Publications

Click on the links below to view the publications organized by topic.

Methods Development   |   Ions Around DNA and RNA   |   DNA and RNA Condensation

DNA-DNA Interactions   |   RNA Folding   |   Conformational Dynamics of Proteins

Protein-Nucleic Acid Interactions   |   RNA Structure

Chronological

Structural enzymology using X-ray free electron lasers
C. Kupitz, J. L. Olmos Jr, M. Holl, L. Tremblay, K. Pande, S. Pandey, D. Oberthür, M. Hunter, M. Liang, A. Aquila, J. Tenboer, G. Calvey, A. M. Katz, Y. Chen, M. O. Wiedorn, J. Knoska, A. Meents, V. Majriani, T. Norwood, I. Poudyal, T. Grant, M. D. Miller, W. Xu, A Tolstikova, A. Morgan, M. Metz, J. M. Martin-Garcia, J. D. Zook, S. Roy-Chowdhury, J. Coe, N. Nagaratnam, D. Meza, R. Fromme, S. Basu, M. Frank, T. White, A. Barty, S. Bajt, O. Yefanov, H. N. Chapman, N. Zatsepin, G. Nelson, U. Weierstall, J. Spence, P. Schwander, L. Pollack, P. Fromme, A. Ourmazd, G. N. Phillips Jr, M. Schmidt.
Struct. Dyn. 4(4):044003 (2017). [Abstract]

Spermine Condenses DNA, but Not RNA Duplexes.
A. M. Katz, I. S. Tolokh, S. A. Pabit, A. V. Onufriev, L. Pollack
Biophys. J. 112(1):22-30 (2017). [Abstract]

Visualizing single-stranded nucleic acids in solution.
A. Plumridge, S. P. Meisburger, L. Pollack
Nucleic Acids Research (2016). [Abstract]

Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core
Y. Chen, J. M. Tokuda, T. Topping, S. P. Meisburger, S. A. Pabit, L. M. Gloss, L. Pollack
Proc. Natl. Acad. Sci. USA. 114(2):334-339 (2016). [Abstract]

Mixing injector enables time-resolved crystallography with high hit rate at X-ray free electron lasers.
G. D. Calvey, A. M. Katz, C. B. Schaffer, L. Pollack
Struct. Dyn. 3(5):054301 (2016). [Abstract]

SAICAR activates PKM2 in its dimeric form
M. Yan, S. Chakravarthy, J. M. Tokuda, L. Pollack, G. D. Bowman, Y.-S. Lee
Biochemistry. 55(33):4731-4736 (2016). [Abstract]

Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA.
A. V. Drozdetski, I. S. Tolokh, L. Pollack, N. A. Baker, A. V. Onufriev
Phys. Rev. Lett. 117(2):028101 (2016). [Abstract]

Multi-shell model of ion-induced nucleic acid condensation.
I. S. Tolokh, A. V. Drozdetski, L. Pollack, N. A. Baker, A. V. Onufriev
J. Chem. Phys. 144(15):115101 (2016). [Abstract]

Extracting water and ion distributions from solution x-ray scattering experiments.
H. T. Nguyen, S. A. Pabit, L. Pollack, D. A. Case
J. Chem. Phys. 144(21):214105 (2016). [Abstract]

Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations.
S. A. Pabit, A. M. Katz, I. S. Tolokh, A. Drozdetski, N. Baker, A. V. Onufriev, L. Pollack
J. Chem. Phys. 144(20):205102 (2016). [Abstract]

SAXS studies of RNA: structures, dynamics, and interactions with partners.
Y. Chen, L. Pollack
Wiley Interdisp Rev RNA. 2016 Apr 12. [Abstract]

Protein-DNA and ion-DNA interactions revealed through contrast variation SAXS
J. M. Tokuda, S. A. Pabit, L. Pollack
Biophys. Rev. 8(2):139-149 (2016). [Abstract]

The Role of Correlation and Solvation in Ion Interactions with B-DNA.
M. L. Sushko, D. G. Thomas, S. A. Pabit, L. Pollack, A. V. Onufriev, N. A. Baker
Biophys. J. 110(2):315-26 (2016). [Abstract]

Tuning RNA Flexibility with Helix Length and Junction Sequence.
J. L. Sutton, L. Pollack
Biophys. J. 109(12):2644-53 (2015). [Abstract]

