Oligomer mismatches

The operation of the mismatch effects may be seen to best advantage when a range of products is possible from a single reactant or set of reactants. The reaction of ethylene oxide with metal salts results in the formation of crown ethers (Fig. 6-30). Obviously, a whole range of different cyclic oligomers and acyclic polymers could be formed from ethylene oxide. If we specifically wanted to obtain 18-crown-6, with a hole size of about 1.4 A, we would expect to use a potassium ion as template (r = 1.38 A). In fact, 18-crown-6 is obtained in good yield from the reaction of ethylene oxide with potassium tetra-fluoroboratc. In contrast, if we wanted 12-crown-4, with a hole size of about 0.8 A, it... 

Melt temperature measurements indicated that the thermodynamic stability of the probe molecules can be adjusted using the oligomer matrix to achieve lower Tm values by as much as 5 °C, with retention of selectivity for discrimination of single base pair mismatches [14]. The enhanced temperature sensitivity may ultimately provide for the development of analytical devices of extremely high selectivity. Devices containing immobilized... 

The luminescence of the hybridized [Ru(phen)2(dppz)]2+ derivative may be used to characterize the molecular assembly (77). Dilution experiments show that intercalation is intramolecular at concentrations <5 mM duplex addition of unmodified duplex to the covalently bound duplex results in <5% change in the luminescence. The results of experiments performed on duplexes containing mismatches in various positions along the duplex are also consistent with intramolecular intercalation. In this series, luminescence is higher for mismatches near the ruthenated end of the oligomer, where the ruthenium complex can intercalate intramolecularly and stabilize the mismatched site. 

The increase of AE with chain length must originate from the difference between the monomer lattice constant and the length of oligomer/polymer repeat unit. Anticipating proportionality between 5AE/5n and lattice mismatch as suggested by studies under pressure (see 5.2), the variation of AE with n can be calculated for arbitrary conversion X from the low conversion value (8AE/8n)x=o ... 

The base analogues 2-amino-6-(2-thienyl)purine and 2-amino-6-(2-furyl)purine (90) have been incorporated into ODN duplexes as potential nonhydrogen bonding base pairs with pyridin-2-one nucleoside. The thienyl derivative opposite pyridin-2-one was more stable than the N -dimethylaminopurine. The 5 -triphosphate derivative of the pyridin-2-one nucleoside was inserted opposite the thienylpurine derivative more efficiently than the natural dNTPs. RNA oligomers have been prepared using the phos-phoramidite monomer derived from 6-trifluoromethylpurine ribonucleoside as potential inhibitors of adenosine deaminase. The presence of the modification was destabilising in an RNA duplex, equivalent to an A-A mismatch. 

Maskos and Southern (1992) designed a linker for the synthesis of oligomers on glass supports which is resistant to ammonia treatment. The system appears to be highly specific in hybridization and sensitive to single mismatches. Their predictable behavior should make this system very useful for hybridization and for the isolation of DNA-binding proteins. 

In most SBH experiments, probe sets are deliberately designed to improve discrimination. The use of probes shorter than 25 bases inherently enhances discrimination. In addition, SBH experiments may use probe molecules with an informative oligomer core of length n surrounded by a few degenerate (variable) bases, e.g. N j-B -N, which helps enhance discrimination [12,19,31]. Using degenerate bases to surround a fixed oligomer core minimizes the problem of end mismatch discrimination because the fixed core is internalized within the probe. 

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