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Items: 1 to 50 of 243

1.

Multiplexed kit based on Luminex technology and achievements in synthetic biology discriminates Zika, chikungunya, and dengue viruses in mosquitoes.

Glushakova LG, Alto BW, Kim MS, Hutter D, Bradley A, Bradley KM, Burkett-Cadena ND, Benner SA.

BMC Infect Dis. 2019 May 14;19(1):418. doi: 10.1186/s12879-019-3998-z.

2.

Hachimoji DNA and RNA: A genetic system with eight building blocks.

Hoshika S, Leal NA, Kim MJ, Kim MS, Karalkar NB, Kim HJ, Bates AM, Watkins NE Jr, SantaLucia HA, Meyer AJ, DasGupta S, Piccirilli JA, Ellington AD, SantaLucia J Jr, Georgiadis MM, Benner SA.

Science. 2019 Feb 22;363(6429):884-887. doi: 10.1126/science.aat0971.

PMID:
30792304
3.

Hydroxymethanesulfonate from Volcanic Sulfur Dioxide: A "Mineral" Reservoir for Formaldehyde and Other Simple Carbohydrates in Prebiotic Chemistry.

Kawai J, McLendon DC, Kim HJ, Benner SA.

Astrobiology. 2019 Apr;19(4):506-516. doi: 10.1089/ast.2017.1800. Epub 2019 Jan 7.

4.

The surprising pairing of 2-aminoimidazo[1,2-a][1,3,5]triazin-4-one, a component of an expanded DNA alphabet.

Laos R, Lampropoulos C, Benner SA.

Acta Crystallogr C Struct Chem. 2019 Jan 1;75(Pt 1):22-28. doi: 10.1107/S2053229618016923. Epub 2019 Jan 1.

PMID:
30601127
5.

Prebiotic plausibility and networks of paradox-resolving independent models.

Benner SA.

Nat Commun. 2018 Dec 12;9(1):5173. doi: 10.1038/s41467-018-07274-y.

6.

Molybdenum(VI)-Catalyzed Rearrangement of Prebiotic Carbohydrates in Formamide, a Candidate Prebiotic Solvent.

Ziegler EW, Kim HJ, Benner SA.

Astrobiology. 2018 Sep;18(9):1159-1170. doi: 10.1089/ast.2017.1742.

PMID:
30204496
7.

"Skinny" and "Fat" DNA: Two New Double Helices.

Hoshika S, Singh I, Switzer C, Molt RW Jr, Leal NA, Kim MJ, Kim MS, Kim HJ, Georgiadis MM, Benner SA.

J Am Chem Soc. 2018 Sep 19;140(37):11655-11660. doi: 10.1021/jacs.8b05042. Epub 2018 Sep 10.

PMID:
30148365
8.

Optimization of cationic (Q)-paper for detection of arboviruses in infected mosquitoes.

Glushakova LG, Alto BW, Kim MS, Wiggins K, Eastmond B, Moussatche P, Burkett-Cadena ND, Benner SA.

J Virol Methods. 2018 Nov;261:71-79. doi: 10.1016/j.jviromet.2018.08.004. Epub 2018 Aug 9.

PMID:
30099053
9.

The challenge of synthetic biology. Synthetic Darwinism and the aperiodic crystal structure.

Karalkar NB, Benner SA.

Curr Opin Chem Biol. 2018 Oct;46:188-195. doi: 10.1016/j.cbpa.2018.07.008. Epub 2018 Aug 9. Review.

PMID:
30098527
10.

Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide.

Singh I, Laos R, Hoshika S, Benner SA, Georgiadis MM.

Nucleic Acids Res. 2018 Sep 6;46(15):7977-7988. doi: 10.1093/nar/gky552.

11.

Nucleoside analogs to manage sequence divergence in nucleic acid amplification and SNP detection.

Yang Z, Kim HJ, Le JT, McLendon C, Bradley KM, Kim MS, Hutter D, Hoshika S, Yaren O, Benner SA.

Nucleic Acids Res. 2018 Jul 6;46(12):5902-5910. doi: 10.1093/nar/gky392.

12.

Artificially Expanded Genetic Information Systems for New Aptamer Technologies.

Biondi E, Benner SA.

Biomedicines. 2018 May 9;6(2). pii: E53. doi: 10.3390/biomedicines6020053. Review.

13.

Multiplexed Isothermal Amplification Based Diagnostic Platform to Detect Zika, Chikungunya, and Dengue 1.

Yaren O, Alto BW, Bradley KM, Moussatche P, Glushakova L, Benner SA.

J Vis Exp. 2018 Mar 13;(133). doi: 10.3791/57051.

14.

Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography.

Koirala D, Shelke SA, Dupont M, Ruiz S, DasGupta S, Bailey LJ, Benner SA, Piccirilli JA.

