Publications by authors named "Aseem Z Ansari"

68Publications

De novo design of programmable inducible promoters.

Nucleic Acids Res 2019 11;47(19):10452-10463

Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.

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http://dx.doi.org/10.1093/nar/gkz772DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821364PMC
November 2019

A chemoprobe tracks its target.

Authors:
Aseem Z Ansari

J Biol Chem 2019 05;294(20):8323-8324

From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706.

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http://dx.doi.org/10.1074/jbc.H119.008945DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6527164PMC
May 2019

Reprogramming cell fate with artificial transcription factors.

FEBS Lett 2018 03 11;592(6):888-900. Epub 2018 Feb 11.

Department of Biochemistry, University of Wisconsin - Madison, WI, USA.

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http://dx.doi.org/10.1002/1873-3468.12993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5869137PMC
March 2018

Combinatorial bZIP dimers display complex DNA-binding specificity landscapes.

Elife 2017 02 10;6. Epub 2017 Feb 10.

Department of Biochemistry, University of Wisconsin-Madison, Madison, United States.

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http://dx.doi.org/10.7554/eLife.19272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5349851PMC
February 2017

Sliding on DNA: From Peptides to Small Molecules.

Angew Chem Int Ed Engl 2016 11 4;55(48):15110-15114. Epub 2016 Nov 4.

Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.

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http://dx.doi.org/10.1002/anie.201606768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217825PMC
November 2016

Engineered Covalent Inactivation of TFIIH-Kinase Reveals an Elongation Checkpoint and Results in Widespread mRNA Stabilization.

Mol Cell 2016 08 28;63(3):433-44. Epub 2016 Jul 28.

Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2016.06.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5122673PMC
August 2016

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin).

J Vis Exp 2016 Jan 20(107):e53510. Epub 2016 Jan 20.

Department of Biochemistry, University of Wisconsin-Madison; The Genome Center, University of Wisconsin-Madison;

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http://dx.doi.org/10.3791/53510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4781686PMC
January 2016

Pathway connectivity and signaling coordination in the yeast stress-activated signaling network.

Mol Syst Biol 2014 Nov 19;10:759. Epub 2014 Nov 19.

Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299600PMC
http://dx.doi.org/10.15252/msb.20145120DOI Listing
November 2014

Controlling gene networks and cell fate with precision-targeted DNA-binding proteins and small-molecule-based genome readers.

Biochem J 2014 Sep;462(3):397-413

‡Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, U.S.A.

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http://dx.doi.org/10.1042/BJ20140400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4205157PMC
September 2014

Mapping polyamide-DNA interactions in human cells reveals a new design strategy for effective targeting of genomic sites.

Angew Chem Int Ed Engl 2014 Sep 27;53(38):10124-8. Epub 2014 Jul 27.

Department of Biochemistry and The Genome Center, University of Wisconsin - Madison, Madison, WI 53706 (USA).

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http://dx.doi.org/10.1002/anie.201405497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160732PMC
September 2014

The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally.

PLoS Genet 2013 17;9(10):e1003839. Epub 2013 Oct 17.

Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

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http://dx.plos.org/10.1371/journal.pgen.1003839
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http://dx.doi.org/10.1371/journal.pgen.1003839DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3798270PMC
March 2014

Gene loops enhance transcriptional directionality.

Science 2012 Nov 27;338(6107):671-5. Epub 2012 Sep 27.

Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.

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http://dx.doi.org/10.1126/science.1224350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3563069PMC
November 2012

Emerging Views on the CTD Code.

Genet Res Int 2012 26;2012:347214. Epub 2012 Feb 26.

Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.

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http://www.hindawi.com/journals/gri/2012/347214/
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http://dx.doi.org/10.1155/2012/347214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3335543PMC
August 2012

Har Gobind Khorana 1922-2011.

Cell 2011 Dec;147(7):1433-5

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http://dx.doi.org/10.1016/j.cell.2011.12.008DOI Listing
December 2011

A partner evokes latent differences between Hox proteins.

Cell 2011 Dec;147(6):1220-1

Department of Biochemistry and The Genome Center, University of Wisconsin, Madison, Madison, WI 53706, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S00928674110144
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http://dx.doi.org/10.1016/j.cell.2011.11.046DOI Listing
December 2011

Fabrication of duplex DNA microarrays incorporating methyl-5-cytosine.

Lab Chip 2012 Jan 5;12(2):376-80. Epub 2011 Dec 5.

McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA.

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http://dx.doi.org/10.1039/c1lc20698bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4205155PMC
January 2012

Jarid2 (Jumonji, AT rich interactive domain 2) regulates NOTCH1 expression via histone modification in the developing heart.

