Sequencing of oligonucleotides

McGuinness, B. F. Lipman, R. Nakanishi, K. Tomasz, M. J. Reaction of sodium dithionite activated mitomycin C with guanine at non-cross-linkable sequences of oligonucleotides. J. Org. Chem. 1991, 56. 

Sistare, M.F. Codden, S.J. Heimlich, G. Thorp, H.H. Effects of base stacking on guanine electron transfer Rate constants for G and GG sequences of oligonucleotides from catalytic electrochemistry. J. Am. Chem. Soc. 2000, 122, 4742-4749. 

This approach to analyze exonuclease ladders seems to be a particularly promising tool to determine rapidly the sequence of oligonucleotides. Compared to conventional methods, based on the laboratory-scale preparation of a large number of samples at different enzyme and substrate concentrations followed by MALDI-MS analysis, the microfluidics approach offers the advantage of saving time and material. Furthermore, due to the limited sample handling, the risks encountered when manipulating biomolecules are also reduced as well as that of sample contamination. 

Figure 8.7 Modification of oligonucleotides to increase stability, (a) Oligonucleotides (here shown as DNA) with a phosphodiester backbone (X = 0) are rapidly degraded by nucleases. Modification to create phosphorothioate analogs (X = S ) greatly increases half-life, (b) Peptide nucleic acids represent another DNA analog that can be used to bind with complementary sequences of oligonucleotides. Dashed lines represent hydrogen bonding which follows Watson-Crick base pairs.

The automated oligonucleotide synthesizers now enable large-quantity, low-cost synthesis of precisely designed different sequences of oligonucleotide based in a parallel fashion. On the other hand, depending on the specificity of sequences for... 

Mass spectrometry sequencing of oligonucleotides is not as common a practice as it is for proteins and peptides. However, the following mass spectrometry-based sequence determination strategies have gained acceptance ... 

R. P. Glover, G. M. A. Sweetman, P. B. Frama-, and G. C. K. Roberts, Sequencing of oligonucleotides using high performance Uquid chromatography and electrospray mass spectrometry. Rapid Commun. Mass Spectrom. 9, 97-102 (1995). 

Table I. Sequences of oligonucleotides employed in these studies, fl = Fluorescein, su = surface.

Oligonucleotides All oligonucleotides were purchased from Sangon, Inc. (Shanghai, China). The sequences of oligonucleotides are listed as follows (see Note 1) ... 

Table 1.3 The sequences of oligonucleotide substrates for the Suzuki-Miyaura reactions [147]. 

McLafferty, F.W. Rapid Sequencing of Oligonucleotides by High-Resolution Mass Spectrometry. J. Am. Chem. Soc. 1994,116,4893-4897. 

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