Building Solutions--One Molecule at a Time

Huneycutt, A. J.; Saykally, Richard J.

doi:10.1126/science.1082269

Cited by 52 publications

(55 citation statements)

References 16 publications

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“…However, spectroscopic studies show that at least four water molecules constitute the first solvent shell (19,20) around cations associated with DNA, so the charge on the alkali ion is also widely dispersed. There is some evidence that tetramethylammonium ions are bound more strongly to DNAs than are sodium ions (13).…”

Section: Discussionmentioning

confidence: 99%

Thermodynamic treatment of oligonucleotide duplex–simplex equilibria

Owczarzy

Dunietz²,

Behlke³

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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Thermodynamic formulations have been devised to obtain ⌬G°v alues directly from spectroscopic data at a fixed common temperature in nucleic acid duplex-simplex melting curves. In addition, the dependence of melting on salt concentration has been expressed in terms of a stepwise stoichiometric representation, which leads to a specific equation for the partition of the added sodium ions between the different oligonucleotide forms. G enerally the free energy of melting of an oligonucleotide duplex, D, into its constituent complementary single strands, S 1 and S 2 , is obtained from the temperature at the midpoint of the melting curve, T m . To compare the ⌬G°s of a series of duplexes of varying composition, one obtains the respective T m values and adjusts them to a common temperature using data for the ⌬HЊ of the transition.It is also possible to obtain ⌬GЊ for a series of duplexes from absorbance data at only one fixed common temperature in the melting curves. We have explored this alternative mode of treatment with a set of duplexes having oligonucleotide lengths of 10 bp.Melting curves of duplex DNA are very sensitive to salt concentration. The dependence of T m and of ⌬GЊ on Na ϩ molarity has been generally formulated on the basis of the following chemical equation for the oligonucleotide equilibrium,

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Section: Discussionmentioning

confidence: 99%

Thermodynamic treatment of oligonucleotide duplex–simplex equilibria

Owczarzy

Dunietz²,

Behlke³

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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“…One strategy to gain a detailed understanding of how ions and water molecules interact is to build up a solution, one molecule of water at a time. [1] Vibrational spectroscopy is a powerful structural tool for investigating hydrated ions, and has been used to investigate the structures of hydrated monovalent cations, including Ag + , [2] H + , [3][4][5][6] Cs + , [7,8] Cu + , [2] K + , [9] Mg + , [10] NH 4 + , [11,12] and Ni + , [13] and hydrated anions, including Cl À , [14,15] e À , [16] F À , [15,17] HO À , [18] and SO 4 2À . [19] Despite serving critical regulatory and structural roles in biology, experimental studies of hydrated, multiply charged ions have lagged behind those of singly charged ions, owing to the great difficulty in producing them in significant abundances; for example, formation of doubly hydrated, divalent calcium by condensation results in rapid dissociation aided by Coulomb repulsion [Eq.…”

Section: Introductionmentioning

confidence: 97%

Hydration of the Calcium Dication: Direct Evidence for Second Shell Formation from Infrared Spectroscopy

2007

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Infrared laser action spectroscopy in a Fourier-transform ion cyclotron resonance mass spectrometer is used in conjunction with ab initio calculations to investigate doubly charged, hydrated clusters of calcium formed by electrospray ionization. Six water molecules coordinate directly to the calcium dication, whereas the seventh water molecule is incorporated into a second solvation shell. Spectral features indicate the presence of multiple structures of Ca(H2O)(7)2+ in which outer-shell water molecules accept either one (single acceptor) or two (double acceptor) hydrogen bonds from inner-shell water molecules. Double-acceptor water molecules are predominantly observed in the second solvent shells of clusters containing eight or nine water molecules. Increased hydration results in spectroscopic signatures consistent with additional second-shell water molecules, particularly the appearance of inner-shell water molecules that donate two hydrogen bonds (double donor) to the second solvent shell. This is the first reported use of infrared spectroscopy to investigate shell structure of a hydrated multiply charged cation in the gas phase and illustrates the effectiveness of this method to probe the structures of hydrated ions.

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“…These pioneering works opened the way to high-resolution spectroscopy in the microwave and infrared spectral ranges [2][3][4][5]. It proved to be a challenging field, experimentally because these weakly bound species are difficult to produce with sufficient density, and theoretically because these complexes show large amplitude motions.…”

Section: Introductionmentioning

confidence: 99%