Publications
Publication 55
Systematically Modulating Aptamer Affinity and Specificity by Guanosine-to-Inosine Substitution
Manuel, B. A., Sterling, S. A., Sanford, A. A., and J. M. Heemstra
Anal. Chem., 94, 17, 6436–6440
2022
Publication 57
Tracking the Message: Applying Single Molecule Localization Microscopy to Cellular RNA Imaging
Arnould, B. Quillin, A. and J. M. Heemstra
ChemBiochem
2023
Publication 56
Stimuli-responsive assembly of bilingual peptide nucleic acids
Argueta-Gonzalez, H. Swenson, C. Song, G. and J. M. Heemstra
RCS Chem. Biol.
2022
Publication 55
Systematically Modulating Aptamer Affinity and Specificity by Guanosine-to-Inosine Substitution
Manuel, B. A., Sterling, S. A., Sanford, A. A., and J. M. Heemstra
Anal. Chem., 94, 17, 6436–6440
2022
Publication 54
Fluorescence Quenching of Xanthene Dyes during Amide Bond Formation using DMTMM
Patterson, K., Romero-Reyes, M. A., and J. M. Heemstra
ChemRxiv
2022
Publication 53
Romero-Reyes, M.A. and J. M. Heemstra
Bioconjugate Chem., 32, 9, 2043-2051
2021
Publication 52
Sweet sensation: Developing a single-cell fluorescent reporter of glycolytic heterogeneity
Karloff, D. B. and J. M. Heemstra
Cell Chem. Biol., 28 (11), 1539-1541
2021
Publication 51
RE-SELEX: restriction enzyme-based evolution of structure-switching aptamer biosensors
A. A. Sanford, A. E. Rangel, T. A. Feagin, R. G. Lowery, H. S. Argueta-Gonzalez, and J. M. Heemstra
Chem. Sci. 2021, Advance Article
2021
Publication 50
Henry, M.A., Shorter, S., Charkoudian, L. K., Heemstra, J. M., Le, B., & Corwin, L. A
International Journal of STEM Education: 8, 43
2021
Publication 49
Direct Immunodetection of Global A‐to‐I RNA Editing Activity with a Chemiluminescent Bioassay
Knutson, S. D., Arthur, R. A., Johnston H. R., and Heemstra, J. M.
Angew. Chem. Int. Ed., 60, 17009
2021
Publication 48
Protein-based molecular recognition tools for detecting and profiling RNA modifications.
Knutson, S. D., Heemstra, J. M.
Curr. Opin. Struct. Biol., 69, 1-10.
2021
Publication 47
Thermoreversible Control of Nucleic Acid Structure and Function with Glyoxal Caging.
Knutson, S. D.*, Sanford, A. A.*, Swenson, C. S., Korn, M. M., Manuel, B. M., and Heemstra, J. M.
J. Am. Chem. Soc.: 142, 41, 17766–17781
2020
Publication 46
Recruit and Retain a Diverse Workforce
Manuel, B. A.; Karloff, D. B.
Nat Rev Chem 4, 435–437
2020
Publication 45
Chemical Profiling of A-to-I RNA Editing Using a Click-Compatible Phenylacrylamide.
Knutson, S. D.; Korn, M. M.; Johnson, R. P.; Monteleone, L. R.; Dailey, D. M.; Swenson, C. S.; Beal, P. A.; Heemstra, J. M.
Chem. Eur. J.; 26(44), 9874-9878.
2020
Publication 44
EndoVIPER-seq for improved detection of A-to-I editing sites in cellular RNA.
Knutson, S. D.; Heemstra, J. M.
Curr. Protoc. Chem. Biol.; 12(2), e82.
2020
Publication 42
Lackey, H. H.; Peterson, E. M.; Harris, J. M.; Heemstra, J. M.
Anal. Chem.; 92, 6909-6917.
2020
Publication 43
Muniz, M. I.; Lackey, H. H.; Heemstra, J. M.; Weber, G
Chem. Phys. Lett; 749, 137413.
2020
Publication 42
Lackey, H. H.; Peterson, E. M.; Harris, J. M.; Heemstra, J. M.
Anal. Chem.; 92, 6909-6917.
2020
Publication 40
Imaging and tracking mRNA in live mammalian cells via fluorogenic photoaffinity labeling.
Ayele, T.; Loya, T.; Valdez-Sinon, A.; Bassell, G.; Heemstra, J.
bioRxiv; 02.10.942482.
