Inverted motif

An inverted motif for the oligonucleotide triplex (RYR) is possible when the central position of a triad is occupied by pseudouridine, as in A-xl/UA (Figure... 

An essential step of NR action is the interaction of these receptors with the specific DNA sequence HREs. Indeed, HREs position the receptors, and the transcriptional complexes recruited by them, close to the target genes. HREs are bipartite elements that are composed of two hexameric core half-site motifs. These consensus nucleotide sequences form direct, indirect, or inverted repeats, which consist of two half-sites separated... 

The operators of discrete rotational groups, best described in terms of both proper and improper symmetry axes, have the special property that they leave one point in space unmoved hence the term point group. Proper rotations, like translation, do not affect the internal symmetry of an asymmetric motif on which they operate and are referred to as operators of the first kind. The three-dimensional operators of improper rotation are often subdivided into inversion axes, mirror planes and centres of symmetry. These operators of the second kind have the distinctive property of inverting the handedness of an asymmetric unit. This means that the equivalent units of the resulting composite object, called left and right, cannot be brought into coincidence by symmetry operations of the first kind. This inherent handedness is called chirality. 

The multipUcity of possible combinations of homodimers and heterodimers of RAR and RXR subtypes, and the various possible RXR heterodimers with other receptors, permits a wide variety of active retinoid receptor complexes that bind to different response elements on DNA. Unlike most hormone response elements on DNA, which are palindromic and bind a symmetrical receptor homodimer, the most common type of retinoid response element is a direct repeat purine-G-(G or T)-T-C-A-(Xn)-purine-G-(G or T)-T-C-A, in which the spacer (Xn) is commonly 5 base pairs, but may be 1 or 2. There are also more complex retinoid response elements, including palindromic and inverted palindromic repeats, as well as hexameric motifs with variable spacing. This means that a wide variety of different genes may be regulated differendy in response to retinoids. 

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-... 

As shown by a UV melting experiment, successful triplex formation can be achieved when this inverted triad is accommodated in T AT triplexes. The two A moieties in the inverted repeat are not likely to be identical, and the issue is yet to be resolved as to whether the two have different glycosidic torsions and so on. These examples involving pseudopyrimidines in the central position have really extended the triplex recognition motifs and allow the construction of additional patterns with pyrimidines involved in nonstandard WC pairs. 

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