Complete journal publication list from 1997 to present.


106. Transliteration of synthetic genetic enzymes
Wang Y, Liu X, Shehabat M, Chim N, and Chaput JC
Nucleic Acids Research 2021, 49, in press.

105. Synthesis and polymerase recognition of threose nucleic acid triphosphates equipped with diverse chemical functionalities
Li Q, Maola VA, Chim N, Hussain J, Lozoya-Colinas A, and Chaput, JC
Journal of the American Chemical Society 2021, 143, in press.

104. REVEALR: A multicomponent XNAzyme-based nucleic acid detection system for SARS-CoV-2
Yang K, and Chaput, JC
Journal of the American Chemical Society 2021, 143, 8957-8961.

103. Functional comparison of laboratory-evolved XNA polymerases for synthetic biology
Medina E, Yik EJ, Herdewijn P, and Chaput, JC
ACS Synthetic Biology 2021, 10, 1429-1437.

102. Following replicative DNA synthesis by time-resolved X-ray crystallography
Chim N, Meza, RA, Trinh, AM, Yang, K, and Chaput, JC
Nature Communications 2021, 12: 2641.

101. Allele-specific RNA knockdown with a biologically stable and catalytically efficient XNAzyme
Nguyen K, Wang Y,  England WE, Chaput JC, and Spitale RC
Journal of the American Chemical Society 2021, 143, 4519-4523.

100. A biologically stable DNAzyme that efficiently silences gene expression in cells
Wang Y, Nguyen K, Spitale RC, and Chaput JC
Nature Chemistry 2021, 13, 319-326.

99. Redesigning the genetic polymers of life
Chaput JC
Accounts of Chemical Research 2021, 54, 1056-1065.

98. Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization
Zhang W, Kim SC, Tam CP, Lelyveld VS, Bala S, Chaput JC, and Szostak JW
Nucleic Acids Research 2021, 49, 646-656.


97. Reading and writing digital information in TNA
Yang K, McCloskey CM, and Chaput JC
ACS Synthetic Biology 2020, 9, 2936–2942

96. In Vitro Selection of an ATP-Binding TNA Aptamer
Zhang L, Chaput JC
Molecules 2020, 25, e4194

95. Engineering Polymerases for Applications in Synthetic Biology
Nikoomanzar A, Chim N, Yik EJ, Chaput JC
Quarterly Reviews of Biophysics 2020, 53, e8, 1-31

94. Synthesis and Polymerase Recognition of a Pyrrolocytidine TNA Triphosphate
Mei H, Wang Y, Yik EJ, Chaput JC
Biopolymers 2020, e23388.

93. Programmed Allelic Mutagenesis of a DNA Polymerase with Single Amino Acid Resolution
Nikoomanzar A, Vallejo D, Yik EJ, Chaput JC
ACS Synthetic Biology 2020, 9, 1873–1881

92. Directed Evolution of Custom Polymerases Using Droplet Microfluidics
Vallejo D, Nikoomanzar A, Chaput JC
Methods in Enzymology 2020, 644, 227-253

91. Generating Biologically Stable TNA Aptamers that Function with High Affinity and Thermal Stability
Dunn MR, McCloskey CM, Buckley P, Rhea K, Chaput JC
Journal of the American Chemical Society 2020, 142, 7721-7724

90. Orthogonal Genetic Systems
Chaput JC, Herdewijn, P, Hollenstein M
ChemBioChem 2020, 21, 10, 1408-1411

89. Evaluating the Catalytic Potential of a General RNA-Cleaving FANA Enzyme
Wang Y, Vorperian A, Shehabat M, Chaput JC
ChemBioChem 2020, 21, 1001-1006


88. P(V) Reagents for the Scalable Synthesis of Natural and Modified Nucleoside Triphosphates
Liao JY, Bala S, Ngor AK, Yik EJ, Chaput JC
Journal of the American Chemical Society 2019, 141, 13286-13289

