonium salt of genistein. The new, metabolically stable analogs of previously studied O-glycosidic genistein derivatives inhibited proliferation of cancer cell lines through inhibition of the cell cycle.

We present density functional theory (DFT) calculations using B3LYP/6-31++G ** method to show relaxation in geometry of base pairs on cation radical formation. The changes in hydrogen bond length and angles show that in the cationic radical form the structure of the base pairs relaxes due to the distribution of charge. According to a recent study, it has been found that, upon excitation hole transfer from base to sugar occurs which results in sugar radical formation and leads to strand breakage [45] [A. Kumar, M.D. Sevilla, J. Phys. Chem. B 110 (2006) 24181]. One hydrogen bond increases, while the other decreases in Adenine-Thymine (AT) base pair and in case of Guanine-Cytosine (GC) base pair, one bond increases and other two decrease. Same is the case with bond angles for both the base pairs. Analysis of the electron density map of Singly Occupied Molecular Orbital (SOMO) reveals that electron is transferred mainly from adenine and guanine bases in the cationic radical formation of AT and GC base pair, respectively. The reactive sites of bases have been analyzed using condensed Fukui functions in a relaxed and frozen core approximation. The effects of relaxation on the reactivity indices are also analyzed.

Synthesis of the Isotope-Labeled Standards. The 5'-d(15 N 5 , 13 C 10-G)pT and 5'-d(15 N 5 , 13 C 10-G)pCpT sequences were synthesized by standard automated phosphoramidite chemistry technique using uniformly labeled 2'-deoxyguanosine phosporamidites (Cambridge Isotope Laboratories), and then oxidized by photochemically generated CO 3  radicals to form the 5'-d(15 N 5 , 13 C 10-G)*pT* and 5'd(15 N 5 , 13 C 10-G)*pCpT* cross-linked products [Yun, B. H., et al. (2011) Chem. Res. Toxicol. 24, 1144-1152]. All isotope-labeled standards were isolated, purified, and desalted by HPLC methods and their identities were confirmed by LC/MS/MS methods. Extraction of DNA from cells. Cellular DNA was extracted using the NaI method. HeLa cells (10 million) were suspended in 350 µL of extraction buffer (10 mM Tris-Cl (pH 8.0) + 5 mM EDTA-Na 2 , 0.15 mM desferrioxamine pH 8.0 and 1% sodium dodecyl sulfate) and subjected to two freezethaw cycles in liquid N 2. RNA was removed by digestion with 20 µL of RNAse A (stock solution: 1 mg/mL in 10 mM Tris-Cl (pH 8), 1 mM EDTA-Na 2 , 2.5 mM desferrioxamine pH 7.4 containing 1% sodium dodecyl sulfate) at 50°C for 30 min. Then, 15 µL of protease (stock solution: 20 mg/ml in water) was added to the samples and incubated at 37˚C for 120 min with frequent vortex. After protease treatment, DNA was precipitated by the addition of 600 µL of NaI solution (stock solution: 7.6 M NaI, 40 mM Tris-Cl (pH 8.0), 20 mM EDTA-Na 2 , 0.3 mM desferrioxamine) followed by the addition of 1 ml of 2-propanol. The sample was centrifuged at 14, 000 g for 30 min at 4˚C. The supernatant was removed and the pellet was washed first with 1 ml of 50% 2-propanol and then 70% ethanol. The pellet was briefly dried under vacuum and stored in the freezer until enzymatic digestion and analysis.

The DNA sequences similarity analysis approaches have been based on the representation and the frequency of sequences components; however, the position inside sequence is important information for the sequence data. Whereas, insufficient information in sequences representations is important reason that causes poor similarity results. Based on three classifications of the DNA bases according to their chemical properties, the frequencies and average positions of group mutations have been grouped into two twelve-components vectors, the Euclidean distances among introduced vectors applied to compare the coding sequences of the first exon of beta globin gene of 11 species.

The ultrafast deactivation processes in the excited state of biomolecules, such as the most stable tautomers of guanine, forbid any state-of-the-art gas phase spectroscopic studies on these species with nanosecond lasers. This drawback can be overcome by grafting a chromophore having a long-lived excited state to the molecule of interest, allowing thus a mass-selective detection by nanosecond R2PI and therefore double resonance IR/UV conformer-selective spectroscopic studies. The principle is presently demonstrated on the keto form of a modified 9-methylguanine, for which the IR/UV double resonance spectrum in the C═O stretch region, reported for the first time, provides evidence for extensive vibrational couplings within the guanine moiety. Such a successful strategy opens up a route to mass-selective IR/UV spectroscopic investigations on molecules exhibiting natural chromophores having ultrashort-lived excited states, such as DNA bases, their complexes as well as peptides containi...

