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Complexometric Titration: Ligands

Complexometric Titration: Ligands

Different monodentate and polydentate ligands are used as complexing agents in complexometric titration reactions. The formation of complexes by mono- and bidentate ligands involves two or more intermediate steps, limiting their use as complexing agents. In comparison, polydentate ligands can form complexes with metal ions in a single-step process, facilitating sharper end points. This means polydentate ligands, such as amino carboxylic acid derivatives, are most commonly employed in...

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EDTA titrations are usually carried out in highly basic conditions, where the fully deprotonated form of EDTA, Y4−, actively complexes with the free metal ions in the solution. Several metal ions precipitate as hydrous oxide (hydroxides, oxides, or oxyhydroxides) under these conditions, lowering the concentration of free metal ions in the solution. For this reason, auxiliary complexing agents or ligands such as ammonia, tartrate, citrate, or triethanolamine are used in EDTA titrations to...

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When a nucleophile and an alkyl halide react, nucleophilic substitution and β-elimination reactions compete to generate products.
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Monochrome Multiplex Quantitative PCR Telomere Length Measurement

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Monovalent and divalent salt correction algorithms for Tm prediction--recommendations for Primer3 usage.

Nicolas von Ahsen¹, Carl T Wittwer, Ekkehard Schütz

¹University Hospital Göttingen, Germany.

Briefings in Bioinformatics

|September 28, 2011

Summary

Primer3 primer design software now offers improved melting temperature (T(m)) predictions by updating salt correction formulas. Accurate T(m) prediction is crucial for selecting compatible primer pairs in polymerase chain reaction (PCR).

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Novel Sequence Discovery by Subtractive Genomics

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Published on: January 25, 2019

Area of Science:

Molecular Biology
Bioinformatics

Background:

Primer3 is a key tool for designing oligonucleotide primers for polymerase chain reaction (PCR).
Recent updates to Primer3's web implementation include revised salt correction formulas for improved melting temperature (T(m)) prediction.
Magnesium ions (Mg2+) are essential for PCR and significantly stabilize double-stranded DNA (dsDNA), necessitating accurate salt correction in primer design.

Purpose of the Study:

To evaluate the accuracy of updated salt correction formulas in Primer3 for predicting oligonucleotide melting temperatures (T(m)).
To assess the impact of different salt correction formula combinations on T(m) prediction, particularly in the presence of divalent cations like Mg2+.

Main Methods:

Utilized a dataset of 475 published T(m) values for various oligonucleotides.
Compared T(m) predictions from Primer3 using different monovalent and divalent salt correction formulas.
Evaluated the performance of the implemented conversion of divalent to monovalent cation concentration with various salt correction models.

Main Results:

The updated Primer3 salt correction formulas provide improved T(m) prediction accuracy.
The combination of specific salt correction formulas significantly impacts T(m) prediction, especially with Mg2+ present.
The SantaLucia salt correction formula is recommended for use with Mg2+ in the current Primer3 version.

Conclusions:

Accurate T(m) prediction in Primer3 relies on the appropriate selection and combination of salt correction formulas.
The current Primer3 implementation shows good performance with the SantaLucia formula when Mg2+ is present.
Future Primer3 releases should incorporate the most recent form of the alternative salt correction formula for enhanced accuracy.