Publications

Publication 55

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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

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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

2021

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

2021

Publication 51

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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

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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

2021

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 

2021

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.  

2021

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

2020

Publication 46

Recruit and Retain a Diverse Workforce

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

 

Nat Rev Chem 4, 435–437

2020

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.

2020

Publication 44

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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

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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.

2020

Publication 43

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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.

2020

Publication 42

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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.

2020

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.

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

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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

2020

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

2020

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

2019

Publication 34

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Small-Molecule Sequestration using Aptamer-Functionalized Membranes.

Romero-Reyes, M.A.; Heemstra, J.M.

 

ACS Materials Lett. 1, 5, 568–572

2019

Publication 36

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A Scientist's Guide to Social Media

Heemstra, J. M.

 

ACS Cent. Sci.; 6, 1, 1–5

2020

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

2020

Publication 33

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Self-care is not the enemy of performance.

Heemstra, J.M.

 

ChemBioChem 20 (2203-2206).

2019

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

2019

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

2018

Publication 32

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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

2019

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.

2019 

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.

2018

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.

2018

Publication 26

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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

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

Tan, Z.; Heemstra, J. M. 

ChemBioChem 19, 1853 - 1857

2018

Publication 24

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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

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

Waterman, R.; Heemstra, J., eds. 

Research Corporation for Science Advancement, Tucson, AZ

2018

Publication 22

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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

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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

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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

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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

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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 15

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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

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

Heemstra, J. M. Beil.

J. Org. Chem. 11, 2713-2720.

2015

Publication 13

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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.