87. What is XNA?
Chaput JC, Herdwijn P.
Angewandte Chemie 2019, 58, 11570-11572

86. A Novel Small RNA-Cleaving Deoxyribozyme with a Short Binding Arm
Wang Y, Yang J, Yuan X, Cao J, Xu J, Chaput JC, Zhe L, Yu H
Scientific Reports 2019, 9, 8224

85. Crystal Structures of a Natural DNA Polymerase that Functions as an XNA Reverse Transcriptase
Jackson LN, Chim N, Shi C, Chaput JC
Nucleic Acid Research 2019, 47, 6973–6983

84. Elucidating the determinants of polymerase specificity by microfluidic-based deep mutational scanning
Nikoomanzar A, Vallejo D, Chaput JC
ACS Synthetic Biology 20198, 1421-1429

83. Fluorescence-activated droplet sorting for single-cell directed evolution
Vallejo D, Nikoomanzar A, Paegel BM, Chaput JC
ACS Synthetic Biology 20198, 1430-1440

82. RNA-catalyzed polymerization of deoxyribose, threose, and arabinose nucleic acids
Horning DP, Bala S, Chaput JC, Joyce GF
ACS Synthetic Biology 20198, 955-961

81. Oligo-Snoop: A non-invasive side channel attack against DNA synthesis machines
Faezi S, Chhetri SR, Malawade AV, Chaput, JC, Grover W, Brisk P, Al Faruque MA
Network and Distributed System Security Symposium 2019, Feb. 24-27. San Diego, CA.

80. Ligase-Mediated Threose Nucleic Acid Synthesis on DNA Templates
McCloskey C, Liao JY, Bala S, Chaput JC
ACS Synthetic Biology 20198, 282–286

79. Activation of innate immune responses by a CpG oligonucleotide sequence composed entirely of threose nucleic acid
Lange MJ, Burke DH, Chaput JC
Nucleic Acid Therapeutics 2019, 29, 51-59


78.  Evolution of a General RNA-cleaving FANA Enzyme
Wang Y, Ngor AK, Nikoomanzar A, Chaput JC
Nature Communications 2018 9, 5067

77. Crystal Structures of DNA Polymerase I Capture Novel Intermediates in the DNA Synthesis Pathway
Chim N, Jackson LN, Trinh AM, Chaput JC
eLife 2018 7, e40444

76. Exploring the Role of AUG Triplets in Human Cap-Independent Translation Enhancing Elements
Juba AN, Chaput JC, Wellensiek BP
Biochemistry 2018 
57, 6308-6318

75. Bacterial Genome Containing Chimeric DNA-RNA Sequences
Mehta, A, Wang, Y, Reed, SA, Supekova, L, Javahishvili, T, Chaput, JC, Schultz, PG
Journal of the American Chemical Society 2018 140, 11464-11473

74. Synthesis of 2’-Deoxy-α-L-Threofuranosyl Nucleoside Triphosphates
Bala S, Liao JY, Zhang L, Tran C, Chim N, Chaput JC
Journal of Organic Chemistry 2018 83, 8840-8850

73. Visualizing Primer Extension Without Enzymes
Chaput JC
eLife 2018 7:37926

72. Synthesis and Evolution of a TNA Aptamer Bearing 7-Deaza-7-Substituted Guanosine Residues
Mei H, Liao JY, Jimenez RM, Wang Y, Bala S, McCloskey C, Switzer C, Chaput JC
Journal of the American Chemical Society 2018 140, 5706-5713

71. Made in Translation
Chaput JC
Nature Chemistry 2018 10, 379-381

70. Expanding the Chemical Diversity of TNA with tUTP Derivatives that are Substrates for a TNA Polymerase
Mei H, Chaput JC
Chemical Communication 2018 54, 1237-1240

69. A Tool for the Import of Natural and Unnatural Nucleoside Triphosphates into Bacteria
Feldman A, Fischer E, Ledbetter M, Liao, JY, Chaput JC, Romesberg FE
Journal of the American Chemical Society 2018 140, 1447-1454


