Eric T Kool

Eric T Kool

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Eric T Kool

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Dual Inhibitors of 8-Oxoguanine Surveillance by OGG1 and NUDT1.

ACS Chem Biol 2019 12 29;14(12):2606-2615. Epub 2019 Oct 29.

Department of Chemistry , Stanford University , Stanford , California 94305 , United States.

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http://dx.doi.org/10.1021/acschembio.9b00490DOI Listing
December 2019

Ultrafast Oxime Formation Enables Efficient Fluorescence Light-up Measurement of DNA Base Excision.

J Am Chem Soc 2019 Dec 27;141(49):19379-19388. Epub 2019 Nov 27.

Department of Chemistry, Stanford Cancer Institute and ChEM-H Institute , Stanford University , Stanford , California 94305 , United States.

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http://dx.doi.org/10.1021/jacs.9b09812DOI Listing
December 2019

A fluorescent hydrazone exchange probe of pyridoxal phosphate for the assessment of vitamin B6 status.

Chem Commun (Camb) 2019 Dec;56(2):317-320

Department of Chemistry and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1039/c9cc08458dDOI Listing
December 2019

Increased MTH1-specific 8-oxodGTPase activity is a hallmark of cancer in colon, lung and pancreatic tissue.

DNA Repair (Amst) 2019 11 5;83:102644. Epub 2019 Jul 5.

Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305-5151, United States. Electronic address:

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http://dx.doi.org/10.1016/j.dnarep.2019.102644DOI Listing
November 2019

Fluorescent reporter assays provide direct, accurate, quantitative measurements of MGMT status in human cells.

PLoS One 2019 27;14(2):e0208341. Epub 2019 Feb 27.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0208341PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6392231PMC
October 2019

Polymerase synthesis of four-base DNA from two stable dimeric nucleotides.

Nucleic Acids Res 2019 10;47(18):9495-9501

Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/nar/gkz741DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6765132PMC
October 2019

Polyacetate and Polycarbonate RNA: Acylating Reagents and Properties.

Org Lett 2019 Jul 3;21(14):5413-5416. Epub 2019 Jul 3.

Department of Chemistry , Stanford University , Stanford , California 94305 , United States.

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http://dx.doi.org/10.1021/acs.orglett.9b01526DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6775763PMC
July 2019

RNA structure maps across mammalian cellular compartments.

Nat Struct Mol Biol 2019 04 18;26(4):322-330. Epub 2019 Mar 18.

MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.

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http://www.nature.com/articles/s41594-019-0200-7
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http://dx.doi.org/10.1038/s41594-019-0200-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6640855PMC
April 2019

Simple alkanoyl acylating agents for reversible RNA functionalization and control.

Chem Commun (Camb) 2019 Apr;55(35):5135-5138

Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

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http://xlink.rsc.org/?DOI=C9CC01598A
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http://dx.doi.org/10.1039/c9cc01598aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6541391PMC
April 2019

Polymerase-amplified release of ATP (POLARA) for detecting single nucleotide variants in RNA and DNA.

Chem Sci 2019 Mar 30;10(11):3264-3270. Epub 2019 Jan 30.

Department of Chemistry , Stanford University , Stanford , CA 94305 , USA . Email:

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http://xlink.rsc.org/?DOI=C8SC03901A
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http://dx.doi.org/10.1039/c8sc03901aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429602PMC
March 2019

Water-Soluble Leaving Group Enables Hydrophobic Functionalization of RNA.

Org Lett 2018 10 9;20(20):6587-6590. Epub 2018 Oct 9.

Department of Chemistry , Stanford University , Stanford , California 94305 , United States.

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http://dx.doi.org/10.1021/acs.orglett.8b02938DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478029PMC
October 2018

Fluorescence Probes for ALKBH2 Allow the Measurement of DNA Alkylation Repair and Drug Resistance Responses.

Angew Chem Int Ed Engl 2018 09 3;57(39):12896-12900. Epub 2018 Sep 3.

Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1002/anie.201807593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478024PMC
September 2018

Fluorescent Probes of DNA Repair.

ACS Chem Biol 2018 07 30;13(7):1721-1733. Epub 2017 Nov 30.

Department of Chemistry , Stanford University , Stanford , California 94305 , United States.

