Proton affinity ladder for uridine and analogs: influence of the hydroxyl group on the sugar ring conformation

Mezzache, S.; Alvès, Sandra; Pèpe, Claude; Quelquejeu, Mélanie; Fournier, Françoise; Valéry, Jean‐Marc; Tabet, Jean‐Claude

doi:10.1002/jms.844

Cited by 11 publications

(4 citation statements)

References 33 publications

(36 reference statements)

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“…Similarly to uracil and thymine, the calculations [33] at the B3LYP/6-31G* level of theory predict that the O 8 (C 5 ) position is the most preferred protonation site for the most stable uridine and thymidine tautomers, 2, and this position is likely to be the most favorable for water binding, 2a.…”

Section: Uracil and Thymine And Their Nucleosidesmentioning

confidence: 99%

Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase

Wincel

2009

J. Am. Soc. Mass Spectrom.

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Thermochemical data, ⌬H o n , ⌬S o n , and ⌬G o n , for the hydration of protonated nucleic acid bases and protonated nucleosides have been experimentally studied by equilibrium measurements using an electrospray high-pressure mass spectrometer equipped with a pulsed ion-beam reaction chamber. For protonated nucleobases the hydration enthalpies were found to be similar for all studied systems and varied between 12.4 -13.1 kcal/mol for the first and 11.2-11.5 kcal/mol for the second water molecule. While for protonated nucleosides the water binding enthalpies (11.7-13.3 kcal/mol) are very close to those for protonated nucleobases, the entropy values are "more negative." The structural and energetic aspects of hydrated ions are discussed in conjunction with the available theoretical data. (J Am Soc Mass Spectrom 2009, 20, 1900 -1905) © 2009 American Society for Mass Spectrometry N ucleic acid bases are amongst the primary building blocks of DNA and RNA, and water is generally considered to be their integral part. Hydration of nucleobases is crucially important for the structure, stability, and biologic functions of DNA [1,2]. Interaction between the DNA constituents and water molecules is important for a better understanding of the mechanistic role of water molecules in conformational transitions and mechanisms of DNA's bioactivity. The effect of hydration of the DNA bases is very local and only a limited number of water molecules contribute to it significantly [1,2]. Many studies on the gas-phase interactions of neutral and anionic forms of nucleic acid bases [3][4][5][6][7][8][9][10][11][12][13] [19] of hydrated adenine and thymine cations. Much less attention has been paid to the hydration of protonated DNA components, although these forms are of considerable interest in view of their potential formation in radiation-induced damage of DNA and RNA, and interaction with a water environment. To our best knowledge, the stabilities of protonated adenine tautomers and their complexes with water molecules [20] have only been investigated computationally, while there have been some experimental and theoretical studies on the hydration of protonated and deprotonated forms of the four mononucleotides (dAMP, dCMP, dGMP, and dTMP) [21]. More recently, the possible tautomeric forms of the monohydrated protonated uracil have been examined in the gas phase by using IR multiple-photon dissociation spectroscopy (IR-MPD) in combination with computational study [22].In this paper, we present the first experimental results on the energetics of hydration of protonated nucleic acid bases, NABs (uracil, Ura; thymine, Thy; adenine, Ade; and hypoxanthine, Hyp), and protonated nucleosides, NSDs (uridine, Urd; thymidine, Thd; adenosine, Ado; and inosine, Ino). These results were obtained from high-pressure mass spectrometry equilibria measurements in the gas phase. Previously, we measured the energetics of hydration of protonated and deprotonated amino acids [23][24][25]. ExperimentalAll experiments were performed on a high-pressure (HP...

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Section: Uracil and Thymine And Their Nucleosidesmentioning

confidence: 99%

Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase

Wincel

2009

J. Am. Soc. Mass Spectrom.

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“…dUrd is highly susceptible to modification at the 5-position such that minor forms of dUrd with halogen, ethyl, methylthio, hydroxymethyl and allyl substituents are known, and these dUrd variants are used as antiviral drugs. [34][35][36] Tabet and coworkers 37 measured the proton affinities (PAs) of Urd and dUrd using the kinetic method 38 and complemented these measurements with theoretical calculations. They found that the PA of dUrd is B10 kJ mol À1 greater than the PA of Urd, and that the sugar configuration exerts only a minor effect on the PA (B2 kJ mol À1 ).…”

Section: Introductionmentioning

confidence: 99%

Diverse mixtures of 2,4-dihydroxy tautomers and O4 protonated conformers of uridine and 2′-deoxyuridine coexist in the gas phase

Frieler

et al. 2015

Phys. Chem. Chem. Phys.