68.  Evaluating the Rate and Substrate Specificity of Laboratory Evolved XNA Polymerases
Nikoomanzar A, Dunn MR, Chaput JC
Analytical Chemistry 2017 89, 12622-12625

67.  Structural Basis for TNA Synthesis by an Engineered TNA Polymerase
Chim N, Shi C, Sau SP, Nikoomanzar A, Chaput JC
Nature Communications 2017 8:1810

66.  Analysis of Aptamer Discovery and Technology
Dunn MR, Jimenez RM, Chaput JC
Nature Reviews Chemistry 2017 1:0076

65.  A Gram-Scale HPLC-Free Synthesis of TNA Triphosphates Using an Iterative Phosphorylation Strategy
Sau S, Chaput JC
Organic Letters 2017 19(16):4379-4382

64.  Synthesis of α-L-Threofuranosyl Nucleoside 3’-Monophosphates, 3’-Phosphoro(2-Methyl)imidazolides, and 3’-Triphosphates
Bala S, Liao J, Mei H, Chaput JC
Journal of Organic Chemistry 2017 82(11):5910−5916

63.  Synthesis and Polymerase Activity of a Fluorescent Cytidine TNA Triphosphate Analogue
Mei H, Shi C, Jimenez RM, Wang Y, Kardouh M, Chaput JC
Nucleic Acids Research 2017 45(10):5629-5638

62.  Engineered Polymerases with Altered Substrate Specificity: Expression and Purification
Nikoomanzar A, Dunn, MR, Chaput, JC
Current Protocols in Nucleic Acids Chemistry 2017 69,4.75.1–4.75.20


61.  A Parallel Stranded G-Quadruplex Composed of Threose Nucleic Acid (TNA)
Liao JY, Anosova I, Bala S, Van Horn WD, Chaput JC
Biopolymers 2016 107:e22999

60.  Reverse Transcription of Threose Nucleic Acid by a Naturally Occurring DNA Polymerase
Dunn MR, Chaput JC
ChemBioChem 2016 17:1804-1808

59.  Structural Insights into Conformational Differences between DNA/TNA and RNA/TNA Chimeric Duplexes
Anosova I, Kowal EA, Sisco NJ, Sau SP, Liao JY, Bala S, Rozners E, Egli M, Chaput JC, Van WD
ChemBioChem 2016 17:1705-1708

58.  A One-Pot Synthesis of α-L Threofuranosyl Nucleoside Triphosphates (tNTPs)
Sau SP and Chaput JC
Bioorganic & Medicinal Chemistry Letters 2016 26(14): 271-3273

57.  Evaluating TNA Stability Under Simulated Physiological Conditions
Culbertson MC, Temburnikar K, Sau SP, Liao JY, Bala S, Chaput JC
Bioorganic & Medicinal Chemistry Letters 2016 26(10): 2418–2421

56.  A Scalable Synthesis of α-L-Threose Nucleic Acid Monomers
Sau SP, Fahmi NE, Liao JY, Bala S, Chaput JC
Journal of Organic Chemistry 2016 81: 2302-2307

55.  A General Strategy for Expanding Polymerase Function by Droplet Microfluidics
Larsen AC, Dunn MR, Hatch A, Sujay, SP, Youngbull C, Chaput JC
Nature Communications 2016 7:11235

54.  Improving Polymerase Activity with Unnatural Substrates by Sampling Mutations in Homologous Protein Architectures
Dunn MR, Otto C, Fenton KE, Chaput JC
ACS Chemical Biology 2016 11(5):1210-1219

53.  The Structural Diversity of Artificial Genetic Polymers
Anosova I, Kowal EA, Dunn MR, Chaput JC, Van Horn WD, Egli M
Nucleic Acids Research 2016 44(3): 1007-1021


52.  Comparative Analysis of Eukaryotic Cell-Free Expression Systems
Hartsough EM, Shah P, Larsen AC, Chaput JC
Biotechniques 2015 59(3):149-151

