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Preparation of a Conditional RNA Switch.

Zakrevsky P, Parlea L, Viard M, Bindewald E, Afonin KA, Shapiro BA.

Methods Mol Biol. 2017;1632:303-324. doi: 10.1007/978-1-4939-7138-1_20.


Oxime Ether Lipids as Transfection Agents: Assembly and Complexation with siRNA.

Puri A, Zampino S, Viard M, Shapiro BA.

Methods Mol Biol. 2017;1632:241-253. doi: 10.1007/978-1-4939-7138-1_16.


Cotranscriptional Production of Chemically Modified RNA Nanoparticles.

Kireeva ML, Afonin KA, Shapiro BA, Kashlev M.

Methods Mol Biol. 2017;1632:91-105. doi: 10.1007/978-1-4939-7138-1_6.


Protocols for Molecular Dynamics Simulations of RNA Nanostructures.

Kim T, Kasprzak WK, Shapiro BA.

Methods Mol Biol. 2017;1632:33-64. doi: 10.1007/978-1-4939-7138-1_3.


Computational Generation of RNA Nanorings.

Sharan R, Bindewald E, Kasprzak WK, Shapiro BA.

Methods Mol Biol. 2017;1632:19-32. doi: 10.1007/978-1-4939-7138-1_2.


Combined single molecule experimental and computational approaches for understanding the unfolding pathway of a viral translation enhancer that participates in a conformational switch.

Le MT, Kasprzak WK, Shapiro BA, Simon AE.

RNA Biol. 2017 Nov 2;14(11):1466-1472. doi: 10.1080/15476286.2017.1325069. Epub 2017 Oct 11.


Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch.

Le MT, Kasprzak WK, Kim T, Gao F, Young MY, Yuan X, Shapiro BA, Seog J, Simon AE.

Elife. 2017 Feb 13;6. pii: e22883. doi: 10.7554/eLife.22883.


Functionally-interdependent shape-switching nanoparticles with controllable properties.

Halman JR, Satterwhite E, Roark B, Chandler M, Viard M, Ivanina A, Bindewald E, Kasprzak WK, Panigaj M, Bui MN, Lu JS, Miller J, Khisamutdinov EF, Shapiro BA, Dobrovolskaia MA, Afonin KA.

Nucleic Acids Res. 2017 Feb 28;45(4):2210-2220. doi: 10.1093/nar/gkx008.


Melanoma Differentiation-associated Gene 7/IL-24 Exerts Cytotoxic Effects by Altering the Alternative Splicing of Bcl-x Pre-mRNA via the SRC/PKCδ Signaling Axis.

Shapiro BA, Vu NT, Shultz MD, Shultz JC, Mietla JA, Gouda MM, Yacoub A, Dent P, Fisher PB, Park MA, Chalfant CE.

J Biol Chem. 2016 Oct 7;291(41):21669-21681. Epub 2016 Aug 12.


Cellular Delivery of RNA Nanoparticles.

Parlea L, Puri A, Kasprzak W, Bindewald E, Zakrevsky P, Satterwhite E, Joseph K, Afonin KA, Shapiro BA.

ACS Comb Sci. 2016 Sep 12;18(9):527-47. doi: 10.1021/acscombsci.6b00073. Epub 2016 Aug 26. Review.


Advances in RNA structure determination.

Shapiro BA, Le Grice SF.

Methods. 2016 Jul 1;103:1-3. doi: 10.1016/j.ymeth.2016.06.006. No abstract available.


Ring Catalog: A resource for designing self-assembling RNA nanostructures.

Parlea L, Bindewald E, Sharan R, Bartlett N, Moriarty D, Oliver J, Afonin KA, Shapiro BA.

Methods. 2016 Jul 1;103:128-37. doi: 10.1016/j.ymeth.2016.04.016. Epub 2016 Apr 26.


Multistrand Structure Prediction of Nucleic Acid Assemblies and Design of RNA Switches.

Bindewald E, Afonin KA, Viard M, Zakrevsky P, Kim T, Shapiro BA.

Nano Lett. 2016 Mar 9;16(3):1726-35. doi: 10.1021/acs.nanolett.5b04651. Epub 2016 Feb 29.


The Use of Minimal RNA Toeholds to Trigger the Activation of Multiple Functionalities.

Afonin KA, Viard M, Tedbury P, Bindewald E, Parlea L, Howington M, Valdman M, Johns-Boehme A, Brainerd C, Freed EO, Shapiro BA.

