B-DNA Helix Stability in a Solvent-Free Environment

Baker, Erin; Bowers, Michael T.

doi:10.1016/j.jasms.2007.03.001

Cited by 54 publications

(70 citation statements)

References 45 publications

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“…This does not necessarily mean that the gas-phase conformations of 6-and 7-charge states are A-and B-helices, but helps to understand conclusions previously derived solely based on more densely charged duplexes. 17,18 When starting from the B-form, MD simulations always show spontaneous hydrogen bonds formation between phosphate groups situated on each side of the minor groove (supporting information Movie S1 and Figure S8). This causes the "zipping" of the minor groove.…”

Section: Resultsmentioning

confidence: 97%

“…16 The Bowers group later explored the gas-phase structure of DNA duplexes by IMS. 17,18 By comparing the experimental collision cross section (CCS) of d(GC) n duplexes with those obtained on duplexes relaxed by short (5-ns) MD, they showed that the gas-phase structures resemble an A-helix for the short duplexes (8)(9)(10)(11)(12)(13)(14)(15)(16)-mer) and a B-helix for longer ones (>18-mer). It is worth noting that Bowers' IMS experiments were performed in non-native solution conditions (49:49:2 mixture of H 2 O:MeOH:NH 4 OH) and on high charge states (1 negative charge per 2 base pairs), raising questions on whether this represents what happens in native conditions.…”

Section: Introductionmentioning

confidence: 99%

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Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry

Porrini

Rosu

Rabin

et al. 2017

Preprint

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ABSTRACT:Native mass spectrometry coupled to ion mobility spectrometry is a promising tool for structural biology. Intact complexes can be transferred to the mass spectrometer and, if native conformations survive, collision cross sections give precious information on the structure of each species in solution. Based on several successful reports for proteins and their complexes, the conformation survival becomes more and more taken for granted. Here we report on the fate of nucleic acids conformation in the gas phase. Disturbingly, we found that DNA and RNA duplexes, at the electrospray charge states naturally obtained from native solution conditions (≥ 100 mM aqueous NH 4 OAc), are significantly more compact in the gas phase compared to the canonical solution structures. The compaction is observed for short (12-bp) and long (36-bp) duplexes, and for DNA and RNA alike. Molecular modeling (density functional calculations on small helices, semi-empirical calculations on up to 12-bp, and molecular dynamics on up to 36-bp duplexes) demonstrates that the compaction is due to phosphate group self-solvation prevailing over Coulomb-driven expansion. Molecular dynamics simulations starting from solution structures do not reproduce the experimental compaction. To be experimentally relevant, molecular dynamics sampling should reflect the progressive structural rearrangements occurring during desolvation. For nucleic acid duplexes, the compaction observed for low charge states results from novel phosphate-phosphate hydrogen bonds formed across both grooves at the very late stages of electrospray.

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Section: Resultsmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry

Porrini

Rosu

Rabin

et al. 2017

Preprint

View full text Add to dashboard Cite

show abstract

“…This does not necessarily mean that the gas-phase conformations of 6– and 7– charge states are A- and B-helices, but it helps to understand conclusions previously derived solely based on more densely charged duplexes. 21,22 …”

Section: Resultsmentioning

confidence: 99%

Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry

et al. 2017

View full text Add to dashboard Cite

We report on the fate of nucleic acids conformation in the gas phase as sampled using native mass spectrometry coupled to ion mobility spectrometry. On the basis of several successful reports for proteins and their complexes, the technique has become popular in structural biology, and the conformation survival becomes more and more taken for granted. Surprisingly, we found that DNA and RNA duplexes, at the electrospray charge states naturally obtained from native solution conditions (≥100 mM aqueous NH4OAc), are significantly more compact in the gas phase compared to the canonical solution structures. The compaction is observed for all duplex sizes (gas-phase structures are more compact than canonical B-helices by ∼20% for 12-bp, and by up to ∼30% for 36-bp duplexes), and for DNA and RNA alike. Molecular modeling (density functional calculations on small helices, semiempirical calculations on up to 12-bp, and molecular dynamics on up to 36-bp duplexes) demonstrates that the compaction is due to phosphate group self-solvation prevailing over Coulomb repulsion. Molecular dynamics simulations starting from solution structures do not reproduce the experimental compaction. To be experimentally relevant, molecular dynamics sampling should reflect the progressive structural rearrangements occurring during desolvation. For nucleic acid duplexes, the compaction observed for low charge states results from novel phosphate–phosphate hydrogen bonds formed across both grooves at the very late stages of electrospray.

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“…Their experimental CCS is far smaller than the one that a B-helix would adopt, and also far smaller than the values reported by the Bowers group on more densely charged duplexes (Baker & Bowers, 2007;Gidden, Ferzoco, Baker, & Bowers, 2004). Multiple co-existing conformations are observed, in that the CCS distributions are much broader than the instrumental peak width.…”

mentioning

confidence: 62%