J Biol Chem 2012 Jan 21;287(2):1235-41. Epub 2011 Nov 21.

Department of Cellular and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1074/jbc.M111.315945DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3256911PMC
January 2012

Mapping E. coli RNA polymerase and associated transcription factors and identifying promoters genome-wide.

Methods Enzymol 2011 ;498:449-71

Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA.

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http://dx.doi.org/10.1016/B978-0-12-385120-8.00020-6DOI Listing
September 2011

Sequence-specificity and energy landscapes of DNA-binding molecules.

Methods Enzymol 2011 ;497:3-30

Department of Biochemistry, The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, USA.

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http://dx.doi.org/10.1016/B978-0-12-385075-1.00001-9DOI Listing
September 2011

Nucleating the assembly of macromolecular complexes.

Chembiochem 2010 Sep;11(14):1955-62

Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.

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http://dx.doi.org/10.1002/cbic.201000255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176617PMC
September 2010

Small-molecule regulators that mimic transcription factors.

Biochim Biophys Acta 2010 Oct-Dec;1799(10-12):768-74. Epub 2010 Sep 6.

Department of Biochemistry and Genome Center, University of Wisconsion-Madison, WI 53706, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S18749399100011
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http://dx.doi.org/10.1016/j.bbagrm.2010.08.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160733PMC
February 2011

Chemical-genomic dissection of the CTD code.

Nat Struct Mol Biol 2010 Sep 29;17(9):1154-61. Epub 2010 Aug 29.

Department of Biochemistry and The Genome Center, University of Wisconsin, Madison, Wisconsin, USA.

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http://dx.doi.org/10.1038/nsmb.1900DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035229PMC
September 2010

Specificity landscapes of DNA binding molecules elucidate biological function.

Proc Natl Acad Sci U S A 2010 Mar 22;107(10):4544-9. Epub 2010 Feb 22.

Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.

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http://dx.doi.org/10.1073/pnas.0914023107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842033PMC
March 2010

Chemical biology: A Notch above other inhibitors.

Nature 2009 Nov;462(7270):171-3

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http://dx.doi.org/10.1038/462171aDOI Listing
November 2009

Cognate Site Identifier analysis reveals novel binding properties of the Sex Inducer homeodomain proteins of Cryptococcus neoformans.

Mol Microbiol 2009 Jun 25;72(6):1334-47. Epub 2009 May 25.

Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Madison, WI 53706, USA.

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http://dx.doi.org/10.1111/j.1365-2958.2009.06719.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776684PMC
June 2009

CSI-FID: high throughput label-free detection of DNA binding molecules.

Bioorg Med Chem Lett 2009 Jul 3;19(14):3779-82. Epub 2009 May 3.

Genome Center of Wisconsin, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.

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http://dx.doi.org/10.1016/j.bmcl.2009.04.097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760306PMC
July 2009

Riboactivators: transcription activation by noncoding RNA.

Authors:
Aseem Z Ansari

Crit Rev Biochem Mol Biol 2009 Jan-Feb;44(1):50-61

Department of Biochemistry & The Genome Center of Wisconsin, University of Wisconsin-Madison, 53706, USA.

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http://dx.doi.org/10.1080/10409230902734044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749515PMC
May 2009

Regulator trafficking on bacterial transcription units in vivo.

Mol Cell 2009 Jan;33(1):97-108

Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.

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http://dx.doi.org/10.1016/j.molcel.2008.12.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747249PMC
January 2009

Targeted chemical wedges reveal the role of allosteric DNA modulation in protein-DNA assembly.

ACS Chem Biol 2008 Apr;3(4):220-9

Department of Biochemistry and The Genome Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1021/cb700258rDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060767PMC
April 2008

Expanding the specificity of DNA targeting by harnessing cooperative assembly.

Biochimie 2008 Jul 4;90(7):1015-25. Epub 2008 Mar 4.

Department of Biochemistry, The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA.

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http://dx.doi.org/10.1016/j.biochi.2008.02.014DOI Listing
July 2008

Quantitative microarray profiling of DNA-binding molecules.

J Am Chem Soc 2007 Oct 19;129(40):12310-9. Epub 2007 Sep 19.

Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.

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http://pubs.acs.org/doi/abs/10.1021/ja0744899
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http://dx.doi.org/10.1021/ja0744899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3066056PMC
October 2007

Chemical inhibition of the TFIIH-associated kinase Cdk7/Kin28 does not impair global mRNA synthesis.

Proc Natl Acad Sci U S A 2007 Apr 28;104(14):5812-7. Epub 2007 Mar 28.