Nano Lett. 2016 Mar 9;16(3):1746-53. doi: 10.1021/acs.nanolett.5b04676. Epub 2016 Feb 29.


Bolaamphiphiles as carriers for siRNA delivery: From chemical syntheses to practical applications.

Gupta K, Afonin KA, Viard M, Herrero V, Kasprzak W, Kagiampakis I, Kim T, Koyfman AY, Puri A, Stepler M, Sappe A, KewalRamani VN, Grinberg S, Linder C, Heldman E, Blumenthal R, Shapiro BA.

J Control Release. 2015 Sep 10;213:142-151. doi: 10.1016/j.jconrel.2015.06.041. Epub 2015 Jul 4.


Oxime ether lipids containing hydroxylated head groups are more superior siRNA delivery agents than their nonhydroxylated counterparts.

Gupta K, Mattingly SJ, Knipp RJ, Afonin KA, Viard M, Bergman JT, Stepler M, Nantz MH, Puri A, Shapiro BA.

Nanomedicine (Lond). 2015;10(18):2805-18. doi: 10.2217/nnm.15.105. Epub 2015 Jun 24.


Inhibition of vemurafenib-resistant melanoma by interference with pre-mRNA splicing.

Salton M, Kasprzak WK, Voss T, Shapiro BA, Poulikakos PI, Misteli T.

Nat Commun. 2015 May 14;6:7103. doi: 10.1038/ncomms8103.


Silver nanoclusters for RNA nanotechnology: steps towards visualization and tracking of RNA nanoparticle assemblies.

Afonin KA, Schultz D, Jaeger L, Gwinn E, Shapiro BA.

Methods Mol Biol. 2015;1297:59-66. doi: 10.1007/978-1-4939-2562-9_4.


Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores.

Song Y, Hua L, Shapiro BA, Wang JT.

BMC Bioinformatics. 2015 Feb 6;16:39. doi: 10.1186/s12859-015-0464-9.


Computational and experimental studies of reassociating RNA/DNA hybrids containing split functionalities.

Afonin KA, Bindewald E, Kireeva M, Shapiro BA.

Methods Enzymol. 2015;553:313-34. doi: 10.1016/bs.mie.2014.10.058. Epub 2015 Feb 10.


Triggering of RNA interference with RNA-RNA, RNA-DNA, and DNA-RNA nanoparticles.

Afonin KA, Viard M, Kagiampakis I, Case CL, Dobrovolskaia MA, Hofmann J, Vrzak A, Kireeva M, Kasprzak WK, KewalRamani VN, Shapiro BA.

ACS Nano. 2015 Jan 27;9(1):251-9. doi: 10.1021/nn504508s. Epub 2014 Dec 18.


Multifunctional RNA nanoparticles.

Afonin KA, Viard M, Koyfman AY, Martins AN, Kasprzak WK, Panigaj M, Desai R, Santhanam A, Grabow WW, Jaeger L, Heldman E, Reiser J, Chiu W, Freed EO, Shapiro BA.

Nano Lett. 2014 Oct 8;14(10):5662-71. doi: 10.1021/nl502385k. Epub 2014 Sep 30.


Modeling of RNA nanotubes using molecular dynamics simulation.

Badu SR, Melnik R, Paliy M, Prabhakar S, Sebetci A, Shapiro BA.

Eur Biophys J. 2014 Nov;43(10-11):555-64. doi: 10.1007/s00249-014-0985-6. Epub 2014 Sep 12.


The 3' untranslated region of Pea Enation Mosaic Virus contains two T-shaped, ribosome-binding, cap-independent translation enhancers.

Gao F, Kasprzak WK, Szarko C, Shapiro BA, Simon AE.

J Virol. 2014 Oct;88(20):11696-712. doi: 10.1128/JVI.01433-14. Epub 2014 Aug 6.


Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway.

Belew AT, Meskauskas A, Musalgaonkar S, Advani VM, Sulima SO, Kasprzak WK, Shapiro BA, Dinman JD.

Nature. 2014 Aug 21;512(7514):265-9. doi: 10.1038/nature13429. Epub 2014 Jul 9.


Protein kinase C and Src family kinases mediate angiotensin II-induced protein kinase D activation and acute aldosterone production.

Olala LO, Shapiro BA, Merchen TC, Wynn JJ, Bollag WB.

Mol Cell Endocrinol. 2014 Jul 5;392(1-2):173-81. doi: 10.1016/j.mce.2014.05.015. Epub 2014 May 22.