Among the low-index single-crystal gold surfaces, the Au(110) surface is the most active toward molecular adsorption and the one with fewest electrochemical adsorption data reported. Cyclic voltammetry (CV), electrochemically controlled scanning tunneling microscopy (EC-STM), and density functional theory (DFT) calculations have been employed in the present study to address the adsorption of the four nucleobases adenine (A), cytosine (C), guanine (G), and thymine (T), on the Au(110)-electrode surface. Au(110) undergoes reconstruction to the (1 × 3) surface in electrochemical environment, accompanied by a pair of strong voltammetry peaks in the double-layer region in acid solutions. Adsorption of the DNA bases gives featureless voltammograms with lower double-layer capacitance, suggesting that all the bases are chemisorbed on the Au(110) surface. Further investigation of the surface structures of the adlayers of the four DNA bases by EC-STM disclosed lifting of the Au(110) reconstruc...

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The Surface Force Apparatus (SFA) measures directly, and with nanoscale resolution, the interaction energy vs. distance profile of planar arrays of biological molecules (e.g., lipids, polymers, or proteins). Through recent advances in the reconstitution and deposition of lipid bilayers, it is now possible to use SFA to study the interactions between membrane-incorporated biomolecules and to reveal any conformational changes and intermediate assembly states. Therein we describe two example systems. First, we show that using bilayers functionalized to carry DNA bases on their lipid headgroups, we can measure a macroscopic nucleosidenucleoside adhesion force, from which one can obtain a molecular binding energy. Second, we describe the use of the SFA to study the interaction between SNARE proteins, which are involved in most of intracellular fusion events. Membrane fusion occurs when SNARE proteins assemble between lipid bilayers in the form of SNAREpins. SFA measurements between SNAREs embedded in lipid bilayers allowed us to elucidate the energetics and dynamics of SNAREpin folding, and to capture an intermediate binding state in SNAREpin assembly.

A novel kinetic approach based on ab initio calculated rate constants has been developed and implemented in the kTSim program. The proposed approach allows prediction of the distribution of reactant and product concentrations over time, based exclusively on computationally obtained rate constants. The newly developed methodology was used to simulate the process of evaporation and tautomerization of guanine and cytosine under thermal (T) 490 K, cytosine; T) 620 K, guanine) and laser (T) 1000 K, 24 ns laser pulse) desorption conditions. Both monomolecular and bimolecular mechanisms of the tautomerization were considered simultaneously. The rates of the reactions were estimated using the values of Gibbs free energies calculated at the MPWB1K/aug-cc-pVDZ level and specified in a kTSim input. We expect that the proposed approach can also be used for accurate kinetic simulation of a wide range of processes.

We are presenting the electronic photo fragment spectra of the protonated pyrimidine DNA bases homo-dimers. Only the thymine dimer exhibits a well structured vibrational progression, while protonated monomer shows broad vibrational bands. This shows that proton bonding can block some non radiative processes present in the monomer.

Recently, DNA molecules have received great attention because of their potential applications in material science. One interesting example is the production of highly fluorescent and tunable DNA-Ag n clusters with cytosine (C) rich DNA strands. Here, we report the UV photofragmentation spectra of gas phase C tosi e…Ag + …C tosi e C 2 Ag +) and C tosi e…H + …C tosi e C 2 H +) complexes together with theoretical calculations. In both cases the excitation energy does not differ significantly from that of isolated cytosine or protonated-cytosine indicating that the excitation takes place on the DNA base. However, the excited state lifetime of the C 2 H + (= 85 fs), estimated from the bandwidth of the spectrum, is at least two orders of magnitude shorter than that of the C 2 Ag + (> 5300 fs). The increased excited state lifetime upon silver complexation is quite unexpected and it clearly opens the question about what factors are controlling the non-radiative decay in pyrimidine DNA bases? This is an important result for the expanding field of metal-mediated base pairing, and may also be important to the photophysical properties of DNA-templated, fluorescent silver clusters.

