Oligonucleotides base composition

Resolution of a mixture of oligonucleotides of 15, 16, 17 and 18 nucleotides long, (b) Resolution of two oligonucleotides each of 18 nucleotides but differing in base composition. Peak 1 is TCACAGTCTGATCTCACC. Peak 2 is TCACAGTCTGATCTC-GAT. 

W.I. Wood, J. Gitschier, L.A. Lasky, R.M. Lawn, Base Composition-independent Hybridization in Tetrame thy-lammonium Chloride A Method for Oligonucleotide Screening of Highly Complex Gene Libraries , Proc. Natl. Acad. Sci. USA, 82(6), 1585-1588 (1985). 

The RNA oligomers studied by these authors [115, 116] are several evolved sequences (hepatitis delta virus), synthetic polymers (poly-U), and various random RNA sequences. The random sequences are obtained from the HDV sequence by a permutation of the nucleotides in which base composition is fixed [115, 116]. The lengths of all RNA oligonucleotide fragments are 85 nucleotides [115, 116],... 

High-resolution in situ STM as well as phase transition dynamics of nucleobases on Au(lll) and other low-index electrode surfaces supported by infrared spectroscopy have been reviewed recently by Nichols and coworkers [142] and Wandlowski and coworkers [143]. We refer to these reviews for details and note instead another aspect of single-molecule dynamics of DNA-based molecules. The observed electronic conductivity of oligonucleotides of variable length and variable base composition has opened almost a Pandora s box of novel DNA-based electronic properties. These include particularly photochemical and interfacial electrochemical ET. We refer to other recent reviews [144, 145] for this, still far from settled, issue but note the following STM-based studies that illuminate the conductivity issue at the single-molecule level (Figure 2.4). 

Figure I. I. Analysis of termini a number of sequences, shown as lelranudeolides and numbered 1 to 5, are roeogni ed and split with diflcreni K, (and/or V, A indicated by K. Ki, etc. Terminal and penultimate nucleotides were isolated from the resulting oligonucleotides, and their base compositions (sec Fig, 1.2) were determined, (From Bernardi et al.. I ," ),...

In order to quantitate protein capture and binding capacity in the TBA coated capillary, eluate was collected after each step (load, wash, and elnte), and total amonnts of protein in each were determined using flnorescence spectroscopy. The experiment was also performed using a bare (unmodified) capillary and a capillary coated with an oligonucleotide that has the same base composition as the TBA bnt in a scrambled sequence that does not form a G-qnadrnplex strnctnre and does not bind with thrombin (Bock et ah, 1992). The resnlts (Table 11.1) showed that the aptamer-coated capillary captures approximately three times as much thrombin as the bare and scrambled oligonucleotide-coated capillaries. The scrambled oligonucleotide yielded no more captnre than the bare snrface, indicating that thrombin capture at the TBA surface is due to specific affinity interactions. Since thrombin capture occurs only if the TBA is in the G-qnadrnplex conformation, we conld further conclude that the immobilized TBA at the surface is able to form the G-quadruplex. 

Figure 4. Genotyping ofHLA-DQaPCR Product, Type 1.1. Seven primers, comprising four different masses containing 5-mass shifting labels (dB)2 and (dC3) (where n=2 or 3), were selected to type HLA PCR product, each primer terminating one base upstream from the site to be typed. Primer PI did not overlap any of these additional polymorphic sites in the target DNA, but primers P2, P5, and P8 did overlap an additional polymorphism. Primers P2, P5, and P8 ere synthesised as pairs of the same sequence, except for two bases indicated by underlining, one at the 5 end and another at the polymorphic position. An additional terminal 5 base was selected and added to each oligonucleotide sequence in the pair, so that each primer in the pair was of the same base composition and mass.

The r,n of a hybrid generally depends on the salt concentration of the buffer and washing solutions, and also on the base composition. For perfectly matched oligonucleotides of between 11 and 22 nucleotides the can be found from the Wallace rule 1) ... 

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