In silico design and enzymatic synthesis of functional RNA nanoparticles.

Afonin KA, Kasprzak WK, Bindewald E, Kireeva M, Viard M, Kashlev M, Shapiro BA.

Acc Chem Res. 2014 Jun 17;47(6):1731-41. doi: 10.1021/ar400329z. Epub 2014 Apr 23.


MPGAfold in dengue secondary structure prediction.

Kasprzak WK, Shapiro BA.

Methods Mol Biol. 2014;1138:199-224. doi: 10.1007/978-1-4939-0348-1_13.


Genomic analyses reveal broad impact of miR-137 on genes associated with malignant transformation and neuronal differentiation in glioblastoma cells.

Tamim S, Vo DT, Uren PJ, Qiao M, Bindewald E, Kasprzak WK, Shapiro BA, Nakaya HI, Burns SC, Araujo PR, Nakano I, Radek AJ, Kuersten S, Smith AD, Penalva LO.

PLoS One. 2014 Jan 22;9(1):e85591. doi: 10.1371/journal.pone.0085591. eCollection 2014.


The favorable IFNL3 genotype escapes mRNA decay mediated by AU-rich elements and hepatitis C virus-induced microRNAs.

McFarland AP, Horner SM, Jarret A, Joslyn RC, Bindewald E, Shapiro BA, Delker DA, Hagedorn CH, Carrington M, Gale M Jr, Savan R.

Nat Immunol. 2014 Jan;15(1):72-9. doi: 10.1038/ni.2758. Epub 2013 Nov 17.


Preliminary findings of the effects of rivastigmine, an acetylcholinesterase inhibitor, on working memory in cocaine-dependent volunteers.

Mahoney JJ 3rd, Kalechstein AD, Verrico CD, Arnoudse NM, Shapiro BA, De La Garza R 2nd.

Prog Neuropsychopharmacol Biol Psychiatry. 2014 Apr 3;50:137-42. doi: 10.1016/j.pnpbp.2013.11.001. Epub 2013 Nov 12.


Co-transcriptional production of RNA-DNA hybrids for simultaneous release of multiple split functionalities.

Afonin KA, Desai R, Viard M, Kireeva ML, Bindewald E, Case CL, Maciag AE, Kasprzak WK, Kim T, Sappe A, Stepler M, Kewalramani VN, Kashlev M, Blumenthal R, Shapiro BA.

Nucleic Acids Res. 2014 Feb;42(3):2085-97. doi: 10.1093/nar/gkt1001. Epub 2013 Nov 4.


Computational and experimental characterization of RNA cubic nanoscaffolds.

Afonin KA, Kasprzak W, Bindewald E, Puppala PS, Diehl AR, Hall KT, Kim TJ, Zimmermann MT, Jernigan RL, Jaeger L, Shapiro BA.

Methods. 2014 May 15;67(2):256-65. doi: 10.1016/j.ymeth.2013.10.013. Epub 2013 Nov 1.


The kissing-loop T-shaped structure translational enhancer of Pea enation mosaic virus can bind simultaneously to ribosomes and a 5' proximal hairpin.

Gao F, Gulay SP, Kasprzak W, Dinman JD, Shapiro BA, Simon AE.

J Virol. 2013 Nov;87(22):11987-2002. doi: 10.1128/JVI.02005-13. Epub 2013 Aug 28.


Computational detection of abundant long-range nucleotide covariation in Drosophila genomes.

Bindewald E, Shapiro BA.

RNA. 2013 Sep;19(9):1171-82. doi: 10.1261/rna.037630.112. Epub 2013 Jul 25.


Effective classification of microRNA precursors using feature mining and AdaBoost algorithms.

Zhong L, Wang JT, Wen D, Aris V, Soteropoulos P, Shapiro BA.

OMICS. 2013 Sep;17(9):486-93. doi: 10.1089/omi.2013.0011. Epub 2013 Jun 29.


Activation of different split functionalities on re-association of RNA-DNA hybrids.

Afonin KA, Viard M, Martins AN, Lockett SJ, Maciag AE, Freed EO, Heldman E, Jaeger L, Blumenthal R, Shapiro BA.

Nat Nanotechnol. 2013 Apr;8(4):296-304. doi: 10.1038/nnano.2013.44. Epub 2013 Mar 31.


Structural complexity of Dengue virus untranslated regions: cis-acting RNA motifs and pseudoknot interactions modulating functionality of the viral genome.