51.  DNA Polymerase-Mediated Synthesis of Unbiased Threose Nucleic Acid (TNA) Polymers Requires 7‑Deazaguanine To Suppress G:G Mispairing during TNA Transcription
Dunn MR, Larsen A, Zahurancik WJ, Fahmi NE, Meyers M, Suo Z, Chaput JC
Journal of the American Chemical Society 2015 137(12):4014-4017


50.  Automated Solid-Phase Synthesis of High Capacity Oligo-dT Cellulose for Affinity Purification of Short Poly-A Tagged Biomolecules
Sau SP, Larsen AC, Chaput JC
Bioorganic & Medicinal Chemistry Letters 2014 24(24): 5692-5694

49.  Replicating an Expanded Genetic Alphabet in Cells
Chaput JC
ChemBioChem 2014 15(3):1869-1871

48.  General Approach for Characterizing In Vitro Selected Peptides with Protein Binding Affinity
Larsen AC, Gillig A, Shah P, Sau SP, Fenton KE, Chaput JC
Analytical Chemistry 2014 86(15):7219-7223

47.  An In Vitro Selection Protocol for Threose Nucleic Acid (TNA) using DNA Display
Dunn MR, Chaput JC
Current Protocols in Nucleic Acids Chemistry 2014 9:8.1-9.8.19

46.  Development of a Full-Length Human Protein Production Pipeline
Saul J, Petritis B, Sau SP, Rauf F, Gaskin M, Ober-Reynolds B, Mineyev I, Magee M, Chaput JC, Qiu J, LaBaer J
Protein Science 23(8):1123-1135


45.  A Leader Sequence Capable of Enhancing RNA Expression and Protein Synthesis in Mammalian Cells
Wellensiek BP, Larsen AC, Flores J, Jacobs BL, Chaput JC
Protein Science 2013 22:1392-1398

44.  Genome-wide Profiling of Human Cap-independent Translation-Enhancing Elements
Wellensiek BP, Larsen AC, Stephens B, Kukurba K, Waern K, Briones N, Liu L, Snyder M, Jacobs BL, Kumar S, Chaput JC
Nature Methods
2013 10(8):747-750

43.  An Efficient and Faithful in Vitro Replication System for Threose Nucleic Acid
Yu H, Zhang H, Dunn MR, Chaput JC
Journal of the American Chemistry Society 2013 135(9):3583-3591

42.  ATP Sequestration by a Synthetic ATP-Binding Protein Leads to Novel Phenotypic Changes in Escherichia Coli
Korch B, Stomel JM, Leon MA, Hamada MA, Stevenson CR, Simpson BW, Gujulla SK, Chaput JC
ACS Chemical Biology 2013 8(2)451-456

41.  Synthesis and Enzymatic Incorporation of α-L-Threofuranosyl Adenine Triphosphate (tATP)
Zhang S, Chaput JC
Bioorganic & Medicinal Chemistry Letters 2013 23(5):1447-1449

40.  Synthesis of Threose Nucleic Acid (TNA) Triphosphates and Oligonucleotides by Polymerase-Mediated Primer Extension
Zhang S, Yu H, Chaput JC
Current Protocols in Nucleic Acids Chemistry 2013 4:5.54:4.54.1–4.54.17


39.  Synthetic Genetic Polymers Capable of Heredity and Evolution
Pinheiro VB, Taylor AI, Cozens C, Abramov M, Renders M, Zhang S, Chaput JC, Wengel J, Peak-Chew SY, McLaughlin SJ, Herdewijn P, Holliger P
Science 2012 336(6079)341-344

38.  Darwinian Evolution of an Alternative Genetic System Provides Support for TNA as an RNA Progenitor
Yu H, Zhang S, Chaput JC
Nature Chemistry 2012 4:183-187

37.  The Emerging World of Synthetic Genetics
Chaput JC, Yu H, Zhang S
Chemistry & Biology 2012 19(11):1360-1371

36.  Solution Structure of a Parallel-Stranded Oligoisoguanine DNA Pentaplex Formed by d(T(iG4)T) in the presence of Cs+ Ions
Kang M, Heuberger B, Chaput JC, Switzer C, Feigon J
Angewandte Chemie International Edition 2012 51:7952-7955

