Inverted repeats

Fig. 3. Example of cniciform formation from an inverted-repeat sequence of DNA which occurs in the plasmid ColEl. The bolded bases are paired with...

FIGURE 12.27 The formation of a cruciform structure from a paliudromic sequence within DNA. The self-complementary Inverted repeats can rearrange to form hydrogen-bonded cruciform loops. 

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... 

Transposons are mobile DNA elements (sizes 2.5-23 kbp) that move from one place to another in the chromosome or onto extrachromosomal genetic elements within the same cell. They are flanked by inverted repeats at then-ends and encode among other proteins a transposase that is needed for the transposition process. Resistance genes in the transposon are often parts of integrons. These are structures that cany an integrase responsible for the insertion of the resistance gene cassettes into the integron. 

HrcA/CIRCE (controling inverted repeat of chaperone expression)... 

Rho-dependent transcription termination signals in E coll also appear to have a distinct consensus sequence, as shown in Figure 37—6. The conserved consensus sequence, which is about 40 nucleotide pairs in length, can be seen to contain a hyphenated or interrupted inverted repeat followed by a series of AT base pairs. As transcription proceeds through the hyphenated, inverted repeat, the generated transcript can form the intramolecular hairpin structure, also depicted in Figure 37-6. 

Figure 37-6. The predominant bacterial transcription termination signal contains an inverted, hyphenated repeat (the two boxed areas) followed by a stretch of AT base pairs (top figure). The inverted repeat, when transcribed into RNA, can generate the secondary structure in the RNA transcript shown at the bottom of the figure. Formation of this RNA hairpin causes RNA polymerase to pause and subsequently the p termination factor interacts with the paused polymerase and somehow induces chain termination.

LaComme, C., Hrubikova, K., and Hein, 1. (2003). Enhancement of virus-induced gene silencing through viral-based production of inverted-repeats. Plant J. 34 543-553. 

Abbreviations IR inverted repeat DR direct repeat ER everted repeat NR no repeat . Numbers of the HREs give the number of pairs separating the half-sites. R purine, Y pyrimidine. NGFI Nerve growth factor induced receptor COLfP-TF Chicken ovalbumin upstream promoter transcription factor ROR Retinoic acid related orphan receptor, a, P und y are receptor subtypes coded by distinct genes. After Mangelsdorf et al., 1995. 

Fig. 4.6. HRE structure of the RXR heterodimer. Shown is the consensus sequence of the HREs of the RXR heterodimers (see Fig. 4.7) and the different possible arrangements of the hexameric half-site sequences. The hexamers can be arranged palindromically as inverted repeats (a), as everted repeats (b), or as direct repeats (c). n indicates the number of base pairs that lie between the two hexamers. RXR receptor for 9-ds retinoic acid RAR receptor for all-trans retinoic acid T3R receptor for the T3 hormon PPAR peroxisome prohferator-activated receptor VDR receptor for vitamin D3.

The bending observed with this and other sequences may be important in the binding of some proteins to DNA A rather common type of DNA sequence is a palindrome. A palindrome is a word, phrase, or sentence that is spelled identically read either forward or backward two examples are ROTATOR and NURSES RUN. The term is applied to regions of DNA with inverted repeats of base sequence having twofold symmetry over two strands of DNA (Fig. 8-20). Such sequences are self-complementary within each strand and therefore have the potential to form hairpin or cruciform (cross-shaped) structures (Fig. 8-21). When the inverted repeat occurs within each individual strand of the DNA, the sequence is called a mirror repeat. Mrror repeats do not have complementary sequences within the same strand and cannot form hairpin or cruciform structures. Sequences of these types are found... 

Chloroplasts contain large 120- to 169-kb circular genomes encoding about 100 proteins (Chapter 23). A characteristic feature of most chloroplast DNA is the presence of long inverted repeat sequences (10,058 bp in the liverwort, 25,339 bp in tobacco).463 464 These are separated by 19,813 and 81,095 bp single copy regions in the liverwort and by similar sized regions in tobacco. Plastid DNA exists as a mixture of monomeric molecules with smaller amounts of dimers, trimers, and tetramers.464... 

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