Additives for the stabilization of double-stranded DNA in UV-MALDI MS

Distler, Anne M.; Allison, John

doi:10.1016/s1044-0305(02)00430-0

Cited by 26 publications

(21 citation statements)

References 31 publications

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“…The only observations of natural polyamineoligonucleotide complexes by mass spectrometry have been reported in the case where spermine was used as matrix additives for oligonucleotide analysis by MALDI-TOF [12][13][14][15]. In this case, protonated sites of the polyamine were expected to bond DNA phosphate in solution to displace alkaline cations [12][13][14] and stabilize duplexes [15]. Ideally, polyamine protons were transferred to DNA phosphates during sample crystallization or desorption/ ionization process and the oligonucleotide free of alkaline cation and polyamine was observed.…”

mentioning

confidence: 99%

A study of noncovalent complexes involving single-stranded DNA and polybasic compounds using nanospray mass spectrometry

Terrier

Tortajada

Buchmann

2007

J. Am. Soc. Mass Spectrom.

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Noncovalent complexes involving a single-stranded DNA oligonucleotide and a polybasic compound (spermine, penta-L-lysine, penta-L-arginine, or polydisperse poly-L-lysine) were detected by nanospray-MS. Several control experiments tended to show that these complexes preexisted in solution and that the interactions were initially ionic ones between oligonucleotide phosphates and protonated basic sites of the polybasic compound. Collision-induced dissociation (CID) experiments carried out with these complexes allowed us to identify some differences in the nature of the interactions between the solution and the gas phase, arising from possible proton transfers. Different dissociation pathways were observed according to the nature of the polybasic compound and to the initial charge state of the complex. The complex involving spermine dissociated by cleavage of noncovalent bonds leading to the separation of the two components, whereas the one involving penta-L-arginine underwent fragmentations of covalent bonds. Both behaviors were independent of the initial charge state of the complex. On the other hand, the dissociation pathway of the complex involving penta-L-lysine has been shown to be clearly charge state dependent. Noncovalent dissociation (separation of the two components) driven by coulomb repulsion occurred for the higher charged complexes, whereas fragmentation of covalent bonds was the main pathway of the lower charged complexes. In the latter case, differences in CID behavior were observed for different lengths of poly-L-lysine. (J Am Soc Mass Spectrom 2007, 18, 346 -358)

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confidence: 99%

A study of noncovalent complexes involving single-stranded DNA and polybasic compounds using nanospray mass spectrometry

Terrier

Tortajada

Buchmann

2007

J. Am. Soc. Mass Spectrom.

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“…Protonated sites of the polyamine were expected to bind with DNA phosphates in solution to displace alkaline cations [24 -26] and stabilize duplexes [27]. Ideally, polyamine protons were transferred to DNA phosphates during sample crystallization or desorption/ionization process and DNA free of alkaline cation and polyamine was observed.…”

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confidence: 99%

Noncovalent complexes between DNA and basic polypeptides or polyamines by MALDI-TOF

Terrier

Tortajada

Zin

et al. 2007

J. Am. Soc. Mass Spectrom.

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MALDI-MS was evaluated as a method for the study of noncovalent complexes involving DNA oligonucleotides and various polybasic compounds (basic polypeptides and polyamines). Complexes involving single-stranded DNA were successfully detected using DHAP matrix in the presence of an ammonium salt. Control experiments confirmed that the interactions involved basic sites of the polybasic compounds and that the complexes were not formed in the gas phase but were pre-existing in the matrix crystals. Moreover, the pre-existence in solution was probed by isothermal titration calorimetry at concentration and ionic strength similar to those used for mass spectrometry. Spectra showed no important difference between negative and positive ion modes. The influence of nature and size of DNA and polybasic compound on the relative intensities and stoichiometries of the complexes was investigated. Despite the fact that relative intensities can be affected by ionization yields and the gas-phase stabilities of the different species, numerous trends observed in the MALDI study were consistent with the expected in-solution behaviors. Experimental conditions related to sample preparation were investigated also. Complex abundance generally decreased when increasing the ammonium acetate concentration. It was dramatically decreased when using ATT instead of DHAP. Penta-L-arginine is an exception to these observations. Lastly, in the case of complexes involving DNA duplex, the ATT matrix was shown to favor the observation of specific DNA duplex but not that of its complex with polybasic compounds. Inversely, DHAP was appropriate for the conservation of DNA-polybasic compound interaction but not for the transfer of intact

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“…Duplex DNA is more difficult to stabilize than RNA. Various additives such as cobalt (III) hexamine and ammonium citrate have been used to stabilize the DNA duplex during the desorption process [119,120]. Duplex RNA appears to be more stable in the desorption process.…”

Section: Matrix Assisted Laser Desorption Ionization (Maldi)mentioning

confidence: 99%