Activation Energies for Dissociation of Double Strand Oligonucleotide Anions:  Evidence for Watson−Crick Base Pairing in Vacuo

Schnier, Paul D.; Klassen, John S.; Strittmatter, Eric F.; Williams, Evan R.

doi:10.1021/ja973534h

Cited by 153 publications

(155 citation statements)

References 68 publications

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“…This method has been used to investigate the effects of individual hydrogen bonds between heme and myoglobin and cytochrome b 5 [8], binding in double stranded DNA [9,10], and to investigate binding of inhibitors to aldose reductase [11], peptides to vancomycin [12], and avoparcin [13], small molecules to carbonic anhydrase [14], peptides to OppA [15], an antibody single chain fragment to a series of structurally related trisaccharides [7,16], and a series of trisaccharides to an antibody single chain fragment [17].…”

mentioning

confidence: 99%

Gas phase noncovalent protein complexes that retain solution binding properties: Binding of xylobiose inhibitors to the β-1, 4 exoglucanase from Cellulomonas fimi

Tešić

Wicki

Poon

et al. 2007

J. Am. Soc. Mass Spectrom.

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Tandem mass spectrometry has been used to compare gas-phase and solution binding of three small-molecule inhibitors to the wild type and three mutant forms of the catalytic domain of Cex, an enzyme that hydrolyses xylan and xylo-oligosaccharides. The inhibitors, xylobiosyldeoxynojirimycin, xylobiosyl-isofagomine lactam, and xylobiosyl-isofagomine consist of a common distal xylose linked to different proximal aza-sugars. The three mutant forms of the enzyme contain the substitutions Asn44Ala, Gln87Met, and Gln87Tyr that alter the binding interactions between Cex and the distal sugar of each inhibitor. An electrospray ionization (ESI) triple quadrupole MS/MS system is used to measure the internal energies, ⌬E int , that must be added to gas-phase ions to cause dissociation of the noncovalent enzyme-inhibitor complexes. Collision cross sections of ions of the apo-enzyme and enzyme-inhibitor complexes, which are required for the calculations of ⌬E int , have also been measured. The results show that, in the gas phase, enzyme-inhibitor complexes have more compact, folded conformations than the corresponding apo-enzyme ions. With the mutant enzymes, the effects of substituting a single residue can be detected. The energies required to dissociate the gas-phase complexes follow the same trend as the values of ⌬G 0 for dissociation of the complexes in solution. This trend is observed both with different inhibitors, which probe binding to the proximal sugar, and with mutants of Cex, which probe binding to the distal sugar. Thus the gas-phase complexes appear to retain much of their solution binding characteristics. (J Am Soc Mass Spectrom 2007, 18, 64 -73)

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confidence: 99%

Gas phase noncovalent protein complexes that retain solution binding properties: Binding of xylobiose inhibitors to the β-1, 4 exoglucanase from Cellulomonas fimi

Tešić

Wicki

Poon

et al. 2007

J. Am. Soc. Mass Spectrom.

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“…In the former case, the mass spectra should ideally directly represent the solution phase chemistry. Gas-phase methods include cone voltage driven dissociation (called the "VC 50 " method) [12,13], collision-induced dissociation [14,15], guided ion beam tandem mass spectrometry [16,17], blackbody infrared radiative dissociation [18,19] and heated capillary dissocation [20,21].…”

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confidence: 99%

Mass spectrometric determination of association constants of adenylate kinase with two noncovalent inhibitors

Daniel

McCombie

Wendt

et al. 2003

J. Am. Soc. Mass Spectrom.

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Noncovalent complexes between chicken muscle adenylate kinase and two inhibitors, P 1 ,P 4 -di(adenosine-5')tetraphosphate (Ap4A) and P 1 ,P 5 -di(adenosine-5') pentaphosphate (Ap5A), were investigated with electrospray ionization mass spectrometry under non-denaturing conditions. The nonconvalent nature and the specificity of the complexes are demonstrated with a number of control experiments. Titration experiments allowed the association constants for inhibitor binding to be determined. Problems with concentration dependent ion yields are circumvented by a data evaluation method that is insensitive to the overall ionization efficiency. The K a values found were 9.0 ϫ 10 4 M Ϫ1 (Ap4A) and 4.0 ϫ S oft ionization mass spectrometry (MS), in particular matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI), is well known for its ability to bring high molecular weight biomolecules into the gase phase and to even preserve noncovalent complexes [1][2][3][4][5][6][7][8][9][10]. Besides its established applications, a recurring question concerns the applicability of mass spectrometry to measuring noncovalent interaction strengths [11]. There are different approaches to measure the interaction strengths in the gas phase as well as in the liquid phase. In the former case, the mass spectra should ideally directly represent the solution phase chemistry. Gas-phase methods include cone voltage driven dissociation (called the "VC 50 " method) [12,13], collision-induced dissociation [14,15], guided ion beam tandem mass spectrometry [16,17], blackbody infrared radiative dissociation [18,19] and heated capillary dissocation [20,21].Some mass spectrometric studies have been reported in the literature for the determination of noncovalent interaction strengths. There are three basic methods to determine association constants that are reflective of those in solution: first, it is possible to record "melting curves" by raising the temperature of the analyte solution and to use MS to determine the percentage of intact complexes. Cheng et al. analyzed complementary DNA strands [22] and Fändrich et al. studied the chaperone GimC/prefolding homologue complex [13] with this method. Second, competition experiments can be used to evaluate the stability of noncovalent complexes. In Jørgensen's method [23,24], the relative intensities of the free host and the different complexes were used, whereas Kempen et al. employed the known concentration of a reference complex to determine the concentration of an unknown complex [25]. Third, a titration of a host with a guest (or vice versa) can be used. In this case, the mass spectrometric signals should accurately represent the concentrations of the species in solution. The titration method is documented in a number of publications, all of them convincingly showing the successful use of mass spectrometry for the quantitative determination of noncovalent binding constants of proteins and small molecules [26 -33]. This aspect was the main focus in most previous research; th...