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http://dx.doi.org/10.1021/acschembio.7b00919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5976523PMC
July 2018

Exceptionally rapid oxime and hydrazone formation promoted by catalytic amine buffers with low toxicity.

Chem Sci 2018 Jun 21;9(23):5252-5259. Epub 2018 May 21.

Department of Chemistry , Stanford University , Stanford , CA 94305 , USA . Email:

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http://dx.doi.org/10.1039/c8sc01082jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6001384PMC
June 2018

ATP-Linked Chimeric Nucleotide as a Specific Luminescence Reporter of Deoxyuridine Triphosphatase.

Bioconjug Chem 2018 05 29;29(5):1614-1621. Epub 2018 Mar 29.

Department of Chemistry , Stanford University , Stanford , California 94305 , United States.

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http://dx.doi.org/10.1021/acs.bioconjchem.8b00124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6484856PMC
May 2018

RNA Cloaking by Reversible Acylation.

Angew Chem Int Ed Engl 2018 03 22;57(12):3059-3063. Epub 2018 Feb 22.

Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1002/anie.201708696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5842138PMC
March 2018

RNA Control by Photoreversible Acylation.

J Am Chem Soc 2018 03 1;140(10):3491-3495. Epub 2018 Mar 1.

Department of Chemistry , Stanford University , Stanford , California 94305 , United States.

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http://dx.doi.org/10.1021/jacs.7b12408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486827PMC
March 2018

Potent and Selective Inhibitors of 8-Oxoguanine DNA Glycosylase.

J Am Chem Soc 2018 02 5;140(6):2105-2114. Epub 2018 Feb 5.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/jacs.7b09316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5823510PMC
February 2018

Measuring deaminated nucleotide surveillance enzyme ITPA activity with an ATP-releasing nucleotide chimera.

Nucleic Acids Res 2017 Nov;45(20):11515-11524

Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/nar/gkx774DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714213PMC
November 2017

Fluorescent nucleobases as tools for studying DNA and RNA.

Nat Chem 2017 11 16;9(11):1043-1055. Epub 2017 Oct 16.

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1038/nchem.2859DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5819341PMC
November 2017

Fingerprints of Modified RNA Bases from Deep Sequencing Profiles.

J Am Chem Soc 2017 11 17;139(47):17074-17081. Epub 2017 Nov 17.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/jacs.7b07914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5819333PMC
November 2017

Luminescent Carbon Dot Mimics Assembled on DNA.

J Am Chem Soc 2017 09 12;139(37):13147-13155. Epub 2017 Sep 12.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/jacs.7b07420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5817913PMC
September 2017

Oximes and Hydrazones in Bioconjugation: Mechanism and Catalysis.

Chem Rev 2017 Aug 22;117(15):10358-10376. Epub 2017 Jun 22.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://pubs.acs.org/doi/10.1021/acs.chemrev.7b00090
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http://dx.doi.org/10.1021/acs.chemrev.7b00090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5580355PMC
August 2017

Color-Change Photoswitching of an Alkynylpyrene Excimer Dye.

Angew Chem Int Ed Engl 2017 06 5;56(23):6497-6501. Epub 2017 May 5.

Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1002/anie.201701235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5665017PMC
June 2017

Fluorogenic Templated Reaction Cascades for RNA Detection.

J Am Chem Soc 2017 04 5;139(15):5405-5411. Epub 2017 Apr 5.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://pubs.acs.org/doi/10.1021/jacs.7b00466
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http://dx.doi.org/10.1021/jacs.7b00466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568022PMC
April 2017

Comparison of SHAPE reagents for mapping RNA structures inside living cells.

RNA 2017 02 22;23(2):169-174. Epub 2016 Nov 22.

Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1261/rna.058784.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5238792PMC
February 2017

DNA as an environmental sensor: detection and identification of pesticide contaminants in water with fluorescent nucleobases.

Org Biomol Chem 2017 Feb;15(8):1801-1809

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1039/c6ob02830fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322131PMC
February 2017

Chemical and structural effects of base modifications in messenger RNA.

Nature 2017 01;541(7637):339-346

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1038/nature21351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5498787PMC
January 2017

Light-Up "Channel Dyes" for Haloalkane-Based Protein Labeling in Vitro and in Bacterial Cells.

