Microarray analysis of the in vivo sequence preferences of a minor groove binding drug.

BMC Genomics
Todd T EckdahlLaurie J Heyer

Abstract

Minor groove binding drugs (MGBDs) interact with DNA in a sequence-specific manner and can cause changes in gene expression at the level of transcription. They serve as valuable models for protein interactions with DNA and form an important class of antitumor, antiviral, antitrypanosomal and antibacterial drugs. There is a need to extend knowledge of the sequence requirements for MGBDs from in vitro DNA binding studies to living cells. Here we describe the use of microarray analysis to discover yeast genes that are affected by treatment with the MGBD berenil, thereby allowing the investigation of its sequence requirements for binding in vivo. A novel approach to sequence analysis allowed us to address hypotheses about genes that were directly or indirectly affected by drug binding. The results show that the sequence features of A/T richness and heteropolymeric character discovered by in vitro berenil binding studies are found upstream of genes hypothesized to be directly affected by berenil but not upstream of those hypothesized to be indirectly affected or those shown to be unaffected. The data support the conclusion that effects of berenil on gene expression in yeast cells can be explained by sequence patterns discovered by i...Continue Reading

References

Nov 1, 1991·Antimicrobial Agents and Chemotherapy·L R Ferguson, R J Sundberg
Sep 11, 1995·Nucleic Acids Research·A Abu-DayaK R Fox
Sep 1, 1994·Nature Structural Biology·J L Kim, S K Burley
Oct 1, 1993·Acta Tropica·S A Agbe, K L Yielding
Feb 21, 1998·Nucleic Acids Research·J M CherryD Botstein
Mar 5, 1999·Journal of Molecular Biology·C AnselmiA Scipioni
Aug 6, 1999·Biochemistry·F G AlbertJ N Anderson
Sep 10, 1999·The Journal of Biological Chemistry·D J Fitzgerald, J N Anderson
Nov 24, 1999·Journal of Biomolecular Structure & Dynamics·K E Reinert
Jun 14, 2000·Journal of Molecular Biology·A Bareket-SamishT E Haran
Jun 21, 2001·Journal of the American Chemical Society·D L BogerM P Hedrick
Jul 31, 2001·Current Drug Targets·P R Turner, W A Denny
Jul 31, 2001·Natural Product Reports·S Neidle
Nov 28, 2002·Nature Genetics·John Quackenbush
Jun 26, 2003·Nucleic Acids Research·Kristian VlahovicekSándor Pongor
Jan 14, 2004·Molecular Biology of the Cell·Isabelle Lesur, Judith L Campbell
Feb 5, 2004·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·A Craig LockhartMace L Rothenberg
Feb 28, 2004·European Journal of Medicinal Chemistry·Anna PućkowskaKrystyna Midura-Nowaczek
Apr 30, 2004·Journal of Medicinal Chemistry·Italo BeriaRomeo Romagnoli
Jun 2, 2004·Medicinal Research Reviews·Pier Giovanni BaraldiRomeo Romagnoli
Jan 14, 2005·Bioinformatics·L J HeyerB K Akin
Feb 25, 2006·Science·A Malcolm CampbellAnne G Rosenwald
Aug 19, 2007·Current Medicinal Chemistry·Antonino LauriaAnna Maria Almerico

❮ Previous
Next ❯

Citations

Feb 19, 2019·MedChemComm·Adeyemi RahmanIsabel Rozas

❮ Previous
Next ❯

Methods Mentioned

BETA
footprinting
PCR
electrophoresis
reverse transcription PCR

Software Mentioned

bend
Berenil
. it
MicroArray Genome Imaging and Clustering ( MAGIC ) Tool
MAGIC Tool
Excel

Related Concepts

Related Feeds

Antivirals

Antivirals are medications that are used specifically for treating viral infections. Discover the latest research on antivirals here.

Antivirals (ASM)

Antivirals are medications that are used specifically for treating viral infections. Discover the latest research on antivirals here.