2020
Publication 41
Covalent live-cell labeling of proteins using a photoreactive fluorogen.
Ayele, T. M.; Knutson, S.D.; Heemstra, J.M.
Methods in Enzymology; 639(16), 355-377.
2020
Publication 39
Selective Enrichment of A-to-I Edited Transcripts from Cellular RNA Using Endonuclease V.
Knutson, S. D.; Arthur, R. A.; Johnston, H. R.; Heemstra, J. M.
J. Am. Chem. Soc. 142, 11, 5241–5251
2020
Publication 38
Peptide Nucleic Acids Harness Dual Information Codes in a Single Molecule.
Swenson, C.S.; Heemstra, J. M.
Chem. Commun.; 56, 1926-1935
2020
Publication 35
Swenson, C.S.; Velusamy, A.; Argueta-Gonzalez, H. S.; Heemstra, J. M.
Journal of the American Chemical Society. 141, 48, 19038-19047
2019
Publication 34
Small-Molecule Sequestration using Aptamer-Functionalized Membranes.
Romero-Reyes, M.A.; Heemstra, J.M.
ACS Materials Lett. 1, 5, 568–572
2019
Publication 36
Publication 37
Lackey, H. H.; Chen, Z.; Harris, J. M.; Peterson, E. M.; Heemstra, J. M.
ACS Synth. Biol.; 9, 2, 249–253
2020
Publication 33
Publication 30
Thermostability Trends of TNA:DNA Duplexes Reveal Strong Purine Dependence.
Lackey, H.; Peterson, E.M.; Chen, Z.; Harris, J.M.; Heemstra, J.M.
ACS Synth. Biol. 8, 5, 1144–1152
2019
Publication 29
Biomolecular Assemblies: Moving from Observation to Predictive Design.
Wilson, C. J.; Bommarius, A. S.; Champion, J. C.; Chernoff, Y. O.; Lynn, D. G.; Paravastu, A. K.; Liang, C.; Hsieh, M.-C.; Heemstra, J. M.
Chem. Rev. 118, 24, 11519–11574
2018
Publication 32
Henry, M.; Shorter, S.; Charkoudian, L.; Heemstra, J.; Corwin, L.
CBE Life Sci. Educ. 18, ar1-rm1
2019
Publication 31
Fluorogenic Photoaffinity Labeling of Proteins in Living Cells.
Ayele, T. M.; Knutson, S. D.; Ellipilli, S.; Hwang, H.; Heemstra, J.M.
Bioconjugate Chem. 30 (5), 1309-1313.
2019
Publication 28
Single-Molecule Kinetic Investigation of Cocaine-Dependent Split Aptamer Assembly.
Morris, F. D.; Peterson, E. M.; Heemstra, J. M.; Harris, J. M.
Anal. Chem. 90, 12964 - 12970.
2018
Publication 27
Chemical Labeling and Affinity Capture of Inosine-Containing RNAs Using Acrylamidofluorescein.
Knutson, S. D.; Ayele, T. M.; Heemstra, J. M.
Bioconjugate Chem. 29, 2899 - 2903.
2018
Publication 26
In Vitro Selection of an XNA Aptamer Capable of Small-Molecule Recognition.
Rangel, A. E.; Chen, Z.; Ayele, T. M.; Heemstra, J. M.
Nucleic Acids Res. 6, 8057 - 8068.
2018
Publication 25
High-Throughput Small-Molecule Enantiopurity Measurement Using Flow Cytometry.
Tan, Z.; Heemstra, J. M.
ChemBioChem 19, 1853 - 1857
2018
Publication 24
Synthesis of comb-shaped oligonucleotides using a non-nucleosidic branching phosphoramidite.
Ellipilli, S.; Phillips, J. D.; Heemstra, J. M.
Org. Biomol. Chem. 16, 4659-4664.
2018
Publication 23
Expanding the Cure Model: Course-based Undergraduate Research Experience.
Waterman, R.; Heemstra, J., eds.
Research Corporation for Science Advancement, Tucson, AZ
2018
Publication 22
Collaborating with Undergraduates to Contribute to Biochemistry Community Resources.
Haas, K. L.; Heemstra, J. M.; Medema, M. H.; Charkoudian, L. K.
Biochemistry in press.
2017
Publication 21
Throwing away the cookbook: implementing course-based undergraduate research experiences (CUREs) in chemistry.
