DNA A-motif

Both lambda Cro and repressor proteins have a specific DNA-binding motif... 

Figure 8.15 Sequence-specific protein-DNA interactions provide a general recognition signal for operator regions in 434 bacteriophage, (a) In this complex between 434 repressor fragment and a synthetic DNA there are two glutamine residues (28 and 29) at the beginning of the recognition helix in the helix-turn-helix motif that provide such interactions with the first three base pairs of the operator region.

Structural studies of a repressor-DNA complex have shown that helices 4 and 5 form a helix-turn-helix motif and that side chains from the recognition helix 5 form water-mediated interactions with bases in the major groove. 

Harrison, S.C., Aggarwal, A.K. DNA recognition by proteins with the helix-tum-helix motif. Anna. Rev. Biochem. 59 933-969, 1990. 

Dimerization of the Ce-zinc cluster transcription factors involves an a-helical coiled coil in the dimerization region. Coiled coils, often called leucine zippers, are also found in a large group of transcription factors that do not contain zinc. The leucine zipper is made up of two a helices in a coiled coil with every seventh residue leucine or some other large hydrophobic residue, such as isoleucine or valine. Leucine zipper transcription factors (b/zip) include factors characterized by heterodimerization, for example Fos and Jun. The a-helical DNA-binding motifs of the heterodimers recognize quite different base sequences and are continous with the a helices of the zipper. 

Nuclear factor kappa B (NF-kB) is the generic term for a family of dimeric eukaryotic transcription factors, composed of members of the Rel family of DNA-binding proteins including the mammalian proteins RelA (or p65), cRel, RelB, p50 and p52, and the Drosophila proteins Dorsal, Dif and Relish. These proteins bind with different affinities to a consensus DNA sequence motif (called the kB site) consisting of the sequence 5 -GGGRNNYYCC-3 in which R is a purine, Y is a pyrimidine, and N is any base. 

FIG. 13 Synthetic DN A motifs for the construction of DNA framework Three- [75] (13) and four-arm (14) DNA junction [8] DNA double-crossover (DX) molecules 15,16 were used for initial studies of enzymatic oligomerization [79]. The DX motif 17, containing four cohesive ends of individual nucleotide sequence, was used for the construction of two-dimensional DNA crystals [80]. 

Wang Y, Griffith J. The ((G/C)3NN)n motif a common DNA repeat that excludes nucleosomes. Proc Natl Acad Sci USA 1996 93 8863-8867. 

The principles whereby a chain of nueleosomes can compact to form a 30 nm chromatin fiber are still not well understood. Nevertheless, important aspects of this process are becoming clear from imaging studies, employing both ECM and SFM. When isolated chicken erythrocyte chromatin or chromatin reconstituted onto six tandem 208 bp nucleosome positioning units were examined by ECM, a linker DNA stem-like architectural motif was observed at the entry-exit sites (Fig. 4) [30]. Particles consistent with an octamer are surrounded with 1.7 turns of DNA, a linker... 

Fig. 8 Schematic representation of DNA junctions and crossover tiles. Motif 1 is a branched DNA junction with three arms and motif 2 with four arms. Every terminal in the arm is an unpaired ssDNA. The ssDNA acts as sticky ends , which may pair with another complementary strand. The two motifs 3 and 4 are two different antiparallel double-crossover molecules containing an even number of half-helical turns between branch points (DAE) or an odd number (DAO). They are more stable and thus usually applied. Oligonucleotide strands are individually represented with different colors...

Applying short ssDNA strands that selectively interact with a specific part of a molecular device is another method to make the device move. A robust rotary device was developed based on multiple crossover motifs [91]. The motivity of the device was the reversible binding of DNA strands. The central axis consists of a couple of ssDNA sections. The conformation of the two ssDNA strands can readily be switched between a PX conformation and its topoisomer conformation. The ssDNA strand replacement can cause the interconversion between the two conformations, and results in an 180° rotation of the end of one strand. This work showed that a rotary nanomechanical device is capable of being cycled by the addition of strands that direct its structure (Fig. 12a). As an application of the DNA nanodevice, a unique DNA nanomechanical device that enables the positional synthesis of products whose sequences are determined by the state of the device has been... 

Several crystal structure analyses of individual repressors and of repressor-operator complexes disclosed a recurrent template on the protein side. It consists of an a-helix/turn/a-helix motif with an almost invariant glycine in the turn region [707-710]. Most of the repressors so far investigated display such a motif but the interactions with the operator DNA, which occur in the major groove are individually different. Here we consider more closely the well-documented complexes between the N-terminal fragment of the repressor from phage 434 and its specific operator DNA [711], and the ternary complex formed between tryptophan repressor, tryptophan and DNA [712, 713]. 

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