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“…The extension of FRET, widely used in solution studies [14] to measure trapped biopolymer ions can provide the capability to directly correlate changes in fluorescence intensity with changes in the average conformation of biopolymer molecules. For example, FRET methods might be applied to further investigate gas phase dissociation dynamics of double strand oligonucleotide anions [15]. In this case, the rf trap offers a unique capability to correlate the in situ fluorescence data with ion mass spectra which could lead to a new approach to study the intermediate states preceding dissociation of the double strand.…”

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confidence: 99%

Pulsed fluorescence measurements of trapped molecular ions with zero background detection

Khoury¹,

Rodriguez‐Cruz²,

Parks³

2002

J Am Soc Mass Spectrom

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Sensitive methods have been developed to measure laser-induced fluorescence from trapped ions by reducing the detection of background scattering to zero levels during the laser excitation pulse. The laser beam diameter has been reduced to ϳ150 m to eliminate scattering on trap apertures and the resulting laser-ion interaction is limited to a volume of ϳ10 Ϫ5 cm 3 which is ϳ0.03-0.15 of the total ion cloud volume depending on experimental conditions. The detection optics collected fluorescence only from within the solid angle defined by laser-ion interaction volume. Rhodamine 640 and Alexa Fluor 350 ions, commonly used as fluorescence resonance energy transfer (FRET) fluorophores, were generated in the gas phase by using electrospray ionization and injected into a radiofrequency Paul trap where they were stored and exposed to Nd:YAG laser pulses at 532 and 355 nm for times up to 10 m. Fluorescence emitted by these ions was investigated for several trap q z values and ion cloud temperatures. Analysis of photon statistics indicated an average of ϳ10 photons were incident on the PMT detector per 15 ns pulse for ϳ10 3 trapped ions in the interaction volume. Fluorescence measurements displayed a dependence on trapped ion number which were consistent with calculations of the space charge limited ion density. To investigate the quantitative capability of these fluorescence techniques, the laser-induced fragmentation of trapped Alexa I on traps provide a controlled environment in which fluorescence measurements can be performed on an ensemble of ions over timescales sufficient to consider small ion numbers and slow reaction rates. Laserinduced fluorescence measurements of trapped ions have been used in spectroscopic studies of atomic structure [1][2][3][4], the vibrational spectra of small molecules [5][6][7][8], as well as to characterize the dynamic cooling [9] and crystallization of atomic ions [10 -12].This paper introduces techniques that eliminate the detection of laser background scattering on trap apertures and internal surfaces allowing measurements to achieve both high sensitivity and large dynamic range. In previous pulsed laser measurements of molecular fluorescence collected from trapped species (discussed in references [5][6][7][8]), the radiative lifetimes were sufficiently long to allow collection of fluorescence radiation after the laser pulse. This greatly simplified methods to reduce the detection of background resulting from scattered laser radiation. However, experiments described in this paper apply the Nd:YAG pulsed laser to excite strongly emitting molecules having fluorescence lifetimes shorter than the laser pulse. This required the reduction of background laser scattering during laser excitation, a more demanding constraint.Techniques described in this paper will help to extend fluorescence measurements as an in situ probe of trapped ion properties including chemical identity, the growth and decay of specific ion populations, ion spectroscopy. Fluorescence emission from trapped ions also presen...

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Activation Energies for Dissociation of Double Strand Oligonucleotide Anions: Evidence for Watson−Crick Base Pairing in Vacuo

Cited by 153 publications

References 68 publications

Gas phase noncovalent protein complexes that retain solution binding properties: Binding of xylobiose inhibitors to the β-1, 4 exoglucanase from Cellulomonas fimi

Gas phase noncovalent protein complexes that retain solution binding properties: Binding of xylobiose inhibitors to the β-1, 4 exoglucanase from Cellulomonas fimi

Mass spectrometric determination of association constants of adenylate kinase with two noncovalent inhibitors

Pulsed fluorescence measurements of trapped molecular ions with zero background detection

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