DNA sequence specificity

The promoter proximal elements are usually 100 to 200 base pairs long and relatively close to the site of initiation of transcription. Within each of these elements there are DNA sequences specifically recognized by several different transcription factors which either interact directly with the preinitiation complex or indirectly through other proteins. 

Larsen H.J., Nielsen P.E. Transcription-mediated binding of peptide nucleic acid (PNA) to double-stranded DNA sequence-specific suicide transcription. Nucleic Acids Res. 1996 24 458-463. 

Fig. 55. DNA assembly of gold nanoparticles. Different sized particles (typically, 8 and 30 nm) are assembled alternately through DNA sequence specificity. Reproduced with permission from Ref. (185). Copyright 2000, American Chemical Society.

Remodelling complexes appear to have no intrinsic DNA sequence specificity. Targeting may therefore occur primarily via interactions with other regulatory proteins or to epitopes on the histones marked by specific modifications. Both these means of recruitment are important and may not be mutually exclusive. They... 

Physical (e.g., heat shock, ionizing radiation) and physiological (e.g., hypoxia) stresses, along with metabolic factors (e.g., glucose), induce specific gene expression by mechanisms involving DNA sequence specific transcription factors (Table 2.1). 

Table 2.1 Examples of DNA sequence specific transcription factors that regulate stress inducible promoters now being used in therapeutic applications. Shown are the stress inducers, transcriptional activating proteins and consensus response elements recognized by the transacting proteins...

Examples of DNA sequence specific transcription factors that regulate stress inducible 15... 

It has been established that steroid binding and activation of receptor results in increased affinity of steroid-receptor complex for sites within nuclei in vivo and for DNA in vitro [4], Such binding is low affinity, non-saturable and lacks DNA sequence specificity, yet clearly steroids regulate the transcription of specific genes. Since any protein which interacts with a specific DNA sequence must also interact with other sequences, albeit with reduced affinities, it is assumed that non-specific... 

Malina J, Hannon MJ, Brabec V (2008) Interaction of dinuclear ruthenium(II) supramolecular cylinders with DNA sequence-specific binding, unwinding, and photocleavage. Chem Eur J 14 10408-10414... 

Hurley LH, et al. Reaction of the antitumor antibiotic CC-1065 with DNA structure of a DNA adduct with DNA sequence specificity. Science 1984 226 843-844. 

Phillips DR, White RJ, Cullinane C. DNA sequence-specific adducts of adriamycin and mitomycin C. FEBS Lett. 1989 246 233-240. 89. 

Burnett R, et al. DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA.TTC repeats in Friedreich s ataxia. Proc. Natl. Acad. Sci. U.S.A. 2006 103 11497. 

Many DDE transposases carry a DNA sequence-specific binding domain in their N-terminal regions and at least one domain involved in multimerization. Generally, the catalytic domain is located in the C-terminal part of the protein. The DDE domain is by far the most studied and best understood catalytic motif involved in transposition. It is found in many different types of transposon from retroviruses to Tc-Mariner, bacterial ISs, and transposons (4). 

Fig. 19.8d). The data indicate that the multiplexed assay is not only DNA sequence-specific, but also can quantitatively and simultaneously identify the different food-home pathogens. Obviously, the multiplex related labor and sample processing reduction, simpficity, and breadth of testing options on one device, and combinational power of multiple biomarkers, [41] will make the assay even more attractive for the nucleic acids-based diagnostics. 

V. Petri, M. Hsieh, E. Jamison and M. Brenowitz. DNA sequence-specific recognition by the Saccharomyces cerevisiae "TATA" binding protein promoter-dependent differences in the thermodynamics and kinetics of binding. Biochemistry 37 (1998) 15842-9. 

E2. Eisenach, K. D., Cave, M. D., Bates, J. H., and Crawford, J. T., Polymerase chain reaction amplification of a repetitive DNA sequence specific for Mycobacterium tuberculosis. J. Infect. 

It is well established that DNA sequence specific transcription factors influence transcription through interactions not only with DNA, but also with co-activator and co-repressor proteins. Given the growing number of examples in which Msx proteins have been found to influence transcription without binding DNA (Catron et al., 1995 Newberry 1997 Zhou and Snead, 2000), it has become increasingly important to identify Msx2 co-factors/interacting proteins. By means of two hybrid and far western screens, as well as candidate approaches, several such molecules have been identified. 

Mapping the major adducts of cis- and frans-DDP on DNA sequence specificity... 

Lang H P, CogdeU RJ, Takaichi S and Hunter CN (1995) Complete DNA sequence, specific Tn5 insertion map, and gene assignment of the carotenoid biosynthesis pathway of Rhodobacter sphaeroides. J Bacteriol 177 2064-2073... 

Elferink, C.J. and J.P. Whitlock, Jr. (1994). Dioxin-dependent, DNA sequence-specific binding of a multiprotein complex containing the Ah receptor. Receptor i, 157-173. 

Tliis method enables the rapid identification of DNA-binding proteins. Immobifized DNA probes haiboring a specific sequence motif ai e incubated with cell or nuclear extract. Proteins are analyzed directly off the solid support by MALDI-TOF. Tlie determined mo-leculai masses aie often sufficient for identification. If not, the proteins ai e subject to MS peptide mapping followed by database seaiches. Apai t from protein identification, the protocol also yields information on post-translational modifications. Tlie protocol was validated by the identification of known prokaiyotic and eukai yotic DNA-binding proteins, and is use provided evidence that poly(ADP-ribose) polymerase exhibits DNA sequence-specific binding to DNA. ... 

---