Inverted direct response sequence

The Inverted Direct Response (IDR)-HSQC-TOCSY pulse sequence is shown in Fig. 18 [58]. The experiment begins with an HSQC segment... 

Fig. 10.18. IDR (Inverted Direct Response)—HSQC-TOCSY pulse sequence. The experiment first uses an HSQC sequence to label protons with the chemical shift of their directly bound carbons, followed by an isotropic mixing period that propagates magnetization to vicinal neighbor and more distant protons. The extent to which magnetization is propagated in the experiment is a function of both the size of the intervening vicinal coupling constants and the duration of the mixing period. After isotropic mixing, direct responses are inverted by the experiment and proton detection begins.

Fig. 8.31 Pulse sequence schematic for the inverted direct response GHSQC-TOCSY experiment. After labeling protons with the respective, directly bound carbon chemical shifts, magnetization is propagated from a given pro-...

Fig. 11. A Pulse sequence to invert direct (one-bond) responses based on HSQC-TOCSY (Domke 1991). B Pulse sequence to invert direct responses based on HMQC-TOCSY (Martin et al. 1992). When the adjustable pulse, P, is set to 180°, the direct responses are inverted as in the original work of Domke (1991). In contrast, when p = 90°, direct responses will be canceled in a manner analogous to the procedure used to calibrate decoupler pulses (Thomas et al. 1981 Bax 1983b). In experiments when the direct response is to be canceled, there is no need of broadband heteronuclear decoupling during acquisition, allowing higher levels of digital resolution in F2 than would otherwise be possible...

Fig. 12A-C. HMQC-TOCSY contour plots recorded for the alkaloid quindoline (3) using the pulse sequence shown in Fig. IIB. The spectrum was recorded with a mixing time of 24 ms. A Contour plot showing all responses. B Contour plot in which only negative contours from inverted direct responses are plotted. C Contour plot in which only the positive TOCSY responses appear...

Steroid and nuclear receptors are differentiated by their mode of DNA binding. GR, PR, AR, and ER all bind as homodimers to inverted-repeat sequences separated by three nucleotides (nnn), although the ER DNA binding domain recognizes a DNA sequence that is shared by the nuclear receptors. Nuclear receptors bind predominantly as heterodimers with RXR to direct-repeat sequences separated by one to five nucleotides. Structural studies have shown that RXR binds to the 50 half-site of the response element, which may be important for ligand-dependent transcriptional regulatory activity of the heterodimeric... 

RAR-RXR heterodimeric complexes bind to a directly repeated, hexanucleotide motif of the consensus sequence 5 -PuGGTCA-3 (where Pu represents a purine, see above). Directly repeated response elements, in contrast to inverted repeats, are not symmetrical, and this renders the microenvironment of each half-site distinct (38). This situation implies that the orientation of RAR-RXR complexes RAREs may be ordered and occur in a non-random manner. Indeed, this is the case Perl-mann and colleagues used biochemical tech-... 

A FIGURE 11-42 Consensus sequences of DNA response elements that bind three nuclear receptors. The response elements for the glucocorticoid receptor (GRE) and estrogen receptor (ERE) contain inverted repeats that bind these homodimeric proteins. The response elements for heterodimeric receptors contain a common direct repeat separated by three to five base pairs, for the vitamin D3 receptor (VDRE), thyroid hormone receptor (TRE), and retinoic acid receptor (RARE). The repeat sequences are indicated by red arrows. [See K. Umesono etal., 1991, Ce//65 1255, and A. M. Naaretal., 1991, Ce//65 1267]... 

The retinoid receptors function as dimers. Thus, the RAR subtypes heterodimerize with the RXR subtypes. The RXRs also can homodimerize or heterodimerize with the vitamin D, thyroid hormone, and the orphan receptors. The receptor dimers act either directly or indirectly to regulate gene function. The dimers bind directly to retinoid response elements (RAREs and RXREs). These response elements (REs) are specific sequences in the promoter regions of retinoid-responsive genes, which typically consist of two conserved sequences of six nucleotide bases that are separated by discrete numbers of bases. For example, RXR-RAR dimers bind to RAREs which are direct repeats of AGGTCA separated by five (synthetic DR-5 sequence) or two (synthetic DR-2) nucleotides or are palindromic, inverted, or more complex in structure [6]. 

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