Nucleic Acids Res. 2018 Mar 16;46(5):2624-2635. doi: 10.1093/nar/gkx1292.

15.

A Direct Prebiotic Synthesis of Nicotinamide Nucleotide.

Kim HJ, Benner SA.

Chemistry. 2018 Jan 12;24(3):581-584. doi: 10.1002/chem.201705394. Epub 2017 Dec 19.

PMID:
29194806
16.

Prebiotic stereoselective synthesis of purine and noncanonical pyrimidine nucleotide from nucleobases and phosphorylated carbohydrates.

Kim HJ, Benner SA.

Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):11315-11320. doi: 10.1073/pnas.1710778114. Epub 2017 Oct 9.

17.

Structure and Biophysics for a Six Letter DNA Alphabet that Includes Imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-Diaminopyrimidine (K).

Singh I, Kim MJ, Molt RW, Hoshika S, Benner SA, Georgiadis MM.

ACS Synth Biol. 2017 Nov 17;6(11):2118-2129. doi: 10.1021/acssynbio.7b00150. Epub 2017 Aug 15.

18.

Detecting Darwinism from Molecules in the Enceladus Plumes, Jupiter's Moons, and Other Planetary Water Lagoons.

Benner SA.

Astrobiology. 2017 Sep;17(9):840-851. doi: 10.1089/ast.2016.1611. Epub 2017 Jun 30.

19.

Detection of chikungunya viral RNA in mosquito bodies on cationic (Q) paper based on innovations in synthetic biology.

Glushakova LG, Alto BW, Kim MS, Bradley A, Yaren O, Benner SA.

J Virol Methods. 2017 Aug;246:104-111. doi: 10.1016/j.jviromet.2017.04.013. Epub 2017 Apr 27.

20.

Point of sampling detection of Zika virus within a multiplexed kit capable of detecting dengue and chikungunya.

Yaren O, Alto BW, Gangodkar PV, Ranade SR, Patil KN, Bradley KM, Yang Z, Phadke N, Benner SA.

BMC Infect Dis. 2017 Apr 20;17(1):293. doi: 10.1186/s12879-017-2382-0.

21.

Adsorption of RNA on mineral surfaces and mineral precipitates.

Biondi E, Furukawa Y, Kawai J, Benner SA.

Beilstein J Org Chem. 2017 Mar 1;13:393-404. doi: 10.3762/bjoc.13.42. eCollection 2017.

22.

Tautomeric equilibria of isoguanine and related purine analogs.

Karalkar NB, Khare K, Molt R, Benner SA.

Nucleosides Nucleotides Nucleic Acids. 2017 Apr 3;36(4):256-274. doi: 10.1080/15257770.2016.1268694. Epub 2017 Mar 23.

PMID:
28332916
23.

Biological phosphorylation of an Unnatural Base Pair (UBP) using a Drosophila melanogaster deoxynucleoside kinase (DmdNK) mutant.

Chen F, Zhang Y, Daugherty AB, Yang Z, Shaw R, Dong M, Lutz S, Benner SA.

PLoS One. 2017 Mar 21;12(3):e0174163. doi: 10.1371/journal.pone.0174163. eCollection 2017.

24.

Biophysics of Artificially Expanded Genetic Information Systems. Thermodynamics of DNA Duplexes Containing Matches and Mismatches Involving 2-Amino-3-nitropyridin-6-one (Z) and Imidazo[1,2-a]-1,3,5-triazin-4(8H)one (P).

Wang X, Hoshika S, Peterson RJ, Kim MJ, Benner SA, Kahn JD.

ACS Synth Biol. 2017 May 19;6(5):782-792. doi: 10.1021/acssynbio.6b00224. Epub 2017 Feb 9.

PMID:
28094993
25.

Unusual Hydrogen Bonding Patterns and the Role of the Backbone in Nucleic Acid Information Transfer.

Benner SA.

ACS Cent Sci. 2016 Dec 28;2(12):882-884. doi: 10.1021/acscentsci.6b00344. Epub 2016 Nov 22. No abstract available.

26.

A Single Deoxynucleoside Kinase Variant from Drosophila melanogaster Synthesizes Monophosphates of Nucleosides That Are Components of an Expanded Genetic System.

Matsuura MF, Winiger CB, Shaw RW, Kim MJ, Kim MS, Daugherty AB, Chen F, Moussatche P, Moses JD, Lutz S, Benner SA.

ACS Synth Biol. 2017 Mar 17;6(3):388-394. doi: 10.1021/acssynbio.6b00228. Epub 2016 Dec 9.

PMID:
27935283
27.

Crystal structures of deprotonated nucleobases from an expanded DNA alphabet.

Matsuura MF, Kim HJ, Takahashi D, Abboud KA, Benner SA.