35.  Synthesis of Threose Nucleic Acid (TNA) Phosphoramidite Monomers and Oligonucleotide Polymers
Zhang S, Chaput JC
Current Protocols in Nucleic Acids Chemistry 2012 Chapter 4, Unit 4.51 


34.  Aptamers can Discriminate Alkaline Proteins with High Specificity
Yu H, Jiang B, Chaput JC
ChemBioChem 2011 12(17):2659-2666

33.  Generating DNA Synbodies from Previously Discovered Peptides
Liu R, Jiang B, Yu H, Chaput JC
ChemBioChem 2011 12(12):1813–1817


32.  The Evolvability of Lead Peptides from Small Library Screens
Zhang J, Williams BA, Nilsson MT, Chaput JC
Chemical Communications 2010 46: 7778-7780

31.  Three-Dimensional Structures Reveal Multiple ADP/ATP Binding Modes for a Synthetic Class of Artificial Proteins
Simmons CR, Magee CL, Smith DA, Lauman L, Chaput JC, Allen JP
Biochemistry 2010 49:8689-8699

30.  The Resurgence of Acyclic Nucleic Acids
Zhang S, Switzer C, Chaput JC
Chemistry & Biodiversity 2010 7:245-258

29.  Synthesis of Glycerol Nucleic Acid (GNA) Phosphoramidite Monomers and Oligonucleotide Polymers
Zhang S, Chaput JC
Current Protocols in Nucleic Acids Chemistry 2010 4.40.1-4.40.18

28.  Synthesis of Peptide-Oligonucleotide Conjugates using a Heterobifunctional Crosslinker
Williams BA, Chaput JC
Current Protocols in Nucleic Acids Chemistry 2010 4.41.1-4.41.20


27.  Creating Protein Affinity Reagents by Combining Peptide Ligands on Synthetic DNA Scaffolds
Williams BA, Diehnelt CW, Belcher P, Greving M, Woodbury NW, Johnston SA, Chaput JC
Journal of the American Chemical Society 2009 131(47):17233-17241

26.  Template-Directed Nucleation and Growth of Inorganic Nanoparticles on DNA Scaffolds
Stearns LA, Chhabra R, Sharma J, Liu Y, Petuskey WT, Yan H, Chaput JC
Angewandte Chemie International Edition 2009 48:8494 -8496

25.  Recognition Imaging of Acetylated Chromatin Using a DNA Aptamer
Lin L, Fu Q, Williams BA, Azzaz AM, Shogren-Knaak M, Chaput JC, Lindsay SM
Biophysical Journal 2009 97:1804-1807

24.  A Man-made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells
Stomel JM, Wilson JW, Leon MA, Stafford P, Chaput JC
Public Library of Science ONE 2009 4:e7385

23.  Conformational Analysis of DNA Repair Intermediates by Time-Resolved Fluorescence Spectroscopy
Lin S, Horning DP, Szostak JW, Chaput JC
The Journal of Physical Chemistry 2009 113:9585-7

22.  A Synthetic Protein Selected for Ligand Binding Affinity Mediates ATP Hydrolysis
Simmons CR, Stomel JM, McConnell MD, Smith DA, Watkins JL, Allen JP, Chaput JC
ACS Chemical Biology 2009 4:649-658

21.  Evolution of a Histone H4-K16 Acetyl-Specific DNA Aptamer
Williams BA, Lin L, Lindsay SM, Chaput JC
Journal of the American Chemical Society 2009 131: 6330-6331

20.  Transcription of an RNA Aptamer by a DNA Polymerase
McCullum EO, Chaput JC
Chemical Communications 2009 20:2938-2940


19.  Creating Protein Biocatalysts as Tools for Future Industrial Applications
Chaput JC, Woodbury NW, Stearns LA, William BA
Expert Opinion on Biological Therapy 
2008 8:1087-1098