A microfabricated fixed path length silicon sample holder improves background subtraction for cryoSAXS.
J. B. Hopkins, A. M. Katz, S. P. Meisburger, M. A. Warkentin, R. E. Thorne, L. Pollack
J. Appl. Cryst. 48:227-237 (2015). [Abstract]

Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements.
S. P. Meisburger, S. A. Pabit, L. Pollack
Biophys. J. 108(12):2886-95 (2015). [Abstract]

Making water-soluble integral membrane proteins in vivo using an amphipathic protein fusion strategy.
D. Mizrachi, Y. Chen, J. Liu, H. M. Peng, A. Ke, L. Pollack, R. J. Turner, R. J. Auchus, M. P. DeLisa
Nat. Commun. 6:6826 (2015). [Abstract]

Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids.
H. T. Nguyen, S. A. Pabit, S. P. Meisburger, L. Pollack, D. A. Case
J. Chem. Phys. 141(22) (2014). [Abstract]

Double-focusing mixing jet for XFEL study of chemical kinetics.
D. Wang, U. Weierstall, L. Pollack, J. Spence
J. Synch. Rad. 21(6):1364-6 (2014). [Abstract]

Why double-stranded RNA resists condensation.
I. S. Tolokh, S. A. Pabit, A. M. Katz, Y. Chen, A. Drozdetski, N. Baker, L. Pollack, A. V. Onufriev
Nucleic Acids Research 42(16):10823-31 (2014). [Abstract]

Revealing transient structures of nucleosomes as DNA unwinds
Y. Chen, J. M. Tokuda, T. Topping, J. L. Sutton, S.P. Meisburger, S. A. Pabit, L. M. Gloss, L. Pollack
Nucleic Acids Research 42(13):8767-76 (2014). [Abstract]

Flavin reduction activates Drosophila cryptochrome
A. T. Vaidya, D. Top, C. C. Manahan, J. M. Tokuda, S. Zhang, L. Pollack, M. W. Young, B. R. Crane
Proc. Natl. Acad. Sci. USA 110(51):20455-60 (2013). [Abstract]

Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET: Beyond the wormlike chain model.
S. P. Meisburger, J. L. Sutton, H. Chen, S.A. Pabit, S. Kirmizialtin, R. Elber, L. Pollack
Biopolymers. 99(12):1032-1045 (2013). [Abstract]

T box RNA decodes both the information content and geometry of tRNA to affect gene expression
J. C. Grigg, Y. Chen, F. J. Grundy, T. M. Henkin, L. Pollack, A. Ke
Proc. Natl. Acad. Sci. USA 110(18):7240-5 (2013). [Abstract]

Role of ion valence in the submillisecond collapse and folding of a small RNA domain.
S. A. Pabit, J. L. Sutton, H. Chen, L. Pollack
Biochemistry. 52(9):1539-46 (2013). [Abstract]

Breaking the radiation damage limit with Cryo-SAXS
S. P. Meisberger, M. Warkentin, H. Chen, J. B. Hopkins, R. E. Gillilan, L. Pollack, R. E. Thorne
Biophys. J. 104(1):227-36 (2012). [Abstract]

Specificity of the double-stranded RNA-binding domain from the RNA-activated protein kinase PKR for double-stranded RNA: insights from thermodynamics and small-angle X-ray scattering.
S. Patel, J. M. Blose, J. E. Solowski, L. Pollack, P. C. Bevilacqua
Biochemistry. 51(46):9312-22 (2012). [Abstract]

Influenza virus-membrane fusion triggered by proton uncaging for single particle studies of fusion kinetics.
D. A. Costello, D. W. Lee, J. Drewes, K. A. Vasquez, K. Kisler, U. Weisner, L. Pollack, G. R. Whittaker, S. Daniel
Anal. Chem. 84(20):8480-9 (2012). [Abstract]

Pyrite footprinting of RNA
J. C. Schlatterer, M. S. Wieder, C. D. Jones, L. Pollack, M. Brenowitz
Biochem. Biophys. Res. Commun. 425(2):374-8 (2012). [Abstract]

RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations
S. Kirmizialtin, S. A. Pabit, S. P. Meisburger, L. Pollack, R. Elber
Biophys. J. 102(4):819-28 (2012). [Abstract]

