Direct measurement of the ion atmosphere around DNA and RNA duplexes.

Figure 1. Features of DNA solvation measured by SAXS and ASAXS [2].

Nucleic acids are highly charged, attracting a cloud of ions from the solutions that surround them (illustrated in Fig. 1). Changes in the ion atmosphere are important to consider in protein-DNA interactions and RNA folding. However, the ion atmosphere is difficult to model accurately and a challenge to observe by conventional methods. I first contributed (as co-author) to the development of a new method for counting the number of ions around DNA using anomalous SAXS (ASAXS), where ion-specific contrast is obtained by tuning the X-ray energy near an absorption edge for the ion [1,5]. Later, I developed similar methods sensitive to the spatial distribution of ions and water [2]. ASAXS data has been particularly useful for testing theory. I contributed data to a computational project led by David Case and co-workers (Rutgers) that improved implicit solvent models for accurate X-ray scattering simulation [3]. In addition, I contributed measurements of RNA duplex and pseudoknot structures to validate all-atom molecular dynamics simulations performed by Serdal Kirmizialtin and Ron Elber (UT Austin) [4].

Research Articles

[1]

Pabit SA, Meisburger SP, Li L, Blose JM, Jones CD, Pollack L. 2010. Counting ions around DNA with anomalous small-angle X-ray scattering. J Am Chem Soc 132(46): 16334-6. PMID: 21047071, DOI: 10.1021/ja107259y

[2]

Meisburger SP, Pabit SA, Pollack L. 2015. Determining the locations of ions and water around DNA from X-Ray scattering measurements. Biophys J 108: 2886-95. PMID: 26083928, DOI: 10.1016/j.bpj.2015.05.006

[3]

Nguyen HT, Pabit SA, Meisburger SP, Pollack L, Case DA. 2014. Accurate small and wide angle X-ray scattering profiles from atomic models of proteins and nucleic acids. J Chem Phys 141: 22D508. PMID: 25494779, DOI: 10.1063/1.4896220

[4]

Kirmizialtin S, Pabit SA, Meisburger SP, Pollack L, Elber R. 2012. RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations. Biophys J 102(4): 819-28. PMID: 22385853, DOI: 10.1016/j.bpj.2012.01.013

[5]

Meisburger SP, Sutton JL, Chen H, Pabit SA, Kirmizialtin S, Elber R, Pollack L. 2013. Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET: beyond the wormlike chain model. Biopolymers 99: 1032-45. PMID: 23606337, DOI: 10.1002/bip.22265