Target Detection Assay (TDA): a versatile procedure to determine DNA binding sites as demonstrated on SP1 protein - PubMed (original) (raw)
Target Detection Assay (TDA): a versatile procedure to determine DNA binding sites as demonstrated on SP1 protein
H J Thiesen et al. Nucleic Acids Res. 1990.
Free PMC article
Abstract
We developed a rapid method designated Target Detection Assay (TDA) to determine DNA binding sites for putative DNA binding proteins. A purified, functionally active DNA binding protein and a pool of random double-stranded oligonucleotides harbouring PCR primer sites at each end are included the TDA cycle which consists of four separate steps: a DNA protein incubation step, a protein DNA complex separation step, a DNA elution step and a polymerase chain reaction (PCR) DNA amplification step. The stringency of selection can be increased in consecutive TDA cycles. Since tiny amounts of retained DNA can be rescued by PCR, buffer systems, salt concentrations and competitor DNA contents can be varied in order to determine high affinity binding sites for the protein of choice. To test the efficiency of the TDA procedure potential DNA binding sites were selected by the DNA binding protein SP1 from a pool of oligonucleotides with random nucleotides at 12 positions. Target sites selected by recombinant SP1 closely matched the SP1 consensus site. If DNA recognition sites have to be determined for known, mutated or putative DNA binding proteins, the Target Detection Assay (TDA) is a versatile and rapid technique for consideration.
Similar articles
- Determination of recognition-sequences for DNA-binding proteins by a polymerase chain reaction assisted binding site selection method (BSS) using nitrocellulose immobilized DNA binding protein.
Nørby PL, Pallisgaard N, Pedersen FS, Jørgensen P. Nørby PL, et al. Nucleic Acids Res. 1992 Dec 11;20(23):6317-21. doi: 10.1093/nar/20.23.6317. Nucleic Acids Res. 1992. PMID: 1475193 Free PMC article. - Identification of the promoter of human transcription factor Sp3 and evidence of the role of factors Sp1 and Sp3 in the expression of Sp3 protein.
Lou Z, Maher VM, McCormick JJ. Lou Z, et al. Gene. 2005 May 23;351:51-9. doi: 10.1016/j.gene.2005.02.007. Epub 2005 Apr 25. Gene. 2005. PMID: 15857802 - Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection.
Blackwell TK, Weintraub H. Blackwell TK, et al. Science. 1990 Nov 23;250(4984):1104-10. doi: 10.1126/science.2174572. Science. 1990. PMID: 2174572 - CASTing for multicomponent DNA-binding complexes.
Wright WE, Funk WD. Wright WE, et al. Trends Biochem Sci. 1993 Mar;18(3):77-80. doi: 10.1016/0968-0004(93)90156-h. Trends Biochem Sci. 1993. PMID: 8386867 Review.
Cited by
- The role of CEMIP in cancers and its transcriptional and post-transcriptional regulation.
Guo S, Guo Y, Chen Y, Cui S, Zhang C, Chen D. Guo S, et al. PeerJ. 2024 Feb 19;12:e16930. doi: 10.7717/peerj.16930. eCollection 2024. PeerJ. 2024. PMID: 38390387 Free PMC article. Review. - A Krüppel-like factor 1 (KLF1) Mutation Associated with Severe Congenital Dyserythropoietic Anemia Alters Its DNA-Binding Specificity.
Kulczynska K, Bieker JJ, Siatecka M. Kulczynska K, et al. Mol Cell Biol. 2020 Feb 12;40(5):e00444-19. doi: 10.1128/MCB.00444-19. Print 2020 Feb 12. Mol Cell Biol. 2020. PMID: 31818881 Free PMC article. - Maximal Expression of the Evolutionarily Conserved Slit2 Gene Promoter Requires Sp1.
Saunders J, Wisidagama DR, Morford T, Malone CS. Saunders J, et al. Cell Mol Neurobiol. 2016 Aug;36(6):955-964. doi: 10.1007/s10571-015-0281-8. Epub 2015 Oct 11. Cell Mol Neurobiol. 2016. PMID: 26456684 Free PMC article. - Differential effects of Sp cellular transcription factors on viral promoter activation by varicella-zoster virus (VZV) IE62 protein.
Khalil MI, Ruyechan WT, Hay J, Arvin A. Khalil MI, et al. Virology. 2015 Nov;485:47-57. doi: 10.1016/j.virol.2015.06.031. Epub 2015 Jul 23. Virology. 2015. PMID: 26207799 Free PMC article. - Determining the specificities of TALENs, Cas9, and other genome-editing enzymes.
Pattanayak V, Guilinger JP, Liu DR. Pattanayak V, et al. Methods Enzymol. 2014;546:47-78. doi: 10.1016/B978-0-12-801185-0.00003-9. Methods Enzymol. 2014. PMID: 25398335 Free PMC article. Review.
References
- Cell. 1987 Dec 24;51(6):1079-90 - PubMed
- Nucleic Acids Res. 1988 Mar 25;16(5):1879-902 - PubMed
- Mol Cell Biol. 1988 Mar;8(3):1319-26 - PubMed
- Cell. 1988 May 20;53(4):617-25 - PubMed
- Nucleic Acids Res. 1988 May 25;16(10):4227-37 - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases