Sequence context

CpG stands for cytosine phosphate guanine dinucleotide in a particular sequence context. CpG motifs are responsible for proliferative effects of antisense oligonucleotides, particularly with respect to B-lymphocytes. Die optimal immune-stimulatory consensus sequence surrounding CpG is R1R2CGY1Y2, where R1 is a purine (mild preference for G), R2 is a purine or T (preference for A), and Y1 and Y2 are pyrimidines (preference for T). 

Fig. 3.6 Polyamide-DNA binding motifs targeting longer DNA sequences. Overlapped and slipped homodimers depending on the sequence context, six-ring polyamides with central p-Ma residues can bind to DNA as fully overlapped homodimers, recognizing 11 bp, or as slipped homodimers, recognizing 13 bp. Extended hairpin extended conformation increases binding site size (to 9 bp) and enhances binding affinity. Cooperative dimer a cooperatively binding hairpin polyamide can...

Thompson, A. J., E. T. Thome et al. (2004). Complementation of notabilis, an abscisic acid-deficient mutant of tomato Importance of sequence context and utility of partial complementation. Plant Cell Environ. 27(4) 459 171. 

U. Knckelkorn, E.A. Ferreira, 1. Drung, U. Eiewer, P.M. Kloetzel, and M. Theobald, The effect of the interferon-y indncible processing machinery on the generation of a naturally tumor-associated human cytotoxic T lymphocyte epitope within a wild type and mntant p53 sequence context, Eur. J. Immunol., 1368-1375 (2002). 

Dunham, S.U. and Lippard, S.J. (1997) DNA sequence context and protein composition modulate HMG-domain protein recognition of cisplatin-modified DNA. Biochemistry 36, 11428-11436. 

Transglutaminases can recognize a broad range of primary amine acyl-acceptor substrates in vitro. However, recognition of the acyl-donor substrate in vivo is restricted to the y-carboxyamide of glutamine within an apparently relatively small subset of sequence contexts... 

The mRNA of eucaryotes does not possess specific initiation sequences. Rather, the AUG start codon is identified by scanning the eucaryotic mRNA the 408 subunit of the ribosome threads the 5 non-translated end of the mRNA and uses the first AUG codon encoimtered to initiate translation. Whether a AUG codon is used as an initiator depends, additionally, upon the sequence context. If the sequence environment is unfavorable for initiation, then the scanning is continued and initiation occurs at one of the next AUG. With the help of this leaky scanning" strategy it is possible to produce proteins with different N-termini from the same mRNA. 8ince there are often signal sequences foimd at the N-terminus, this mechanism may lead to alternative com-partmentalization of a protein. 

Rodriguez H, Loechler EL. 1993. Mutational specificity of the (+) - anti-diol epoxide of benzo [a] pyrine in a supF gene of an Escherichia coli plasmid DNA sequence context influences hotspots, mutagenic specificity and the extent of SOS enhancements of mutagenesis. Carcinogenesis 14(3) 373-383. 

Incorporation of selenocysteyl-tRNASer into protein in response to the UGA codon requires SELB (the protein product of the selB gene in E. coli). SELB is homologous in sequence to EF-Tu and probably replaces it in translation by specifically recognizing selenocysteyl-tRNA and UGA in the appropriate sequence context. Selenocysteyl-tRNASer, in combination with SELB, must be capable of competing with termination factors for the translation of the termination codon when it occurs in the right context of bases. This process is known as site-specific variation in translation elongation. 

Table 2.1. Sequence context of mutation types and their frequencies observed after application of error-prone PCR as described herein and sequencing of cloned genes. Targets T7 RNAP, coding sequence of T7 RNA polymerase, Poll, coding sequence of E. coli DNA polymerase I, Inti on, cDNA of Tetrahymena thermophila intron,...

Contrary to H-bonded nucleic acid base pairs discussed in the previous section, the nature of intermolecular interactions in complexes of stacked bases was analyzed more extensively. The values of minimal, maximal, and average total stabilization energies, corrected for BSSE, for a set comprising over 80 stacked bases, are plotted in Fig. 20.1. In the case of guanine-adenine and adenine-cytosine complexes, the results are presented for two sequence contexts, i.e., A/G-G/A and A/C-C/A. The symbol AA denotes the 2-oxo-adenine - complexes of oxidized bases, and this... 

Finally, the sequence context of the Pt-DNA adduct can have a significant impact on the strength of the protein-DNA interaction [ 134]. In a study... 

Thus, it appears that mutagenesis induced by cisplatin in vivo shows a correlation with the theoretical DNA-binding sites of the drug but can also be influenced by the sequence context of the adducts as well as the chromatin structure of the DNA region. 

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