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What happens to DNA duplexes in the gas phase?

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What happens to DNA duplexes in the gas phase?

Massimiliano Porrini, Frederic Rosu, Valérie Gabelica

To cite this version:

Massimiliano Porrini, Frederic Rosu, Valérie Gabelica. What happens to DNA duplexes in the gas phase?. 63rd ASMS Conference on Mass Spectrometry and Allied Topics (ASMS 2015), May 2015, St Louis, United States. Proceedings of the ASMS Annual Conference 2015 St. Louis, 2015. �hal-01562195�

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What Happens to DNA Duplexes in the Gas Phase?

1Univ. Bordeaux, IECB, ARNA Laboratory, F-33600 Pessac, France, 2Inserm, U869, ARNA Laboratory,

F-33000 Bordeaux, France, 3CNRS UMS 3033, IECB, University of Bordeaux, F-33600 Pessac, France.

Massimiliano Porrini,

1,2

Frédéric Rosu

3

& Valérie Gabelica

1,2

Funding: ERC « DNAFOLDIMS ». We would like to thank Clémence Rabin for helping with the processing of ion mobility data.

 It is generally believed that DNA double helix is maintained from solution to the gas phase [1‐5].

 In contrast, we found that (12‐mer)2

duplexes sprayed from physiological

conditions (predominant charge: 5‐) have much lower CCS than expected from either a B‐helix or an A‐helix.

[1] Schnier, (…) & Williams, (1998) JACS, 120, 9605. [2] Gabelica & De Pauw (2002) IJMS, 219, 251. [3] Rueda (…) & Orozco (2003). JACS, 125, 8007. [4] Gidden (…) & Bowers (2004) JACS, 126, 15132. [5] Baker & Bowers, (2007) JASMS, 18, 1188.

Key findings

 DNA strands from Eurogentec, annealed in 100 mM

NH4OAc, injected at 20 µM duplex,        no organic co‐solvents.

 Agilent 6560 IMS‐Q‐TOF (drift tube IMS)

 DTIMS operated in Helium, p = 3.85 mbar, T = 296 K.

 In those conditions, IMS performance tested on [TG4T]45‐ model is: resolution = 41, CCS accuracy better than 1%.

Ion mobility experiments

 Softness controlled mostly by source  (fragmentor) and the trapping region (height of the well). Trapping : 0.6 ms.

DT-IMS experimental results

Modeling of DNA duplex gas-phase structure

► A‐helix? Better trend, but no quantitative match 

for native charge states 4‐ and 5‐. Could be OK for 6‐.

► Major groove‐zipped conformation? Stable in the gas phase 

and has a CCS compatible with experiment on 4‐ and 5‐ ions.

► MD starting from B‐helix? Zipping of minor groove  

due to phosphate self‐solvation. No match with experiment.

Molecular modeling details

4- 5- 6-[dCGCGGGCCCGCG]2 [dCGCGAATTCGCG]2 [dCGTAAATTTACG]2 CCS (Ų) CCS (Ų) CCS (Ų) 696 Ų 763 Ų 729 Ų 700 Ų 702 Ų 767 Ų 726 Ų 809 Ų 796 Ų 887 Ų 819 Ų 898 Ų 741 Ų 787 Ų 705 Ų 500 600 700 800 900 1000 (100%GC) 5-(66%GC) 5-(33%GC) 5-Exp. (soft) CCS (Ų)  Native charge states are very compact (< 800 Å²) 500 600 700 800 900 1000 500 600 700 800 900 1000 500 600 700 800 900 1000 [dCGCGAATTCGCG]25- Compaction ~720 Å² 726 Ų 809 Ų CCS (Ų) 724 Ų 744 Ų 719 Ų 741 Ų Eint Fragmentor ↗ V(trapping) ↗ Softest conditions  The compact duplex DNA gas‐phase structure at low charge states most probably involves zipping of the 

major groove due to self‐solvation (extra H‐bonds 

formed between phosphates).

► Globular? Correct size but original  

H‐bonding or stacking not preserved (contradicts past MS/MS results).

Calc. B‐form Calc. A‐form Calc. Globular Calc. Major  groove  zipping CCS (Ų) CCS (Ų) CCS (Ų) CCS (Ų) (100%) 6-(66%) 6-(33%) 6-Exp. (soft)  Amber, parmBCS1 ff (Orozco et al.), pmemd module in solution, sander module in vacuo.

 Lowest energy protonation isomers compatible  with 5‐ charge state were selected.

 Simulated annealing (globular conformations):  60 ps at 550 K, cooling to 0K, minimization.

 Major groove zipping: minimization with

restrained H‐bonds, then 1 µs free in gas phase.  CCS Calc: EHSSrot, radii param of Siu et al.

Simulated annealing  CCS (Ų) (100%GC) 5-(33%GC) 5-(66%GC)

5-63rd ASMS

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