Bioconjug Chem 2016 Dec 1;27(12):2839-2843. Epub 2016 Dec 1.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/acs.bioconjchem.6b00613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5572799PMC
December 2016

The Discovery of Rolling Circle Amplification and Rolling Circle Transcription.

Acc Chem Res 2016 11 24;49(11):2540-2550. Epub 2016 Oct 24.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/acs.accounts.6b00417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568012PMC
November 2016

DNA polymerase θ specializes in incorporating synthetic expanded-size (xDNA) nucleotides.

Nucleic Acids Res 2016 Nov 2;44(19):9381-9392. Epub 2016 Sep 2.

Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA

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http://dx.doi.org/10.1093/nar/gkw721DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100566PMC
November 2016

Fluorogenic Real-Time Reporters of DNA Repair by MGMT, a Clinical Predictor of Antitumor Drug Response.

PLoS One 2016 1;11(4):e0152684. Epub 2016 Apr 1.

Department of Chemistry, Stanford University, Stanford, CA, 94305, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152684PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4818092PMC
August 2016

Dark Hydrazone Fluorescence Labeling Agents Enable Imaging of Cellular Aldehydic Load.

ACS Chem Biol 2016 08 24;11(8):2312-9. Epub 2016 Jun 24.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/acschembio.6b00269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5503141PMC
August 2016

Efficient synthesis of fluorescent alkynyl C-nucleosides via Sonogashira coupling for the preparation of DNA-based polyfluorophores.

Org Biomol Chem 2016 Jul;14(27):6407-12

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1039/c6ob01199cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4935563PMC
July 2016

A Chimeric ATP-Linked Nucleotide Enables Luminescence Signaling of Damage Surveillance by MTH1, a Cancer Target.

J Am Chem Soc 2016 07 18;138(29):9005-8. Epub 2016 Jul 18.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/jacs.6b02895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5500214PMC
July 2016

Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution.

Nucleic Acids Res 2016 05 7;44(8):3820-8. Epub 2016 Apr 7.

Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA

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http://dx.doi.org/10.1093/nar/gkw220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4857003PMC
May 2016

Kinetic selection vs. free energy of DNA base pairing in control of polymerase fidelity.

Proc Natl Acad Sci U S A 2016 Apr 4;113(16):E2277-85. Epub 2016 Apr 4.

Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089;

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http://dx.doi.org/10.1073/pnas.1600279113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843490PMC
April 2016

7SK-BAF axis controls pervasive transcription at enhancers.

Nat Struct Mol Biol 2016 Mar 15;23(3):231-8. Epub 2016 Feb 15.

Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1038/nsmb.3176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4982704PMC
March 2016

Fluorescence Monitoring of the Oxidative Repair of DNA Alkylation Damage by ALKBH3, a Prostate Cancer Marker.

J Am Chem Soc 2016 Mar 15;138(11):3647-50. Epub 2016 Mar 15.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/jacs.6b00986DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5105888PMC
March 2016

ATP-Releasing Nucleotides: Linking DNA Synthesis to Luciferase Signaling.

Angew Chem Int Ed Engl 2016 Feb 6;55(6):2087-91. Epub 2016 Jan 6.

Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1002/anie.201509131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4955596PMC
February 2016

Epigenetics: A new methyl mark on messengers.

Nature 2016 Feb;530(7591):423-4

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1038/530423aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5498786PMC
February 2016

Correction: Pattern-based detection of anion pollutants in water with DNA polyfluorophores.

Chem Sci 2015 08 24;6(8):5086. Epub 2015 Jun 24.

Department of Chemistry , Stanford University , Stanford , California 94305-5080 , USA . Email: ; ; Tel: +1 650 724 4741.

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http://dx.doi.org/10.1039/c5sc90036kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063258PMC
August 2015

In Vitro Fluorogenic Real-Time Assay of the Repair of Oxidative DNA Damage.

Chembiochem 2015 Jul 12;16(11):1637-46. Epub 2015 Jun 12.

Department of Chemistry, Stanford University, Stanford, CA 94305 (USA).

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http://dx.doi.org/10.1002/cbic.201500184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4586133PMC
July 2015

RNA structural analysis by evolving SHAPE chemistry.

Wiley Interdiscip Rev RNA 2014 Nov-Dec;5(6):867-81. Epub 2014 Aug 15.