Acta Crystallogr C Struct Chem. 2016 Dec 1;72(Pt 12):952-959. Epub 2016 Nov 7.

PMID:
27918296
28.

Evaporite Borate-Containing Mineral Ensembles Make Phosphate Available and Regiospecifically Phosphorylate Ribonucleosides: Borate as a Multifaceted Problem Solver in Prebiotic Chemistry.

Kim HJ, Furukawa Y, Kakegawa T, Bita A, Scorei R, Benner SA.

Angew Chem Int Ed Engl. 2016 Dec 19;55(51):15816-15820. doi: 10.1002/anie.201608001. Epub 2016 Nov 9.

PMID:
27862722
29.

Alternative Watson-Crick Synthetic Genetic Systems.

Benner SA, Karalkar NB, Hoshika S, Laos R, Shaw RW, Matsuura M, Fajardo D, Moussatche P.

Cold Spring Harb Perspect Biol. 2016 Nov 1;8(11). pii: a023770. doi: 10.1101/cshperspect.a023770. Review.

30.

Laboratory evolution of artificially expanded DNA gives redesignable aptamers that target the toxic form of anthrax protective antigen.

Biondi E, Lane JD, Das D, Dasgupta S, Piccirilli JA, Hoshika S, Bradley KM, Krantz BA, Benner SA.

Nucleic Acids Res. 2016 Nov 16;44(20):9565-9577. Epub 2016 Oct 3.

31.

Expanded Genetic Alphabets: Managing Nucleotides That Lack Tautomeric, Protonated, or Deprotonated Versions Complementary to Natural Nucleotides.

Winiger CB, Shaw RW, Kim MJ, Moses JD, Matsuura MF, Benner SA.

ACS Synth Biol. 2017 Feb 17;6(2):194-200. doi: 10.1021/acssynbio.6b00193. Epub 2016 Oct 7.

PMID:
27648724
32.

Aptamers against Cells Overexpressing Glypican 3 from Expanded Genetic Systems Combined with Cell Engineering and Laboratory Evolution.

Zhang L, Yang Z, Le Trinh T, Teng IT, Wang S, Bradley KM, Hoshika S, Wu Q, Cansiz S, Rowold DJ, McLendon C, Kim MS, Wu Y, Cui C, Liu Y, Hou W, Stewart K, Wan S, Liu C, Benner SA, Tan W.

Angew Chem Int Ed Engl. 2016 Sep 26;55(40):12372-5. doi: 10.1002/anie.201605058. Epub 2016 Sep 7.

33.

A norovirus detection architecture based on isothermal amplification and expanded genetic systems.

Yaren O, Bradley KM, Moussatche P, Hoshika S, Yang Z, Zhu S, Karst SM, Benner SA.

J Virol Methods. 2016 Nov;237:64-71. doi: 10.1016/j.jviromet.2016.08.012. Epub 2016 Aug 18.

PMID:
27546345
34.

Standard and AEGIS nicking molecular beacons detect amplicons from the Middle East respiratory syndrome coronavirus.

Yaren O, Glushakova LG, Bradley KM, Hoshika S, Benner SA.

J Virol Methods. 2016 Oct;236:54-61. doi: 10.1016/j.jviromet.2016.07.008. Epub 2016 Jul 12.

35.

Polymerase Interactions with Wobble Mismatches in Synthetic Genetic Systems and Their Evolutionary Implications.

Winiger CB, Kim MJ, Hoshika S, Shaw RW, Moses JD, Matsuura MF, Gerloff DL, Benner SA.

Biochemistry. 2016 Jul 19;55(28):3847-50. doi: 10.1021/acs.biochem.6b00533. Epub 2016 Jul 8.

PMID:
27347689
36.

Synthesis and Enzymology of 2'-Deoxy-7-deazaisoguanosine Triphosphate and Its Complement: A Second Generation Pair in an Artificially Expanded Genetic Information System.

Karalkar NB, Leal NA, Kim MS, Bradley KM, Benner SA.

ACS Synth Biol. 2016 Jul 15;5(7):672-8. doi: 10.1021/acssynbio.5b00276. Epub 2016 Feb 25.

PMID:
26914388
37.

Assays To Detect the Formation of Triphosphates of Unnatural Nucleotides: Application to Escherichia coli Nucleoside Diphosphate Kinase.

Matsuura MF, Shaw RW, Moses JD, Kim HJ, Kim MJ, Kim MS, Hoshika S, Karalkar N, Benner SA.

ACS Synth Biol. 2016 Mar 18;5(3):234-40. doi: 10.1021/acssynbio.5b00172. Epub 2016 Feb 1.

PMID:
26829203
38.

A Strategy for Origins of Life Research.

