Technical report: Part 1. Basic requirements for designing optimal oligonucleotide probe sequences

Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations

“…Mitsuhashi (32) suggested an even larger value of β and combined eq 5 with an earlier T m sodium correction function derived by Schildkraut and Lifson (45):…”

“…Mitsuhashi suggested an even larger value of β and combined eq with an earlier T m sodium correction function derived by Schildkraut and Lifson : The accuracy of eq was not reported. Equations − are routinely used for solutions containing magnesium ions in the presence, or absence, of other monovalent ions.…”

“…The “equivalent” Na + concentration is defined as the concentration of sodium ions in a buffer that stabilizes duplexes to the same extent as the magnesium buffer. The following formula was suggested, where concentrations are in mol/L ,, . Effects of magnesium and monovalent ions are assumed to be additive in eq .…”

“…The total concentration of monovalent ions, [Mon + ], is the sum of concentrations of alkali metal and amine cations (Na + , K + , Tris + ). Values from 3.3 to 4.0 have been used for the parameter β ,, . The equivalent [Na + eq ] values are entered into the T m corrections for sodium salts , to correct melting temperatures for magnesium solutions.…”

Polymorphism analysis and gene detection by minisequencing on an array of gel-immobilized primers

“…The melting temperature (T m ) of primers calculated using different formulae (21,22) did not correlate well with the experimental values. In addition, as shown earlier, T m was different for duplexes formed on a microchip and in solution (23).…”