# What happens to DNA duplexes in the gas phase?

Massimiliano Porrini, Frédéric Rosu, Valérie Gabelica

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Massimiliano Porrini, Frédéric 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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Submitted on 18 Jul 2017

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# What Happens to DNA Duplexes in the Gas Phase?

Massimiliano Porrini,¹,² Frédéric Rosu³ & Valérie Gabelica¹,²

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.

## Key findings

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

[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.

* 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.

* 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).

<figure><img src="image_2.png" /></figure>

## Ion mobility experiments

* 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.

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

<figure><img src="image_3.png" /></figure>

* In those conditions, IMS performance tested on [TG₄T]₄ 5-model is: resolution = 41, CCS accuracy better than 1%.

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

## DT-IMS experimental results

### [dCGCGGCCCGCG]₂

<figure><img src="image_4.png" /></figure>

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /></figure>

### [dCGCGAATTCGCG]₂

<figure><img src="image_7.png" /></figure>

<figure><img src="image_8.png" /></figure>

<figure><img src="image_9.png" /></figure>

### [dCGTAAATTTACG]₂

<figure><img src="image_10.png" /></figure>

<figure><img src="image_11.png" /></figure>

<figure><img src="image_12.png" /></figure>

* Native charge states are very compact (< 800 Å²)

### [dCGCGAATTCGCG]₂ 5- Eint → Compaction ~720 Å²

<figure><img src="image_13.png" /></figure>

Softest conditions

<figure><img src="image_14.png" /></figure>

Fragmentor →

<figure><img src="image_15.png" /></figure>

V(trapping) →

## Molecular modeling details

* 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.

## Modeling of DNA duplex gas-phase structure

* **MD starting from B-helix?** Zipping of minor groove due to phosphate self-solvation. No match with experiment.

<figure><img src="image_16.png" /></figure>

* **A-helix?** Better trend, but no quantitative match for native charge states 4- and 5-. Could be OK for 6-.

<figure><img src="image_17.png" /></figure>

* **Globular?** Correct size but original H-bonding or stacking not preserved (contradicts past MS/MS results).

Simulated annealing →

<figure><img src="image_18.png" /></figure>

* **Major groove-zipped conformation?** Stable in the gas phase and has a CCS compatible with experiment on 4- and 5- ions.

<figure><img src="image_19.png" /></figure>

<figure><img src="image_20.png" /></figure>

Exp. (soft)
(100%GC)⁵-
(66%GC)⁵-
(33%GC)⁵-

Calc.
B-form

CCS (Å²)

Exp. (soft)
(100%)⁶-
(66%)⁶-
(33%)⁶-
CCS (Å²)

Calc.
A-form

CCS (Å²)

Calc.
Globular

CCS (Å²)

Calc.
Major
groove
zipping

CCS (Å²)