Sztuba-Solinska J, Teramoto T, Rausch JW, Shapiro BA, Padmanabhan R, Le Grice SF.

Nucleic Acids Res. 2013 May;41(9):5075-89. doi: 10.1093/nar/gkt203. Epub 2013 Mar 26.


In Silico, In Vitro, and In Vivo Studies Indicate the Potential Use of Bolaamphiphiles for Therapeutic siRNAs Delivery.

Kim T, Afonin KA, Viard M, Koyfman AY, Sparks S, Heldman E, Grinberg S, Linder C, Blumenthal RP, Shapiro BA.

Mol Ther Nucleic Acids. 2013 Mar 19;2:e80. doi: 10.1038/mtna.2013.5.


Co-transcriptional assembly of chemically modified RNA nanoparticles functionalized with siRNAs.

Afonin KA, Kireeva M, Grabow WW, Kashlev M, Jaeger L, Shapiro BA.

Nano Lett. 2012 Oct 10;12(10):5192-5. doi: 10.1021/nl302302e. Epub 2012 Sep 27.


The role of salt concentration and magnesium binding in HIV-1 subtype-A and subtype-B kissing loop monomer structures.

Kim T, Shapiro BA.

J Biomol Struct Dyn. 2013;31(5):495-510. doi: 10.1080/07391102.2012.706072. Epub 2012 Aug 13.


A method for discovering common patterns from two RNA secondary structures and its application to structural repeat detection.

Hua L, Wang JT, Ji X, Malhotra A, Khaladkar M, Shapiro BA, Zhang K.

J Bioinform Comput Biol. 2012 Aug;10(4):1250001. doi: 10.1142/S0219720012500011. Epub 2012 Jun 22.


A ribosome-binding, 3' translational enhancer has a T-shaped structure and engages in a long-distance RNA-RNA interaction.

Gao F, Kasprzak W, Stupina VA, Shapiro BA, Simon AE.

J Virol. 2012 Sep;86(18):9828-42. doi: 10.1128/JVI.00677-12. Epub 2012 Jul 3.


Multiscale modeling of double-helical DNA and RNA: a unification through Lie groups.

Wolfe KC, Hastings WA, Dutta S, Long A, Shapiro BA, Woolf TB, Guthold M, Chirikjian GS.

J Phys Chem B. 2012 Jul 26;116(29):8556-72. doi: 10.1021/jp2126015. Epub 2012 Jun 7.


The Proto-oncogene PKCι regulates the alternative splicing of Bcl-x pre-mRNA.

Shultz JC, Vu N, Shultz MD, Mba MU, Shapiro BA, Chalfant CE.

Mol Cancer Res. 2012 May;10(5):660-9. doi: 10.1158/1541-7786.MCR-11-0363. Epub 2012 Apr 20.


Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine.

Afonin KA, Grabow WW, Walker FM, Bindewald E, Dobrovolskaia MA, Shapiro BA, Jaeger L.

Nat Protoc. 2011 Dec 1;6(12):2022-34. doi: 10.1038/nprot.2011.418.


Multistrand RNA secondary structure prediction and nanostructure design including pseudoknots.

Bindewald E, Afonin K, Jaeger L, Shapiro BA.

ACS Nano. 2011 Dec 27;5(12):9542-51. doi: 10.1021/nn202666w. Epub 2011 Nov 17.


Correlating SHAPE signatures with three-dimensional RNA structures.

Bindewald E, Wendeler M, Legiewicz M, Bona MK, Wang Y, Pritt MJ, Le Grice SF, Shapiro BA.

RNA. 2011 Sep;17(9):1688-96. doi: 10.1261/rna.2640111. Epub 2011 Jul 13.


A boost for the emerging field of RNA nanotechnology.

Shukla GC, Haque F, Tor Y, Wilhelmsson LM, Toulmé JJ, Isambert H, Guo P, Rossi JJ, Tenenbaum SA, Shapiro BA.

ACS Nano. 2011 May 24;5(5):3405-18. doi: 10.1021/nn200989r.


Identification of cis-acting elements in the 3'-untranslated region of the dengue virus type 2 RNA that modulate translation and replication.

Manzano M, Reichert ED, Polo S, Falgout B, Kasprzak W, Shapiro BA, Padmanabhan R.

J Biol Chem. 2011 Jun 24;286(25):22521-34. doi: 10.1074/jbc.M111.234302. Epub 2011 Apr 22.

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