Small-angle X-ray scattering and single-molecule FRET spectroscopy produce highly divergent views of the low-denaturant unfolded state
T. Y. Yoo, S. P. Meisburger, J. Hinshaw, L. Pollack, G. Haran, T. R. Sosnick, K. Plaxco
J. Mol. Biol. 418(3-4):226-36 (2012). [Abstract]

Ionic strength-dependent persistence lengths of single-stranded RNA and DNA
H. Chen, S. P. Meisburger, S. A. Pabit, J. L. Sutton, W. W. Webb, L. Pollack
Proc. Natl. Acad. Sci. USA 109(3):799-804 (2012). [Abstract]

Double stranded RNA resists condensation
L. Li, S. A. Pabit, S. Meisburger, L. Pollack
Phys. Rev. Lett., 106, 108101 (2011). [Abstract]

Effects of a protecting osmolyte on the ion atmosphere surrounding DNA duplexes
J. M. Blose, S. A. Pabit, S. P. Meisburger, L. Li, C. D. Jones, L. Pollack
Biochemistry. 50(40):8540-7 (2011). [Abstract]

A microfluidic device that generates hydroxyl radicals to probe the solvent accessible surface of nucleic acids.
C. D. Jones, J. C. Schlatterer, M. Brenowitz, L. Pollack
Lab Chip. 11(20):3458-64 (2011). [Abstract]

SAXS studies of ion-nucleic acid interactions
L. Pollack
Annu. Rev. Biophys. 40:225-42 (2011). [Abstract]

Time resolved SAXS and RNA folding
L. Pollack
Biopolymers, 95, 54. (2011). [Abstract]

Counting ions around DNA with ASAXS
S. A. Pabit, S. P. Meisburger, L. Li, J. M. Blose, C. D. Jones, L. Pollack
L. Am. Chem Soc. 132 (46), pp 16336 (2010). [Abstract]

Electrostatics of strongly charged biological polymers: Ion-mediated interactions and self-organization in nucleic acids and proteins
Gerard C.L. Wong, Lois Pollack
Annual Review of Physical Chemistry Volume 61 (2010). [Abstract]

Illuminating solution responses of a LOV-domain protein with photocoupled small angle x-ray scattering
J. S. Lamb, B. Zoltowski, S. Pabit, L. Li, B. Crane, and L. Pollack
Journal of Molecular Biology 393, 909-919 (2009). [Abstract]

Reconstructing three dimensional shape envelopes from time resolved small angle x-ray scattering data
J.S. Lamb, L. Kwok, X. Qiu, K. Andresen, H. Park and L. Pollack
J. App. Cryst. 41, 1046 (2008). [Abstract]

Closing the lid on DNA end-to-end stacking interactions
L. Li, S.A. Pabit, J.S. Lamb, H.Y. Park and L. Pollack
Appl. Phys. Lett. 92, 223901 (2008). [Abstract]

Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared to dsDNA
S.A. Pabit, X. Qiu, J.S. Lamb, L. Li, S.P. Meisburger and L. Pollack
Nucleic Acids Research 37(12):3887-96 (2009). [Abstract]

Using anomalous small angle x-ray scattering to probe the ion atmosphere around nucleic acids
S. A. Pabit, K.D. Finkelstein and L. Pollack
Methods In Enzymology, Vol 469: Biophysical, Chemical, And Functional Probes Of RNA Structure, Interactions And Folding, Pt B Volume: 469 Pages: 391-410 (2009). [Abstract]

Time resolved x-ray scattering and RNA folding
L. Pollack and S. Doniach, Methods In Enzymology, Vol 469: Biophysical, Chemical, And Functional Probes Of RNA Structure, Interactions And Folding, Pt B   Volume: 469 Pages: 253-268 (2009). [Abstract]

Abrupt transition from free, repulsive to condensed, attractive DNA phase, induced by multivalent polyamine cations
X. Qiu, K. Andresen, J.S. Lamb, L.W. Kwok and L. Pollack
Phys. Rev. Lett. 101, 228101 (2008). [Abstract]

Time-resolved dimerization of a PAS-LOV protein measured with photocoupled small angle x-ray scattering
J.S. Lamb, B. Zoltowski, S. A. Pabit, B. R. Crane and L. Pollack
J. Amer. Chem. Soc. 130, 12226 (2008). [Abstract]

