Inverted repeat sequences

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...

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... 

Following the discovery of the IS elements it was found that transposable elements named transposons could transfer resistance to antibiotics between bacteria. All of these transposable elements have inverted repeat sequences at the ends. For example, IS1 contains the following sequence at both ends but with opposite orientation as if in a... 

PALINDROME A length of DNA containing inverted repeat sequences capable of buckling to form a base-paired loop with either strand or both strands of previously linear, helical DNA. 

Yes. After the RNA polymerase transcribes the inverted repeat sequence, it is the ability of this region to form a hairpin in the single-strand transcript that is responsible, at least in part, for termination of the chain. 

One more interesting structure, also representing an unusual metal-binding center, is the DNA cruciform (or four-way junction) structure. This type of structure results from rearrangement of palindromes (inverted repeat sequences) and may be formed reversibly under certain conditions (e.g. to relax strain in supercoiled DNA). The relative efficiency of different divalent metal ions in promoting the formation of DNA cruciform structures is Mg + > Mn + > Co + >... 

Base sequence of (a) the DNA of the E. coli trp operon at which transcription termination occurs and of (b) the y terminus of the mRNA molecule. The inverted-repeat sequence is indicated by reversed arrows. The mRNA molecule is folded to form a stem-and-loop structure. 

Two classes of constitutive lac mutants that result in expression of the lac operon even in the absence of inducer (A) The lac operator mutants that change the nucleotide sequence within the Lac repressor binding site, a region that contains an inverted repeat sequence. (B) The lac repressor (LacI) mutants that alter the amino-acid sequence within the DNA binding domain of the Lac repressor and thereby disrupt DNA binding function. 

Mechanism of transcriptional derepression of the lac operon by IPTG. Note that the Lac repressor binds to the lac operator as a tetramer, which is shown here schematically as two dimers binding the inverted repeat sequences. 

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... 

Class I elements (Figure 25.35) encode a transposase but not a resolvase, and are of two types. The simplest is called an insertion sequence (IS), which consists simply of a gene for transposase, flanked by two short inverted repeat sequences of about 15 to 25 base pairs. A less simple structure, called a composite transposon, consists of a protein-encoding gene, such as a gene conferring antibiotic resistance, flanked by two insertion sequences, or IS-like elements. These elements may be in either identical or inverted orientations. 

Flanking these structural genes are two direct repeats, the long terminal repeats (LTRs) of about 250 to 1400 base pairs each. Each LTR is flanked in turn by short inverted repeat sequences, 5 to 13 base pairs in length. Integration occurs by a mechanism that duplicates the target site, so that the integrated viral sequence, called a provirus, is flanked by direct repeats of host cell DNA (5 to 13 base pairs each). 

Because symmetry is a recurring theme for protein-DNA interactions, the DNA sequence may have functional importance. One possibility is that the DNA sequence could be a binding site for a dimeric regulatory protein. Alternatively, inverted repeat sequences sometimes serve as hot spots for genetic rearrangements because they may form hairpin secondary structures that block DNA polymerases or are processed by structure-specific endonucleases. 

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