Heemstra, J. M.; Waterman, R.; Antos, J. M.; Beuning, P. J.; Bur, S. K.; Columbus, L.; Feig, A. L.; Fuller, A. A.; Gillmore, J. G.; Leconte, A. M.; Londergan, C. H.; Pomerantz, W. C. K.; Prescher, J. A.; Stanley, L. M.
ACS Symp. Series 1248, 33-63.
2017
Publication 20
Reversible Oligonucleotide Chain Blocking Enables Bead Capture and Amplification of T-Cell Receptor α and β Chain mRNAs.
Hanson, W. M.; Chen, Z.; Jackson, L. K.; Attaf, M.; Sewell, A. K.; Heemstra, J. M.; Phillips, J. D.
J. Am. Chem. Soc. 138, 11073-11076.
2016
Publication 19
Effect of Buffer Conditions and Organic Co-Solvents on the Rate of Strain-Promoted Azide-Alkyne Cycloaddition.
Price, E. K.; Davis, D. L.; Aderibigbe, S. O.; Larkin, M. X.-H.; Barlow, E. D.; Chen, R.; Ford, L. C.; Gray, Z. T.; Gren, S. H.; Jin, Y.; Keddington, K. S.; Kent, A. D.; Kim, D.; Lewis, A.; Marrouche, R. S.; O’Dair, M. K.; Powell, D. R.; Scadden, M. H. C.; Session, C. B.; Tao, J.; Trieu, J.; Whiteford, K. N.; Yuan, Z.; Yun, G.; Zhu, J.; Heemstra, J. M.
J. Org. Chem. 81, 6816-6819
2016
Publication 18
Synthesis and Polymerase Incorporation of β,γ-Modified α-L-Threofuranosyl Thymine Triphosphate Mimics.
Chen, Z.; Meek, K. N.; Rangel, A. E.; Heemstra, J. M.
Bioorg. Med. Chem. Lett. 26, 3958-3962.
2016
Publication 17
Temporal Control of Aptamer Biosensors Using Covalent Self-Caging to Shift Equilibrium.
Tan, Z.; Feagin, T. A.; Heemstra, J. M.
J. Am. Chem. Soc. 138, 6328-6331.
2016
Publication 16
Publication 15
Size-dependent unzipping of duplexes of A-form DNA-RNA, A-form DNA-PNA, and B-form DNA-DNA in the alpha-hemolysin nanopore.
Perera, R. T.; Fleming, A. M.; Peterson, A. M.; Heemstra, J. M.; Burrows, C. J.; White, H. S.
Biophys. J. 110, 306-314
2016
Publication 14
Learning from the Unexpected in Life and DNA Self-Assembly.
Heemstra, J. M. Beil.
J. Org. Chem. 11, 2713-2720.
2015
Publication 13
Modulating the Substrate Selectivity of DNA Aptamers Using Surfactants.
Peterson, A. M.; Jahnke, F. M.; Heemstra, J. M.
Langmuir 31, 11769-11773.
2015
Publication 12
3,3’-Dioctadecyloxacarbocyanine Perchlorate (DiO) as a Fluorogenic Probe for Measurement of Critical Micelle Concentration.
Peterson, A. M.; Tan, Z.; Kimbrough, E. M.; Heemstra, J. M.
Anal. Methods 2015 7, 6877-6882.
Publication 11
Accelerating Strain-Promoted Azide-Alkyne Cycloaddition using Micellar Catalysis.
Anderton, G. I.; Bangerter, A. S.; Davis, T. C.; Feng, Z.; Furtak, A. J.; Larsen, J. O.; Scroggin, T. L.; Heemstra, J. M.
Bioconjugate Chem. 26, 1687-1691.
2015
Publication 10
High-Throughput Enantiopurity Analysis using Enantiomeric DNA-Based Sensors.
Feagin, T. A.; Olsen, D. P. V.; Headman, Z. C.; Heemstra, J. M.
J. Am. Chem. Soc. 137, 4198-4206.
2015
Publication 9
Controlling Self-Assembly of DNA-Polymer Conjugates for Applications in Imaging and Drug Delivery.
Peterson, A. M.; Heemstra, J. M.
WIREs Nanomed. Nanobiotechnol., 7, 282-297.
2015
Publication 8
Fluorescent RNA Labeling Using Self-Alkylating Ribozymes.