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.

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http://www.rafrna.com/s/Spitale_et_al-2014-Wiley_Interdiscip
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http://dx.doi.org/10.1002/wrna.1253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5592018PMC
June 2015

Pattern-Based Detection of Anion Pollutants in Water with DNA Polyfluorophores.

Chem Sci 2015 Apr;6(4):2575-2583

Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States. ; Tel: +650 724 4741.

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http://dx.doi.org/10.1039/C4SC03992KDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486361PMC
April 2015

Structural imprints in vivo decode RNA regulatory mechanisms.

Nature 2015 Mar 18;519(7544):486-90. Epub 2015 Mar 18.

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA.

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http://dx.doi.org/10.1038/nature14263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376618PMC
March 2015

Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification.

J Am Chem Soc 2015 Feb 2;137(5):2107-15. Epub 2015 Feb 2.

Department of Chemistry, ‡Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/ja513080vDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405242PMC
February 2015

New organocatalyst scaffolds with high activity in promoting hydrazone and oxime formation at neutral pH.

Org Lett 2015 Jan 29;17(2):274-7. Epub 2014 Dec 29.

Department of Chemistry, Stanford University , Stanford, California 94305-5017, United States.

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http://dx.doi.org/10.1021/ol503372jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4301078PMC
January 2015

Large-scale detection of metals with a small set of fluorescent DNA-like chemosensors.

J Am Chem Soc 2014 Oct 3;136(41):14576-82. Epub 2014 Oct 3.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/ja507932aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4210079PMC
October 2014

Dissecting the chemical interactions and substrate structural signatures governing RNA polymerase II trigger loop closure by synthetic nucleic acid analogues.

Nucleic Acids Res 2014 May 1;42(9):5863-70. Epub 2014 Apr 1.

Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA

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http://dx.doi.org/10.1093/nar/gku238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027217PMC
May 2014

Pattern-based detection of toxic metals in surface water with DNA polyfluorophores.

Angew Chem Int Ed Engl 2014 May 22;53(21):5361-5. Epub 2014 Apr 22.

Department of Chemistry, Stanford University, Stanford, CA 94305 (USA).

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http://dx.doi.org/10.1002/anie.201403235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4095765PMC
May 2014

Fast alpha nucleophiles: structures that undergo rapid hydrazone/oxime formation at neutral pH.

Org Lett 2014 Mar 21;16(5):1454-7. Epub 2014 Feb 21.

Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States.

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http://dx.doi.org/10.1021/ol500262yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3993714PMC
March 2014

Identification of a selective polymerase enables detection of N(6)-methyladenosine in RNA.

J Am Chem Soc 2013 Dec 11;135(51):19079-82. Epub 2013 Dec 11.

Department of Chemistry, Stanford University , Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/ja4105792DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905807PMC
December 2013

Fast hydrazone reactants: electronic and acid/base effects strongly influence rate at biological pH.

J Am Chem Soc 2013 Nov 13;135(47):17663-6. Epub 2013 Nov 13.

Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States.

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http://dx.doi.org/10.1021/ja407407hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874453PMC
November 2013

Artificial genetic sets composed of size-expanded base pairs.

Angew Chem Int Ed Engl 2013 Nov 7;52(48):12498-508. Epub 2013 Nov 7.

Department of Chemistry, Stanford University, Stanford, CA 94305 (USA).

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http://dx.doi.org/10.1002/anie.201305267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5497059PMC
November 2013

DNA-polyfluorophore Chemosensors for Environmental Remediation: Vapor-phase Identification of Petroleum Products in Contaminated Soil.

Chem Sci 2013 Aug;4(8):3184-3190

Department of Chemistry, Stanford University, Stanford, California, 94305-5080, United States. ; Tel: +650 724 4741.

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http://dx.doi.org/10.1039/C3SC50985KDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3713804PMC
August 2013

Monitoring eukaryotic and bacterial UDG repair activity with DNA-multifluorophore sensors.

Nucleic Acids Res 2013 Jul 3;41(12):e127. Epub 2013 May 3.

Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

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https://academic.oup.com/nar/article/41/12/e127/1028577
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http://dx.doi.org/10.1093/nar/gkt309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695528PMC
July 2013

Importance of ortho proton donors in catalysis of hydrazone formation.

