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. 1998 Sep 23;120(37):9605-13.
doi: 10.1021/ja973534h.

Activation energies for dissociation of double strand oligonucleotide anions: evidence for watson-crick base pairing in vacuo

P D Schnier  1 , J S Klassen, E F Strittmatter, E R Williams
Affiliations

Activation energies for dissociation of double strand oligonucleotide anions: evidence for watson-crick base pairing in vacuo

P D Schnier et al. J Am Chem Soc. .

Abstract

The dissociation kinetics of a series of complementary and noncomplementary DNA duplexes, (TGCA)(2) (3-), (CCGG)(2) (3-), (AATTAAT)(2) (3-), (CCGGCCG)(2) (3-), A(7)*T(7) (3-), A(7)*A(7) (3-), T(7)*T(7) (3-), and A(7)*C(7) (3-) were investigated using blackbody infrared radiative dissociation in a Fourier transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Activation energies range from 1.2 to 1.7 eV, and preexponential factors range from 10(13) to 10(19) s(-1). Dissociation of the duplexes results in cleavage of the noncovalent bonds and/or cleavage of covalent bonds leading to loss of a neutral nucleobase followed by backbone cleavage producing sequence-specific (a - base) and w ions. Four pieces of evidence are presented which indicate that Watson-Crick (WC) base pairing is preserved in complementary DNA duplexes in the gas phase: i. the activation energy for dissociation of the complementary dimer, A(7)*T(7) (3-), to the single strands is significantly higher than that for the related noncomplementary A(7)*A(7) (3-) and T(7)*T(7) (3-) dimers, indicating a stronger interaction between strands with a specific base sequence, ii. extensive loss of neutral adenine occurs for A(7)*A(7) (3-) and A(7)*C(7) (3-) but not for A(7)*T(7) (3-) consistent with this process being shut down by WC hydrogen bonding, iii. a correlation is observed between the measured activation energy for dissociation to single strands and the dimerization enthalpy (-DeltaH(d)) in solution, and iv. molecular dynamics carried out at 300 and 400 K indicate that WC base pairing is preserved for A(7)*T(7) (3-) duplex, although the helical structure is essentially lost. In combination, these results provide strong evidence that WC base pairing can exist in the complete absence of solvent.

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Figures

Figure 1
Figure 1
Electrospray ionization Fourier transform mass spectra from 50:50 H2O/CH3CN solutions containing (a) 10−4 M p(dA)7 and p(dT)7 (inset shows the absorbance (260 nm) versus temperature profile (temperature melt) indicating the presence of double-helix DNA in this solution (Tm ≈ 32 °C)) and (b) 10−4 M p(dA)7 and p(dC)7.
Figure 2
Figure 2
Blackbody infrared radiative dissociation spectra of DNA duplexes with three negative charges taken from the kinetic data (a) (TGCA)2, (300 s, 57 °C), (b) A7·T7 (120 s, 117 °C), (c) (AATTAAT)2 (45 s, 137 °C), (d) (CCGGCCG)2 (150 s, 171 °C), (e) A7·A7 (10 s, 150 °C), (f) T7·T7 (20 s, 107 °C), and (g) (CCGG)2 (30 s, 90 °C). An asterisk indicates a harmonic of the precursor ion. Checks indicate unejected ions; these ions do not interfere with the dissociation kinetics of interest. The spectrum shown in g was background subtracted.
Figure 3
Figure 3
Arrhenius plots for the dissociation of double-strand DNA (•) (TGCA)23−, (○) T7·T73−, (▪) (AATTAAT)23−, (□) A7·A73−, (*) A7·T73−, (♦) (CCGGCCG)23−, and (+) (CCGG)23−.
Figure 4
Figure 4
Plot of calculated dimerization enthalpies (−ΔHd) for DNA duplexes in solution versus gas-phase activation energies for dissociation to monomer. The point for (CCGGCCG)2 is a lower limit since no monomer is observed in the dissociation spectra (see text).
Figure 5
Figure 5
Structure obtained from molecular dynamics simulations of A7·T73−, A7·A73−, and T7·T73− after 100 ps at 300 K: (a) A7·T73− (the dark strand corresponds to T7), (b) A7·A73−, and (c) T7·T73−. Hydrogen bonds are indicated by dashed lines. Location of the charge sites are indicated by the arrows. Hydrogen atoms not involved in hydrogen bonding are omitted for clarity.
Figure 6
Figure 6
Structure of A7·T73− obtained by molecular dynamic simulations after 300 ps at 400 K. The structure in Figure 5a was used as the starting geometry (400 ps total simulation time). Six of the seven Watson–Crick base pairs remain; the two terminal unpaired bases are indicated by asterisks.
Figure 7
Figure 7
BIRD spectra of (a) (AATTAAT)23− and (b) AATTAAT2− with a reaction delay of 105 s at 124 °C.
Figure 8
Figure 8
BIRD spectra of (a) (CCGGCCG)23− and (b) CCGGCCG2− with a reaction delay of 90 s at 181 °C.
Scheme 1
Scheme 1
Scheme 2
Scheme 2
Scheme 3
Scheme 3
Scheme 4
Scheme 4
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