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The gas-phase conformations of protonated uridine, [Urd+H](+), and its modified form, protonated 2'-deoxyuridine, [dUrd+H](+), generated by electrospray ionization are investigated using infrared multiple photon dissociation (IRMPD) action spectroscopy techniques. IRMPD action spectra of [Urd+H](+) and [dUrd+H](+) are measured over the IR fingerprint and hydrogen-stretching regions. [Urd+H](+) and [dUrd+H](+) exhibit very similar IRMPD spectral profiles. However, the IRMPD yields of [Urd+H](+) exceed those of [dUrd+H](+) in both the IR fingerprint and hydrogen-stretching regions. The measured spectra are compared to the linear IR spectra predicted for the stable low-energy structures of these species computed at the B3LYP/6-311+G(d,p) level of theory to determine the tautomeric conformations populated by electrospray ionization. Both B3LYP and MP2 methods find O4 and O2 protonated canonical as well as 2,4-dihydroxy tautomers among the stable low-energy structures of [Urd+H](+) and [dUrd+H](+). Comparison between the measured IRMPD and calculated linear IR spectra suggests that these species exist in their ring-closed forms and that both 2,4-dihydroxy tautomers as well as O4 protonated canonical conformers coexist in the population generated by electrospray ionization for both [Urd+H](+) and [dUrd+H](+). The 2'-deoxy modification of [dUrd+H](+) reduces the variety of 2,4-dihydroxy tautomers populated in the experiments vs. those of [Urd+H](+).

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“…Such analytical methods started contributing to PNA structural investigations in 199322 and allowed identification of PNA/DNA23 duplexes, and PNA/DNA/PNA24, 25 triplexes as well as DNA/PNA/DNA (within triplex or duplex invasion configurations) 26. Mass spectrometry efficiently provided information on: (1) thermochemical properties (relative basicity/acidity scales),27–31 (2) the stoichiometry of the noncovalent complexes constituted by DNA and PNA oligomers23, 32 and (3) gas‐phase conformation of oligonucleotide associations by ion mobility33 and by collision‐induced dissociation (CID)34 or blackbody infrared dissociation (BIRD) 35. It is important to note that the hydrogen‐bonding and electrostatic interactions, such as cation–π and π–π,36–44 which impart rigidity to their conformations, are known to be preserved during their transfer from the solution to the gas phase.…”

Section: Introductionmentioning

confidence: 99%

Charge dependent behavior of PNA/DNA/PNA triplexes in the gas phase

Delvolvé¹,

Tabet²,

Bregant³

et al. 2006

J. Mass Spectrom.

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Intact noncovalent complexes were studied in the gas phase using negative ion nano-ESI mass spectrometry. Among various noncovalent systems studied in the gas phase, the interaction of DNA strands with peptide nucleic acids (PNAs) presents a strong interest as biologically relevant systems. PNAs originally described by Nielsen are used as DNA mimics as possible medical agents by imprisoning DNA single strands into stable noncovalent complexes. Two types of PNAs were investigated in the PNA/DNA multiplex: the original Nielsen's PNA and a modified backbone PNA by the introduction of syn- and anti-(aminoethyl)thiazolidine rings. We first investigated the stoichiometry of PNA/DNA multiplexes formed in solution and observed them in the gas phase via qualitative kinetics of complementary strand associations. It resulted in observing PNA2/DNA triplexes (ts) as the multiply deprotonated species, most stable in both the solution and gas phase. Second, charge-dependant decompositions of these species were undertaken under low-energy collision conditions. It appears that covalent bond cleavages (base releasing or skeleton cleavage) occur from lower ts charge states rather than ts unzipping, which takes place from higher charge states. This behavior can be explained by considering the presence of zwitterions depending on the charge state. They result in strong salt-bridge interactions between the positively charged PNA side chain and the negatively charged DNA backbone. We propose a general model to clearly display the involved patterns in the noncovalent triplex decompositions. Third, the relative stability of three PNA2/DNA complexes was scrutinized in the gas phase by acquiring the breakdown curves of their ts(6-) form, corresponding to the ts unzipping. The chemical structures of the studied PNAs were chosen in order to evidence the possible influence of backbone stereochemistry on the rigidity of PNA2/DNA complexes. It provided significantly different stabilities via V(m) measurements. The relative gas-phase stability order obtained was compared to that found in solution by Chassaing et al., and shows qualitative agreement.

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Proton affinity ladder for uridine and analogs: influence of the hydroxyl group on the sugar ring conformation

Cited by 11 publications

References 33 publications

Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase

Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase

Diverse mixtures of 2,4-dihydroxy tautomers and O4 protonated conformers of uridine and 2′-deoxyuridine coexist in the gas phase

Charge dependent behavior of PNA/DNA/PNA triplexes in the gas phase

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