The ubiquitous nature and persistence of exocyclic DNA adducts suggest their involvement as initiators of carcinogenesis. We have investigated the misincorporation properties of the exocyclic DNA adduct, 3,N 4-ethenocytosine, using DFT and DFT-D methods. Computational investigations have been carried out by using the B3LYP, M062X, and wB97XD methods with the 6-31+G* basis set to determine the hydrogen bonding strengths, binding energy, and physical parameters. The single point energy calculations have been carried out at MP2/6-311++G** on corresponding optimized geometries. The energies were compared among the 3,N 4ethenocytosine adduct with DNA bases to find the most stable conformer. The solvent phase calculations have also been carried out using the CPCM model. The computed reaction enthalpy values provide computational insights to the earlier experimental observation in in vitro, E.coli, and mammalian cells of a high level of substitution mutation in which C → A transversion results from εC−T pairing [εC−T3 and εC−T4] in the adduct containing DNA sequence.

The scanning tunneling microscope has been used to obtain images of DNA that reveal its major and minor grooves and the direction of helical coiling, but sufficient resolution has not yet been achieved to identify its bases. To determine if this technology is capable of identifying individual DNA bases, we have examined the molecular arrangements of adenine and thymine attached to the basal plane of highly oriented pyrolytic graphite. Both molecules form highly organized lattices following deposition on heated graphite. Lattice dimensions, structural periodicities, and the epitaxy of adenine and thymine molecules with respect to the basal plane of graphite have been determined. Images of these molecules at atomic resolution reveal that the aromatic regions are strongly detected in both molecules while the various side-groups are not well-resolved. These studies provide the first evidence that tunneling microscopy can be used to discriminate between purines and pyramidines.

Gas-phase interactions between Ba 2+ and deprotonated cytosine (C(-H)) were studied in [C(-H)Ba] + and [C(-H)BaC] + complexes by IRMPD spectroscopy coupled to tandem mass-spectrometry in combination with DFT calculations. For the [C(-H)BaC] + complex only one [C(-H)KAN1O-Ba-Canti] + isomer was found, although the presence of another structure cannot be neglected. This isomer features a central tetracoordinated Ba 2+ that simultaneously interacts with keto-amino [C(-H)]deprotonated on N1 and neutral keto-amino C. Both moieties are in different planes as a consequence of an additional NH ••• O=C hydrogen bond between C and [C(-H)]-. A sequential IRMPD dynamics is observed in this complex. For the [C(-H)Ba] + complex produced by electrospray ionization two isomers ([C(-H)KAN1OBa] + and [C(-H)KAN3OBa] +) were identified, in which Ba 2+ interacts simultaneously with the C=O group and the N1 or N3 atom of the keto-amino [C(-H)]-, respectively. A comparison with the related [C(-H)Pb] + complex (

We present density functional theory (DFT) calculations using B3LYP/6-31++G ** method to show relaxation in geometry of base pairs on cation radical formation. The changes in hydrogen bond length and angles show that in the cationic radical form the structure of the base pairs relaxes due to the distribution of charge. According to a recent study, it has been found that, upon excitation hole transfer from base to sugar occurs which results in sugar radical formation and leads to strand breakage [45] [A. Kumar, M.D. Sevilla, J. Phys. Chem. B 110 (2006) 24181]. One hydrogen bond increases, while the other decreases in Adenine-Thymine (AT) base pair and in case of Guanine-Cytosine (GC) base pair, one bond increases and other two decrease. Same is the case with bond angles for both the base pairs. Analysis of the electron density map of Singly Occupied Molecular Orbital (SOMO) reveals that electron is transferred mainly from adenine and guanine bases in the cationic radical formation of AT and GC base pair, respectively. The reactive sites of bases have been analyzed using condensed Fukui functions in a relaxed and frozen core approximation. The effects of relaxation on the reactivity indices are also analyzed.

The ionization of the four DNA bases is investigated by means of ab initio calculations. Accurate values of the gas-phase vertical and adiabatic ionization potentials (IP) are obtained at the MP2/6-31G(2d(0.8,R d),p) level of theory. The need of introducing extra polarization to the standard 6-31G(d,p) basis set is demonstrated by test calculations and an optimal value of R d) 0.1 is obtained. Ionization to electronically excited radical cations is also considered. The low-lying excited states of the cations are characterized for the first time. The topology of the corresponding potential energy surfaces is qualitatively described in terms of the stationary points (minima and saddle points) located on these surfaces. A conical intersection is characterized for the first time on the ground-state potential energy surface of all cations. It arises from the crossing of the adiabatic surfaces of the ground and first excited state at planar geometries. A nonplanar minimum is observed for the cytosine cation only. The geometry and electronic changes occurring along these surfaces are analyzed, leading to a comparison between the different nucleobase cations. The study of larger ionized systems related to DNA is rendered possible thanks to the optimized medium size basis set proposed in this work, as exemplified by the calculation of the IP of a stacked dimer of guanines.