Hinge stiffness is a barrier to RNA folding
J. Schlatterer, L.W. Kwok, J.S. Lamb, H.Y. Park, K. Andresen, M. Brenowitz and L. Pollack
J. Mol. Biol. 379, 859 (2008). [Abstract]

Mono and tri-valent ions around DNA: a small angle scattering study of competition and interactions
K. Andresen, X. Qiu, S. A. Pabit, J. S. Lamb, H.Y. Park, L.W. Kwok and L. Pollack
Biophys. J., 95, 287 (2008). [Abstract] [PDF]

Conformational changes of calmodulin upon Ca2+ binding studied with a microfluidic mixer
H. Y. Park, S. A. Kim, J. Korlach, E. Rhoades, L. W. Kwok, W. R. Zipfel, M. N. Waxham, W. W. Webb, and L. Pollack
Proc. Natl Acad Sci USA, 105(2), 542 (2008). [Abstract]

Inter-DNA attraction mediated by divalent counterions
X. Qiu, K. Andresen, L.W. Kwok, J.S. Lamb, H.Y. Park, and L. Pollack
Phys. Rev. Lett., 99 038104 (2007). [Abstract]

Focusing capillary optics for use in solution SAXS
J.S. Lamb, S. Cornaby, K. Andresen, L.W. Kwok, H.Y. Park, X. Qiu, D.M. Smilgies, D.H. Bilderback and L. Pollack,
J. Appl. Cryst., 40, 193 (2007). [Abstract]

Achieving uniform mixing in a microfluidic device: hydrodynamic focusing prior to mixing
H.Y. Park, X. Qiu, E. Rhoades, J. Korlach, L.W. Kwok, W.R. Zipfel, W.W. Webb and L. Pollack
Anal. Chem., 78, 4465 (2006). [Abstract]

Measuring inter-DNA potentials in solution
X. Qiu, L.W. Kwok, H.Y. Park, J.S. Lamb, K. Andresen, and L. Pollack
Phys. Rev. Lett., 96 138101 (2007). [Abstract]

Concordant measurements of folding kinetics from local and global perspective
L.W. Kwok, I.Shcherbakova, J.S. Lamb, H.Y. Park, K. Andresen, H. Smith, M. Brenowitz and L. Pollack, J. Mol. Biol., 355, 282 (2006). [Abstract]

Spatial distribution of competing ions around DNA
K. Andresen, R. Das, H.Y. Park, L.W. Kwok, J.S. Lamb, H. Smith, D. Herschlag, K.D. Finkelstein and L. Pollack
Phys. Rev. Lett., 93, 248103, (2004). [Abstract]

Counterion distribution around DNA probed by x-ray scattering
R. Das, T. T. Mills,  L. W. Kwok, G. S. Maskel, I.S. Millett, D. Doniach, K. D. Finkelstein, D. Herschlag and L. Pollack
Phys. Rev. Lett., 90, 188103 (2003). [Abstract]

The fastest global events in RNA folding
R. Das, L.W. Kwok, I.S.  Millett, Y. Bai, T.T. Mills, J. Jacob, G.S.  Maskel, S. Seifert, S.G.J. Mochrie, P. Thiyagarajan, S.  Doniach, L. Pollack, and D. Herschlag
J. Mol. Biol., 332, 311 (2003). [Abstract]

Rapid compaction during RNA folding
R. Russell, I. S. Mil.ett, M. W. Tate, L. W. Kwok, B. Nakatani, S. M. Gruner, S. G. J. Mochrine, V. Pande, S. Doniach, D. Herschlag, and L. Pollack
Proc. Natl. Acad. Sci. 99, p. 4266 (2002). [Abstract]

Time-resolved collapse of a folding protein observed with small angle x-ray scattering
L. Pollack, M. W. Tate, A. C. Finnefrock, C. Kalidas, S. Trotter, N. C. Darnton, L. Lurio, R. H. Austin, C. A. Batt, S. M. Gruner, and S. G. J. Mochrine
Phys. Rev. Lett. 86, p. 4692 (2001). [Abstract]

Compactness of the denatured state of a fast-folding protein measured by submillisecond small angle x-ray scattering
L. Pollack, M. W. Tate, N. C. Darnton, J. B. Knight, S. M. Gruner, W. A. Eaton, and R. H. Austin
Proc. Natl. Acad. Sci. USA 96, 10115-10117 (1999). [Abstract]