These results would indicate that differences in transfer frequency are only related to the nucleotide sequence of the DNA positions on which homologous recombination occurs.
In mammalian genomic DNA, position 5 of the cytosine residue within a cytosine-phosphate-guanine dinucleotide (CpG) motif is methylated, resulting in the formation of 5-methylcytosine [ 7].
DOI: http://dx.doi.org/10.7554/eLife.06516.005 10.7554/eLiFigure16.006 Figure 2 figure supplement 1. Copy number and T-DNA positions of the GFP -tailswap transgene in three independently derived transgenic lines.
For each DNA, the position of the potential promoter (TATA box) sequence TATATAA preceding the ORFs is indicated in Table 2.
However, because all observed intermolecular NOEs are from the bidppz ligand to the sugar protons of the DNA, the position of the bidppz moiety in the minor groove can be well determined.
The number of DNA positions included in each gene partition after using SOAP is indicated in Table 4.
Namely, self-avoidance of DNA, specific positioning of one or few DNA loci (such as origin or terminus) together with the action of DNA compaction proteins (that organize the chromosome into topological domains) are sufficient to get a linear arrangement of the chromosome along the cell axis.
To refine the DNA sequence positions of known cancer-associated breakpoints, we utilized the known sequence coordinates of 387 cancer-associated genes.
For example, in the minor groove of duplex DNA, the positions of the O2 atoms of pyrimidines and the N3 atoms of purines (both hydrogen bond acceptors) are almost identical for all four correct Watson Crick base pairs, but not for mispairs.
At the DNA level, positions of the disease-associated mutations, including substitution, insertion and deletion, as well as SNPs are shown on a set of exon sequences or genomic DNA sequence with/without the open-reading frame for the gene of interest (Fig. 4A).