The energies and aromaticity of a series of R substituted imidazoles [R = NH 2 , OH, H, CH 3 , F, Cl, CN, NO, NO 2 ], their anions and protonated forms in the gas phase have been calculated with the DFT/B3LYP and MP2 methods at the 6-311++G(d,p) level. We have analyzed the change of local aromaticity using several aromaticity indicators (Pozharsky Index, HOMA, NICS, ASE and pEDA) and found a considerable ring aromaticity for imidazoles, imidazolate anions and their protonated forms. In each class anion forms have the most aromaticity and in neutral forms, 1-H imidazoles have less aromaticity character. The HOMA and structural AI show good correlation with each other but NICS (0) values showed a poor correlation with other scales. The geometrical indices seem to be better correlate with substituent effect.

Carbohydrate-aromatic interactions are highly relevant for many biological processes. Nevertheless, experimental data in aqueous solution relating structure and energetics for sugararene stacking interactions are very scarce. Here, we evaluate how structural variations in a monosaccharide including carboxyl, N-acetyl, fluorine and methyl groups affect stacking interactions with aromatic DNA bases. We find small differences on stacking interaction among the natural carbohydrates examined. The presence of fluorine atoms within the pyranose ring slightly increases the interaction with the C-G DNA base pair. Carbohydrate hydrophobicity is the most determinant factor. However, gradual increase in hydrophobicity of the carbohydrate does not translate directly into a steady growth in stacking interaction. The energetics correlates better with the amount of apolar surface buried upon sugar stacking on top of the aromatic DNA base pair.

Carbohydrate-aromatic interactions are highly relevant for many biological processes. Nevertheless, experimental data in aqueous solution relating structure and energetics for sugararene stacking interactions are very scarce. Here, we evaluate how structural variations in a monosaccharide including carboxyl, N-acetyl, fluorine and methyl groups affect stacking interactions with aromatic DNA bases. We find small differences on stacking interaction among the natural carbohydrates examined. The presence of fluorine atoms within the pyranose ring slightly increases the interaction with the C-G DNA base pair. Carbohydrate hydrophobicity is the most determinant factor. However, gradual increase in hydrophobicity of the carbohydrate does not translate directly into a steady growth in stacking interaction. The energetics correlates better with the amount of apolar surface buried upon sugar stacking on top of the aromatic DNA base pair.

We point out the possibility to distinguish the DNA bases (adenine, cytosine, guanine and thymine) by using the high-order harmonics sources. Moreover, we find the intensity peaks of the high-order harmonics emitted by thymine base while this molecule is near the stable states (keto and enol) as well as at the transition state along the chemical reaction path of a tautomerism process. This finding shows the possibility of tracking the DNA tautomerism. Our investigation is based on the simulation method. The structures of four DNA bases and the ketoenol tautomerism of thymine are simulated by the molecular dynamics method within the Born-Oppenheimer approximation. High-order harmonics, emitted from the bases while molecules are exposed to ultrashort laser pulses are calculated by the strong-field approximation within the Lewenstein model. The calculated data then are used as 'experimental' high-order harmonics sources for investigation.

Carbohydrate-aromatic interactions are highly relevant for many biological processes. Nevertheless, experimental data in aqueous solution relating structure and energetics for sugararene stacking interactions are very scarce. Here, we evaluate how structural variations in a monosaccharide including carboxyl, N-acetyl, fluorine and methyl groups affect stacking interactions with aromatic DNA bases. We find small differences on stacking interaction among the natural carbohydrates examined. The presence of fluorine atoms within the pyranose ring slightly increases the interaction with the C-G DNA base pair. Carbohydrate hydrophobicity is the most determinant factor. However, gradual increase in hydrophobicity of the carbohydrate does not translate directly into a steady growth in stacking interaction. The energetics correlates better with the amount of apolar surface buried upon sugar stacking on top of the aromatic DNA base pair.