Sharma, A. K.; Plant, J. J.; Rangel, A. E.; Khoe, K. N.; Anamisis, A. J.; Hollien, J.; Heemstra, J. M.
ACS Chem. Biol. 9, 1680-1684.
2014
Publication 7
Differential DNA and RNA Sequence Discrimination by PNA Having Charged Side Chains.
De Costa, N. T. S.; Heemstra, J. M.
Bioorg. Med. Chem. Lett. 24, 2360-2363.
2014
Publication 6
General Approach for Engineering Small-Molecule-Binding DNA Split Aptamers.
Kent, A. D.; Spiropulos, N. G.; Heemstra, J. M.
Anal. Chem. 85, 9916-9923.
2013
Publication 5
Evaluating the Effect of Ionic Strength on Duplex Stability for PNA Having Negatively or Positively Charged Side Chains.
De Costa, N. T. S.; Heemstra, J. M.
PLOS ONE 8, e58670.
2013
Publication 4
Templating Effect in DNA Proximity Ligation Enables use of Non-Bioorthogonal Chemistry in Biological Fluids.
Spiropulos, N. G.; Heemstra, J. M.
Artificial DNA: PNA & XNA 3, 123-128.
2012
Publication 3
Enzyme-Linked Small-Molecule Detection using Split Aptamer Ligation.
Sharma, A. K.; Kent, A. D.; Heemstra, J. M.
Anal. Chem. 84, 6104-6109.
2012
Publication 2
Convenient and Scalable Synthesis of Fmoc-Protected Peptide Nucleic Acid Backbone.
Feagin, T. A.; Shah, N. I.; Heemstra, J. M.
J. Nucleic Acids. 354549.
2012
Publication 1
Small Molecule-Dependent Split Aptamer Ligation.
Sharma, A. K.; Heemstra, J. M.
J. Am. Chem. Soc. 133, 12426-12429.
2011
Undergraduate, Graduate, and Postdoctoral:
12. Heemstra, J. M.; Liu, D. R. Templated Synthesis of Peptide Nucleic Acids via Sequence-Selective Base-Filling Reactions. J. Am. Chem. Soc. 2009 131, 11347-11349.
11. Kowtoniuk, W. E.; Shen, Y.; Heemstra, J. M.; Agarwal, I.; Liu, D. R. A chemical screen for biological small molecule-RNA conjugates reveals CoA-linked RNA. Proc. Nat. Acad. Sci. U.S.A. 2009 106, 7768-7773.
10. Heemstra, J. M.; Kerrigan, S. A.; Doerge, D. R.; Helferich, W. G.; Boulanger, W. A. Total Synthesis of (S)-Equol.Org. Lett. 2006 8, 5441-5443.
9. Stone, M. T.; Heemstra, J. M.; Moore, J. S. The Chain Length Dependence Test. Acc. Chem. Res. 2006 39, 11-20.
8. Heemstra, J. M.; Moore, J. S. Enhanced Methylation Rate within a Foldable Molecular Receptor. J. Org. Chem. 2004 69, 9234-9237.
7. Heemstra, J. M.; Moore, J. S. Helix stabilization through pyridinium-? interactions. Chem. Commun. 2004 1480-1481.
6. Heemstra, J. M.; Moore, J. S. A novel indicator series for measuring pKa values in acetonitrile. Tetrahedron2004, 60, 7287-7292.
5. Goto, H.; Heemstra, J. M.; Hill, D. J.; Moore, J. S. Single-Site Modifications and Their Effect on the Folding Stability of m-Phenylene Ethynylene Oligomers. Org. Lett. 2004 6, 889-892.
4. Heemstra, J. M.; Moore, J. S. Pyridine-Containing m-Phenylene Ethynylene Oligomers Having Tunable Basicities. Org. Let. 2004 6, 659-662.
3. Heemstra, J. M.; Moore, J. S. Folding-Promoted Methylation of a Helical DMAP Analog. J. Am. Chem. Soc. 2004 126, 1648-1649.
2. Cary (Heemstra), J. M.; Moore, J. S. Hydrogen Bond Stabilized Helix Formation of a m-Phenylene Ethynylene Oligomer. Org. Lett. 2002 4, 4663-4666.
1. Nowick, J. S.; Cary (Heemstra), J. M.; Tsai, J. H. A Triply Templated Artificial β-Sheet. J. Am. Chem. Soc. 2001 123, 5176-5180.