Scharf C, Virgo N, Cleaves HJ 2nd, Aono M, Aubert-Kato N, Aydinoglu A, Barahona A, Barge LM, Benner SA, Biehl M, Brasser R, Butch CJ, Chandru K, Cronin L, Danielache S, Fischer J, Hernlund J, Hut P, Ikegami T, Kimura J, Kobayashi K, Mariscal C, McGlynn S, Menard B, Packard N, Pascal R, Pereto J, Rajamani S, Sinapayen L, Smith E, Switzer C, Takai K, Tian F, Ueno Y, Voytek M, Witkowski O, Yabuta H.

Astrobiology. 2015 Dec;15(12):1031-42. doi: 10.1089/ast.2015.1113.

39.

Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA.

Glushakova LG, Sharma N, Hoshika S, Bradley AC, Bradley KM, Yang Z, Benner SA.

Anal Biochem. 2015 Nov 15;489:62-72. doi: 10.1016/j.ab.2015.08.015. Epub 2015 Aug 21.

40.

A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair.

Hernandez AR, Shao Y, Hoshika S, Yang Z, Shelke SA, Herrou J, Kim HJ, Kim MJ, Piccirilli JA, Benner SA.

Angew Chem Int Ed Engl. 2015 Aug 17;54(34):9853-6. doi: 10.1002/anie.201504731. Epub 2015 Jul 16.

PMID:
26223188
41.

Nearly Forty Years after Viking: Are We Ready for a New Life-Detection Mission?

Schulze-Makuch D, Rummel JD, Benner SA, Levin G, Parro V, Kounaves S.

Astrobiology. 2015 Jun;15(6):413-9. doi: 10.1089/ast.2015.1336. Epub 2015 Jun 8. No abstract available.

PMID:
26053735
42.

Evolution of functional six-nucleotide DNA.

Zhang L, Yang Z, Sefah K, Bradley KM, Hoshika S, Kim MJ, Kim HJ, Zhu G, Jiménez E, Cansiz S, Teng IT, Champanhac C, McLendon C, Liu C, Zhang W, Gerloff DL, Huang Z, Tan W, Benner SA.

J Am Chem Soc. 2015 Jun 3;137(21):6734-7. doi: 10.1021/jacs.5b02251. Epub 2015 May 20.

43.

Structural basis for a six nucleotide genetic alphabet.

Georgiadis MM, Singh I, Kellett WF, Hoshika S, Benner SA, Richards NG.

J Am Chem Soc. 2015 Jun 3;137(21):6947-55. doi: 10.1021/jacs.5b03482. Epub 2015 May 18.

44.

Helicase-Dependent Isothermal Amplification of DNA and RNA by Using Self-Avoiding Molecular Recognition Systems.

Yang Z, McLendon C, Hutter D, Bradley KM, Hoshika S, Frye CB, Benner SA.

Chembiochem. 2015 Jun 15;16(9):1365-70. doi: 10.1002/cbic.201500135. Epub 2015 May 7.

45.

Prebiotic glycosylation of uracil with electron-donating substituents.

Kim HJ, Benner SA.

Astrobiology. 2015 Apr;15(4):301-6. doi: 10.1089/ast.2014.1264.

PMID:
25860300
46.

Abiotic regioselective phosphorylation of adenosine with borate in formamide.

Furukawa Y, Kim HJ, Hutter D, Benner SA.

Astrobiology. 2015 Apr;15(4):259-67. doi: 10.1089/ast.2014.1209. Epub 2015 Mar 31.

PMID:
25826074
47.

Solubility of polyethers in hydrocarbons at low temperatures. A model for potential genetic backbones on warm titans.

McLendon C, Opalko FJ, Illangkoon HI, Benner SA.

Astrobiology. 2015 Mar;15(3):200-6. doi: 10.1089/ast.2014.1212.

PMID:
25761113
48.

High-throughput multiplexed xMAP Luminex array panel for detection of twenty two medically important mosquito-borne arboviruses based on innovations in synthetic biology.

Glushakova LG, Bradley A, Bradley KM, Alto BW, Hoshika S, Hutter D, Sharma N, Yang Z, Kim MJ, Benner SA.

J Virol Methods. 2015 Mar;214:60-74. doi: 10.1016/j.jviromet.2015.01.003. Epub 2015 Feb 11.

49.

Paradoxes in the origin of life.

Benner SA.

Orig Life Evol Biosph. 2014 Dec;44(4):339-43. doi: 10.1007/s11084-014-9379-0. Epub 2015 Jan 22. No abstract available.

PMID:
25608919
50.

Hominids adapted to metabolize ethanol long before human-directed fermentation.

Carrigan MA, Uryasev O, Frye CB, Eckman BL, Myers CR, Hurley TD, Benner SA.

Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):458-63. doi: 10.1073/pnas.1404167111. Epub 2014 Dec 1.

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