18.  Searching Combinatorial Libraries for Native Proteins with Novel Folds
Watkins J and Chaput JC
ChemBioChem 2008 9:1361-1363

17.  Synthesis of Two Mirror Image 4-Helix Junctions Derived from Glycerol Nucleic Acid
Zhang S, McCullum E, Chaput JC
Journal of the American Chemical Society 2008 130: 5846-5847


16.  In Vitro Selection of Histone H4 Aptamers for Recognition Imaging Microscopy
Lin L, Hom D, Lindsay SM, Chaput JC
Journal of the American Chemical Society 2007 129(47):14568-14569

15.  Experimental Evidence that GNA and TNA Were Not Sequential Polymers in the Prebiotic Evolution of RNA
Yang YW, Zhang S, McCullum E, Chaput JC
Journal of Molecular Evolution 2007 65(3): 289-295

14.  Structure and Evolutionary Analysis of a Non-Biological ATP Binding Protein
Mansy SS, Zhang J, Kummerle R, Nilsson M, Chou JJ, Szostak JW, Chaput JC
Journal of Molecular Biology
2007 371:501-513

13.  Structural Insights into the Evolution of a Non-Biological Protein: Importance of Surface Residues in Protein Fold Optimization
Smith MD, Rosenow MA, Wang M, Allen JP, Szostak JW, Chaput JC
Public Library of Science ONE 2007 2: e467

12.  Self-Assembled Peptide Nanoarrays: A New Approach to Studying Protein-Protein Interactions
Williams BAR, Lund K, Liu Y, Yan H, Chaput JC
Angewandte Chemie International Edition 2007 46:3051-3054


11.  Kinetic Analysis of an Efficient DNA-Dependent TNA Polymerase
Horhota A, Keyong Z, Ichida JK, McLaughlin LW, Szostak JW, Chaput JC
Journal of the American Chemical Society 2005 127:7427-7434


10.  Evolutionary Optimization of a Nonbiological ATP-Binding Protein for Improved Folding Stability
Chaput JC, Szostak JW
Chemistry & Biology 2004 11(6):865-874


9. TNA Synthesis by DNA Polymerases
Chaput JC, Szostak JW
Journal of the American Chemical Society 2003 125: 9274-9275

8.  DNA Polymerase-Mediated DNA Synthesis on a TNA Template
Chaput JC, Ichida JK, Szostak JW
Journal of the American Chemical Society 2003 125:856-857


7.  5-Propynyluracil • Diaminopurine: An Efficient Base-Pair for Non-Enzymatic Transcription of DNA
Chaput JC, Sinha S, Switzer C
Chemical Communications 2002 1568-1569


6.  Probing DNA Structure and Function with Alternative Nucleic Acids Bearing 2′,5′-Linked, Zwitterionic and iso-Cytosine • iso-Guanine Components
Chaput JC, Switzer C
Methods: A Compendium to Methods in Enzymology 2001 23:141-148


5.  Non-Enzymatic Transcription of an isoG:isoC Base Pair
Chaput JCC, Switzer C
Journal of the American Chemical Society 2000 122: 12866-12867

4.  Nonenzymatic Oligomerization on Templates Containing Phosphodiester-Linked Acyclic Glycerol Nucleic Acid Analogues
Chaput JC, Switzer C
Journal of Molecular Evolution 2000 51: 464-470

3.  RecA Protein Promotes Strand Exchange with DNA Substrates Containing isoGuanine and 5-Methyl isoCytosine
Rice KP, Chaput JC, Cox MM, Switzer C
Biochemistry 2000 39: 10177-10188


2.  A DNA Pentaplex Incorporating Nucleobase Quintets
Chaput JC, Switzer C
Proceedings of the National Academy of Sciences of the United States of America 1999 96:10614-10619


1.  Beyond Guanine Quartets: Cation-Induced Formation of Homogenous and Chimeric DNA Tetraplexes Incorporating Iso-Guanine and Guanine
Roberts C, Chaput JC, Switzer C
Chemistry & Biology 1997 4(12):899-908