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


Publication 50


Quantifying fear of failure in STEM: Modifying and evaluating the Performance Failure Appraisal Inventory (PFAI) for use with STEM undergraduates


Henry, M.A., Shorter, S., Charkoudian, L. K., Heemstra, J. M., Le, B., & Corwin, L. A


International Journal of STEM Education: 8, 43


Publication 49

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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 


Publication 48

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Protein-based molecular recognition tools for detecting and profiling RNA modifications.


Knutson, S. D., Heemstra, J. M.


Curr. Opin. Struct. Biol., 69, 1-10.  


Publication 47

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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


Publication 46

Recruit and Retain a Diverse Workforce

Manuel, B. A.; Karloff, D. B.


Nat Rev Chem 4, 435–437


Publication 45

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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.


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.


Publication 42


Probing the Mechanism of Structure-Switching Aptamer Assembly by Super-Resolution Imaging of Single-Molecule Association Kinetics.

Lackey, H. H.; Peterson, E. M.; Harris, J. M.; Heemstra, J. M.


Anal. Chem.; 92, 6909-6917.


Publication 43


DNA/TNA mesoscopic modeling of melting temperatures suggest weaker hydrogen bonding of CG than in DNA/RNA.

Muniz, M. I.; Lackey, H. H.; Heemstra, J. M.; Weber, G


Chem. Phys. Lett; 749, 137413.


Publication 42


Probing the Mechanism of Structure-Switching Aptamer Assembly by Super-Resolution Imaging of Single-Molecule Association Kinetics.

Lackey, H. H.; Peterson, E. M.; Harris, J. M.; Heemstra, J. M.


Anal. Chem.; 92, 6909-6917.


Publication 40

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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.


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.


Publication 39

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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


Publication 38

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Peptide Nucleic Acids Harness Dual Information Codes in a Single Molecule.

Swenson, C.S.; Heemstra, J. M.


Chem. Commun.; 56, 1926-1935


Publication 35

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Bilingual Peptide Nucleic Acids: Encoding the Languages of Nucleic Acids and Proteins in a Single Self-Assembling Biopolymer

Swenson, C.S.; Velusamy, A.; Argueta-Gonzalez, H. S.; Heemstra, J. M.


Journal of the American Chemical Society. 141, 48, 19038-19047


Publication 34


Small-Molecule Sequestration using Aptamer-Functionalized Membranes.

Romero-Reyes, M.A.; Heemstra, J.M.


ACS Materials Lett. 1, 5, 568–572


Publication 36

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A Scientist's Guide to Social Media

Heemstra, J. M.


ACS Cent. Sci.; 6, 1, 1–5


Publication 37

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Single-Molecule Kinetics Show DNA Pyrimidine Content Strongly Affects RNA:DNA and TNA:DNA Heteroduplex Dissociation Rates

Lackey, H. H.; Chen, Z.; Harris, J. M.; Peterson, E. M.; Heemstra, J. M.


ACS Synth. Biol.; 9, 2, 249–253


Publication 33

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Self-care is not the enemy of performance.

Heemstra, J.M.


ChemBioChem 20 (2203-2206).


Publication 30

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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


Publication 29

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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


Publication 32


FAIL is not a four-letter word: A theoretical framework for exploring student approaches to academic challenge and responses to failure.

Henry, M.; Shorter, S.; Charkoudian, L.; Heemstra, J.; Corwin, L.


CBE Life Sci. Educ. 18, ar1-rm1


Publication 31

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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.


Publication 28

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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.


Publication 27

Chemical Labeling and Affinity Capture o

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.


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.


Publication 25


High-Throughput Small-Molecule Enantiopurity Measurement Using Flow Cytometry. 

Tan, Z.; Heemstra, J. M. 

ChemBioChem 19, 1853 - 1857


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.


Publication 23


Expanding the Cure Model: Course-based Undergraduate Research Experience. 

Waterman, R.; Heemstra, J., eds. 

Research Corporation for Science Advancement, Tucson, AZ


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.


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.


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.


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


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.


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.


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


Publication 14


Learning from the Unexpected in Life and DNA Self-Assembly. 

Heemstra, J. M. Beil.

J. Org. Chem. 11, 2713-2720.


Publication 13


Modulating the Substrate Selectivity of DNA Aptamers Using Surfactants. 

Peterson, A. M.; Jahnke, F. M.; Heemstra, J. M. 

Langmuir 31, 11769-11773.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


Publication 1


Small Molecule-Dependent Split Aptamer Ligation. 

Sharma, A. K.; Heemstra, J. M. 

J. Am. Chem. Soc. 133, 12426-12429.


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.

Publication 52

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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