Department of Biochemistry and Genome Center of Wisconsin, University of Wisconsin, Madison, WI 53706, USA.

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http://dx.doi.org/10.1073/pnas.0611505104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851574PMC
April 2007

Minimization of a protein-DNA dimerizer.

J Am Chem Soc 2007 Mar 10;129(9):2660-8. Epub 2007 Feb 10.

Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1021/ja067971kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064071PMC
March 2007

A TAD further: exogenous control of gene activation.

ACS Chem Biol 2007 Jan;2(1):62-75

Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA.

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http://dx.doi.org/10.1021/cb600463wDOI Listing
January 2007

Chemical crosshairs on the central dogma.

Authors:
Aseem Z Ansari

Nat Chem Biol 2007 Jan;3(1):2-7

Genome Center of Wisconsin, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1038/nchembio0107-2DOI Listing
January 2007

Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase.

Mol Cell 2006 Dec;24(5):735-746

Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin 53706. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2006.10.023DOI Listing
December 2006

Defining the sequence-recognition profile of DNA-binding molecules.

Proc Natl Acad Sci U S A 2006 Jan 17;103(4):867-72. Epub 2006 Jan 17.

Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0509843102
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http://dx.doi.org/10.1073/pnas.0509843102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347994PMC
January 2006

Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo.

Mol Cell 2005 Nov;20(3):357-66

Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1016/j.molcel.2005.10.011DOI Listing
November 2005

Unraveling the mechanism of a potent transcriptional activator.

J Biol Chem 2005 Aug 10;280(33):29689-98. Epub 2005 May 10.

Department of Biochemistry, University of Wisconsin, Madison, 53706, USA.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M504895200
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http://dx.doi.org/10.1074/jbc.M504895200DOI Listing
August 2005

Temperature-sensitive protein-DNA dimerizers.

Proc Natl Acad Sci U S A 2005 Apr 21;102(14):5008-13. Epub 2005 Mar 21.

Department of Biochemistry and the Genome Center, University of Wisconsin, Madison, WI 53706, USA.

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http://dx.doi.org/10.1073/pnas.0501289102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC555971PMC
April 2005

Transcriptional activating regions target attached substrates to a cyclin-dependent kinase.

Proc Natl Acad Sci U S A 2005 Feb 1;102(7):2346-9. Epub 2005 Feb 1.

Department of Biochemistry and Genome Center, University of Wisconsin, Madison, WI 53706, USA.

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http://dx.doi.org/10.1073/pnas.0409671102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC549008PMC
February 2005

Two cyclin-dependent kinases promote RNA polymerase II transcription and formation of the scaffold complex.

Mol Cell Biol 2004 Feb;24(4):1721-35

Division of Basic Sciences, Fred Hutchinson Cancer Research Center and Howard Hughes Medical Institute, Seattle, Washington 98109, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC344185PMC
http://dx.doi.org/10.1128/mcb.24.4.1721-1735.2004DOI Listing
February 2004

Toward artificial developmental regulators.

J Am Chem Soc 2003 Nov;125(44):13322-3

California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1021/ja0371395DOI Listing
November 2003

Fingers reach for the genome.

Authors:
Aseem Z Ansari

Nat Biotechnol 2003 Mar;21(3):242-3

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http://www.nature.com/articles/nbt0303-242
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http://dx.doi.org/10.1038/nbt0303-242DOI Listing
March 2003

RNA sequences that work as transcriptional activating regions.

Nucleic Acids Res 2003 Mar;31(5):1565-70

Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC149820PMC
http://dx.doi.org/10.1093/nar/gkg227DOI Listing
March 2003

Modular design of artificial transcription factors.

Curr Opin Chem Biol 2002 Dec;6(6):765-72

Department of Biochemistry and The Genome Center, 433 Babcock Drive, University of Wisconsin-Madison, Madison, WI 53706, USA.

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http://dx.doi.org/10.1016/s1367-5931(02)00377-0DOI Listing
December 2002

Transcriptional activating regions target a cyclin-dependent kinase.

Proc Natl Acad Sci U S A 2002 Nov 4;99(23):14706-9. Epub 2002 Nov 4.

Program in Molecular Biology, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.232573899
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http://dx.doi.org/10.1073/pnas.232573899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137483PMC
November 2002

Design of artificial transcriptional activators with rigid poly-L-proline linkers.

J Am Chem Soc 2002 Nov;124(44):13067-71

Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1021/ja0208355DOI Listing
November 2002

A target essential for the activity of a nonacidic yeast transcriptional activator.

Proc Natl Acad Sci U S A 2002 Jun;99(13):8591-6

Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA.

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http://dx.doi.org/10.1073/pnas.092263499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC124323PMC
June 2002