Randomized region

Use a word processing program to analyze random sequences for equal occurrence of AA, AC, AG, and AT motifs in the random regions (repeat for C, G, and T). If one or more of these motifs predominate or the base composition is not random in the random sequences, the pool may not contain enough different sequences for a successful SELEX experiment. 

B DNA, randomized Region mi DNA, Primer Binding Site Primer E3 DNA, T7 Promotersequence RNA, randomized Region E3 RNA, Primer Binding Site O Matrix Target... 

In almost every published SELEX protocol, the experiment starts with a pool of chemically synthesized ssDNA. The DNA usually consists of a central randomized region of 20-60 nucleotides that is flanked by two constant regions that are necessary for primer binding. 

The randomized region is obtained by using a mixture of all four bases in each synthesis step. In most cases, the four building blocks are mixed with balanced stoichiometry (IUB mix code N ). However, pools may also be synthesized for the selection of aptamers that contain only three different bases in the randomized region [12] or unequal frequencies of the four bases [13]. 

Variable length random region of modified RNA transcript (25 -200 bases)... 

Tig. 11.10. Z-score distribution for two randomized regions of an Fd fragment (PDB file laqk, chain H). White bars residues 100, 104—106 (part of antigen binding region), black bars residues 153, 180, 182, 184 (in loop of C-terminal half of the chain). The arrow marks the z-score of tire wild type. 

Fig. 3.4.3. Construction of a combinatorial RNA library. First, a DNA template having a random region of N positions between two fixed primer binding sites (primer A and B) is synthesized. AT7 promoter can be introduced...

It is possible to constrain peptides by introducing two codons for cysteine in both sites of the random region. Constraining a peptide in its active conformation is an advantage, but if it is constrained into an incorrect conformation, binding to the target molecule can be prevented. Several peptides have been isolated from cyclic libraries. The screening of pools... 

The cloned sequences often (but not always) have obvious secondary structures in common, leading to visual truncations by which the fixed sequences and other unnecessary sequences from the random regions are eliminated from the aptamer, often resulting in slightly increased affinity over the starting full-length aptamer. When visual truncation is not possible, experimental truncation is done instead. After truncation the aptamer may be further altered by substituting nuclease-resistant purines for the normal... 

Before looking directly at these results, let us first set out a formal combination of helical and random dispersion on the assumption that helical and disordered structures contribute to the total rotatory dispersion in a strictly proportional manner. By this means, the way in which the dispersion parameters may be expected to vary with helical content will become clear. The optical rotation of a mixture of random regions and helical segments within a single molecule can be expressed as the sum of the mean residue rotations for a random coil and a helix, [m ]x and [m ]f, respectively, each weighted according to that fraction, fp or / , of the total number of residues which is embodied in the respective conformation. The net rotation of the mixture is thus... 

Figure 12.14. A SEM image of the film grown on Pt(l 11) for 40h. (A) oriented region and (B) random region [402],...

Fig. 10.12 Nucleotide sequences in the random region of the RNA subunit from the pool obtained after the sixth round of in vitro selection. A possible consensus sequence UGC-GGUAG A indicated bold...

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