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Schnier PD, Klassen JS, Strittmatter EF, et al. Activation energies for dissociation of double strand oligonucleotide anions: evidence for watson-crick base pairing in vacuo. J Am Chem Soc. 1998;120(37):9605-13doi: 10.1021/ja973534h.
Schnier, P. D., Klassen, J. S., Strittmatter, E. F., & Williams, E. R. (1998). Activation energies for dissociation of double strand oligonucleotide anions: evidence for watson-crick base pairing in vacuo. Journal of the American Chemical Society, 120(37), 9605-13. https://doi.org/10.1021/ja973534h
Schnier, P D, et al. "Activation energies for dissociation of double strand oligonucleotide anions: evidence for watson-crick base pairing in vacuo." Journal of the American Chemical Society vol. 120,37 (1998): 9605-13. doi: https://doi.org/10.1021/ja973534h
Schnier PD, Klassen JS, Strittmatter EF, Williams ER. Activation energies for dissociation of double strand oligonucleotide anions: evidence for watson-crick base pairing in vacuo. J Am Chem Soc. 1998 Sep 23;120(37):9605-13. doi: 10.1021/ja973534h. PMID: 16498487; PMCID: PMC1380309.
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J Am Chem Soc. 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.

Journal of the American Chemical Society

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

Affiliations

  1. Contribution from the Department of Chemistry, University of California, Berkeley, California 94720, USA.

PMID: 16498487 PMCID: PMC1380309 DOI: 10.1021/ja973534h

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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