Org Lett 2013 Apr 11;15(7):1646-9. Epub 2013 Mar 11.

Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States.

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http://dx.doi.org/10.1021/ol400427xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3618716PMC
April 2013

Genetically encoded multispectral labeling of proteins with polyfluorophores on a DNA backbone.

J Am Chem Soc 2013 04 16;135(16):6184-91. Epub 2013 Apr 16.

Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA.

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http://dx.doi.org/10.1021/ja4004393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646636PMC
April 2013

Selective fluorogenic chemosensors for distinct classes of nucleases.

Chembiochem 2013 Mar 1;14(4):440-4. Epub 2013 Feb 1.

College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 702-701, Korea.

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March 2013

Water-soluble organocatalysts for hydrazone and oxime formation.

J Org Chem 2013 Feb 15;78(3):1184-9. Epub 2013 Jan 15.

Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA.

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February 2013

RNA SHAPE analysis in living cells.

Nat Chem Biol 2013 Jan 25;9(1):18-20. Epub 2012 Nov 25.

Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1038/nchembio.1131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706714PMC
January 2013

Fluorescence quenchers for hydrazone and oxime orthogonal bioconjugation.

Bioconjug Chem 2012 Sep 28;23(9):1969-80. Epub 2012 Aug 28.

Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA.

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http://dx.doi.org/10.1021/bc300344bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3447104PMC
September 2012

Steric restrictions of RISC in RNA interference identified with size-expanded RNA nucleobases.

ACS Chem Biol 2012 Aug 12;7(8):1454-61. Epub 2012 Jun 12.

Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1021/cb300174cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3423588PMC
August 2012

Templated chemistry for monitoring damage and repair directly in duplex DNA.

Chem Commun (Camb) 2012 Aug 10;48(65):8069-71. Epub 2012 Jul 10.

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1039/c2cc34060gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3417126PMC
August 2012

DNA-multichromophore systems.

Chem Rev 2012 Jul 16;112(7):4221-45. Epub 2012 Mar 16.

Department of Chemistry, Stanford University, California 94305, United States.

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http://pubs.acs.org/doi/10.1021/cr100351g
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July 2012

DNA polyfluorophores for real-time multicolor tracking of dynamic biological systems.

Angew Chem Int Ed Engl 2012 Jul 8;51(29):7176-80. Epub 2012 Jun 8.

Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489938PMC
July 2012

Amplified microRNA detection by templated chemistry.

Nucleic Acids Res 2012 May 25;40(9):e65. Epub 2012 Jan 25.

Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.

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http://dx.doi.org/10.1093/nar/gkr1313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351153PMC
May 2012

Dissecting chemical interactions governing RNA polymerase II transcriptional fidelity.

J Am Chem Soc 2012 May 2;134(19):8231-40. Epub 2012 May 2.

Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, California 92093-0625, United States.

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http://dx.doi.org/10.1021/ja302077dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367139PMC
May 2012

Direct fluorescence monitoring of DNA base excision repair.

Angew Chem Int Ed Engl 2012 Feb 12;51(7):1689-92. Epub 2012 Jan 12.

Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1002/anie.201108135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528074PMC
February 2012

Measurement and theory of hydrogen bonding contribution to isosteric DNA base pairs.

J Am Chem Soc 2012 Feb 2;134(6):3154-63. Epub 2012 Feb 2.

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293652PMC
February 2012

Surprising repair activities of nonpolar analogs of 8-oxoG expose features of recognition and catalysis by base excision repair glycosylases.

J Am Chem Soc 2012 Jan 9;134(3):1653-61. Epub 2012 Jan 9.

Department of Chemistry, University of California, Davis, Davis, California 95616, USA.

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January 2012

Fluorescent DNA-based enzyme sensors.

Authors:
Nan Dai Eric T Kool

Chem Soc Rev 2011 Dec 2;40(12):5756-70. Epub 2011 Feb 2.

Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5575859PMC
December 2011

Fluorescent DNA chemosensors: identification of bacterial species by their volatile metabolites.

Chem Commun (Camb) 2011 Nov 21;47(41):11435-7. Epub 2011 Sep 21.

Department of Chemistry, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1039/c1cc14871kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5494280PMC
November 2011

Encoding phenotype in bacteria with an alternative genetic set.

