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Items: 1 to 20 of 21

1.

Disordered RNA chaperones can enhance nucleic acid folding via local charge screening.

Holmstrom ED, Liu Z, Nettels D, Best RB, Schuler B.

Nat Commun. 2019 Jun 5;10(1):2453. doi: 10.1038/s41467-019-10356-0.

2.

Accurate Transfer Efficiencies, Distance Distributions, and Ensembles of Unfolded and Intrinsically Disordered Proteins From Single-Molecule FRET.

Holmstrom ED, Holla A, Zheng W, Nettels D, Best RB, Schuler B.

Methods Enzymol. 2018;611:287-325. doi: 10.1016/bs.mie.2018.09.030. Epub 2018 Nov 16.

PMID:
30471690
3.

Transition path times of coupled folding and binding reveal the formation of an encounter complex.

Sturzenegger F, Zosel F, Holmstrom ED, Buholzer KJ, Makarov DE, Nettels D, Schuler B.

Nat Commun. 2018 Nov 9;9(1):4708. doi: 10.1038/s41467-018-07043-x.

4.

Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments.

Grotz KK, Nueesch MF, Holmstrom ED, Heinz M, Stelzl LS, Schuler B, Hummer G.

J Phys Chem B. 2018 Dec 13;122(49):11626-11639. doi: 10.1021/acs.jpcb.8b07537. Epub 2018 Oct 17.

PMID:
30285443
5.

Tests of Kramers' Theory at the Single-Molecule Level: Evidence for Folding of an Isolated RNA Tertiary Interaction at the Viscous Speed Limit.

Dupuis NF, Holmstrom ED, Nesbitt DJ.

J Phys Chem B. 2018 Sep 27;122(38):8796-8804. doi: 10.1021/acs.jpcb.8b04014. Epub 2018 Sep 18.

PMID:
30078323
6.

Incorporation of isotopic, fluorescent, and heavy-atom-modified nucleotides into RNAs by position-selective labeling of RNA.

Liu Y, Holmstrom E, Yu P, Tan K, Zuo X, Nesbitt DJ, Sousa R, Stagno JR, Wang YX.

Nat Protoc. 2018 May;13(5):987-1005. doi: 10.1038/nprot.2018.002. Epub 2018 Apr 12.

PMID:
29651055
7.

Conformational Plasticity of Hepatitis C Virus Core Protein Enables RNA-Induced Formation of Nucleocapsid-like Particles.

Holmstrom ED, Nettels D, Schuler B.

J Mol Biol. 2018 Aug 3;430(16):2453-2467. doi: 10.1016/j.jmb.2017.10.010. Epub 2017 Oct 16.

8.

Biophysical Insights from Temperature-Dependent Single-Molecule Förster Resonance Energy Transfer.

Holmstrom ED, Nesbitt DJ.

Annu Rev Phys Chem. 2016 May 27;67:441-65. doi: 10.1146/annurev-physchem-040215-112544. Review.

PMID:
27215819
9.

Mechanistic Insights into Cofactor-Dependent Coupling of RNA Folding and mRNA Transcription/Translation by a Cobalamin Riboswitch.

Polaski JT, Holmstrom ED, Nesbitt DJ, Batey RT.

Cell Rep. 2016 May 3;15(5):1100-1110. doi: 10.1016/j.celrep.2016.03.087. Epub 2016 Apr 21.

10.

Single-Molecule FRET Reveals Three Conformations for the TLS Domain of Brome Mosaic Virus Genome.

Vieweger M, Holmstrom ED, Nesbitt DJ.

Biophys J. 2015 Dec 15;109(12):2625-2636. doi: 10.1016/j.bpj.2015.10.006.

11.

Synthesis and applications of RNAs with position-selective labelling and mosaic composition.

Liu Y, Holmstrom E, Zhang J, Yu P, Wang J, Dyba MA, Chen D, Ying J, Lockett S, Nesbitt DJ, Ferré-D'Amaré AR, Sousa R, Stagno JR, Wang YX.

Nature. 2015 Jun 18;522(7556):368-72. doi: 10.1038/nature14352. Epub 2015 May 4.

12.

Kinetic and thermodynamic origins of osmolyte-influenced nucleic acid folding.

Holmstrom ED, Dupuis NF, Nesbitt DJ.

J Phys Chem B. 2015 Mar 5;119(9):3687-96. doi: 10.1021/jp512491n. Epub 2015 Feb 18.

PMID:
25621404
13.

Single-molecule conformational dynamics of a biologically functional hydroxocobalamin riboswitch.

Holmstrom ED, Polaski JT, Batey RT, Nesbitt DJ.

J Am Chem Soc. 2014 Dec 3;136(48):16832-43. doi: 10.1021/ja5076184. Epub 2014 Nov 19.

14.

Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics.

Dupuis NF, Holmstrom ED, Nesbitt DJ.

Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8464-9. doi: 10.1073/pnas.1316039111. Epub 2014 May 21.

15.

Single-molecule fluorescence resonance energy transfer studies of the human telomerase RNA pseudoknot: temperature-/urea-dependent folding kinetics and thermodynamics.

Holmstrom ED, Nesbitt DJ.

J Phys Chem B. 2014 Apr 10;118(14):3853-63. doi: 10.1021/jp501893c. Epub 2014 Mar 28. Erratum in: J Phys Chem B. 2014 Jun 5;118(22):6048.

16.

Pulsed IR heating studies of single-molecule DNA duplex dissociation kinetics and thermodynamics.

Holmstrom ED, Dupuis NF, Nesbitt DJ.

Biophys J. 2014 Jan 7;106(1):220-31. doi: 10.1016/j.bpj.2013.11.008.

17.

Single-molecule kinetics reveal cation-promoted DNA duplex formation through ordering of single-stranded helices.

Dupuis NF, Holmstrom ED, Nesbitt DJ.

Biophys J. 2013 Aug 6;105(3):756-66. doi: 10.1016/j.bpj.2013.05.061.

18.

The role of counterion valence and size in GAAA tetraloop-receptor docking/undocking kinetics.

Fiore JL, Holmstrom ED, Fiegland LR, Hodak JH, Nesbitt DJ.

J Mol Biol. 2012 Oct 19;423(2):198-216. doi: 10.1016/j.jmb.2012.07.006. Epub 2012 Jul 14.

PMID:
22796627
19.

Thermodynamic origins of monovalent facilitated RNA folding.

Holmstrom ED, Fiore JL, Nesbitt DJ.

Biochemistry. 2012 May 8;51(18):3732-43. doi: 10.1021/bi201420a. Epub 2012 Apr 23.

20.

Entropic origin of Mg2+-facilitated RNA folding.

Fiore JL, Holmstrom ED, Nesbitt DJ.

Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2902-7. doi: 10.1073/pnas.1114859109. Epub 2012 Feb 1.

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