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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


Publication 57


Tracking the Message: Applying Single Molecule Localization Microscopy to Cellular RNA Imaging


Arnould, B. Quillin, A. and J. M. Heemstra




Publication 56


Stimuli-responsive assembly of bilingual peptide nucleic acids


Argueta-Gonzalez, H. Swenson, C. Song, G. and J. M. Heemstra


RCS Chem. Biol.


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


Publication 54

Fluorescence Quenching of Xanthene Dyes during Amide Bond Formation using DMTMM


Patterson, K., Romero-Reyes, M. A., and J. M. Heemstra




Publication 53


Sequestration and Removal of Multiple Small-Molecule Contaminants Using an Optimized Aptamer-Based Ultrafiltration System


Romero-Reyes, M.A. and J. M. Heemstra


Bioconjugate Chem., 32, 9, 2043-2051


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


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.

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