J Am Chem Soc 2011 Nov 21;133(45):18447-51. Epub 2011 Oct 21.

Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255458PMC
November 2011

Multi-path quenchers: efficient quenching of common fluorophores.

Bioconjug Chem 2011 Nov 28;22(11):2345-54. Epub 2011 Oct 28.

Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3226780PMC
November 2011

Importance of steric effects on the efficiency and fidelity of transcription by T7 RNA polymerase.

Biochemistry 2011 Nov 1;50(47):10343-9. Epub 2011 Nov 1.

Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222776PMC
November 2011

Improved templated fluorogenic probes enhance the analysis of closely related pathogenic bacteria by microscopy and flow cytometry.

Bioconjug Chem 2011 Sep 26;22(9):1869-77. Epub 2011 Aug 26.

Department of Chemistry, Stanford University, Stanford, CA 94305-5080, United States.

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http://dx.doi.org/10.1021/bc2003567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178687PMC
September 2011

Chemistry of nucleic acids: impacts in multiple fields.

Chem Commun (Camb) 2011 Jul 11;47(25):7018-24. Epub 2011 Apr 11.

Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445425PMC
July 2011

Protease probes built from DNA: multispectral fluorescent DNA-peptide conjugates as caspase chemosensors.

Angew Chem Int Ed Engl 2011 May 31;50(22):5105-9. Epub 2011 Mar 31.

Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

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May 2011

Fluorescent xDNA nucleotides as efficient substrates for a template-independent polymerase.

Nucleic Acids Res 2011 Mar 14;39(4):1586-94. Epub 2010 Oct 14.

Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.

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http://dx.doi.org/10.1093/nar/gkq853DOI Listing
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March 2011

Differentiating between fluorescence-quenching metal ions with polyfluorophore sensors built on a DNA backbone.

J Am Chem Soc 2011 Mar 4;133(8):2664-71. Epub 2011 Feb 4.

Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA.

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March 2011

Multispectral labeling of antibodies with polyfluorophores on a DNA backbone and application in cellular imaging.

Proc Natl Acad Sci U S A 2011 Mar 14;108(9):3493-8. Epub 2011 Feb 14.

Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.

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http://dx.doi.org/10.1073/pnas.1017349108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048162PMC
March 2011

The components of xRNA: synthesis and fluorescence of a full genetic set of size-expanded ribonucleosides.

Org Lett 2011 Feb 7;13(4):676-9. Epub 2011 Jan 7.

Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA.

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February 2011

Two successive reactions on a DNA template: a strategy for improving background fluorescence and specificity in nucleic acid detection.

Chemistry 2011 Feb 10;17(7):2168-75. Epub 2011 Jan 10.

Department of Chemistry, Stanford University, Stanford, CA-94305-5080, USA.

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http://dx.doi.org/10.1002/chem.201002426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428681PMC
February 2011

Differentiating a diverse range of volatile organic compounds with polyfluorophore sensors built on a DNA scaffold.

Chemistry 2011 Jan 10;17(1):174-83. Epub 2010 Dec 10.

Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.

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http://dx.doi.org/10.1002/chem.201002836DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130889PMC
January 2011

Selective sensor for silver ions built from polyfluorophores on a DNA backbone.

Org Lett 2010 Nov;12(21):4820-3

Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2966516PMC
November 2010

Sandwich probes: two simultaneous reactions for templated nucleic acid detection.

Chem Commun (Camb) 2010 Nov 7;46(43):8154-6. Epub 2010 Oct 7.

Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1039/c0cc01968bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5504956PMC
November 2010

Templated chemistry for sequence-specific fluorogenic detection of duplex DNA.

Chembiochem 2010 Oct;11(15):2132-7

Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.

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http://dx.doi.org/10.1002/cbic.201000329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4418650PMC
October 2010

Polyfluorophores on a DNA backbone: sensors of small molecules in the vapor phase.

Angew Chem Int Ed Engl 2010 Sep;49(39):7025-9

Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

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http://doi.wiley.com/10.1002/anie.201002701
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September 2010

Double displacement: An improved bioorthogonal reaction strategy for templated nucleic acid detection.

Bioconjug Chem 2010 Jun;21(6):1115-20

Department of Chemistry, Stanford University, California 94305-5080, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2891565PMC
June 2010