Custom DNA Oligos Modifications

Fluorescent Dyes Labels

The most important fluorescent compounds used to label oligonucleotides are fluorescein and various fluorescein analogs. Fluorescein is a multi-ring aromatic compound that is strongly fluorescent.

* The fluorescent color was calculated with the maximum emission wavelength, for your reference only.

Dual Labels

Dual-labeled fluorescent probes typically contain a 5' fluorophore and a 3' quencher. The probes are often designed to anneal between the upstream and the downstream primer in a PCR reaction. These are commonly used with quantitative PCR, mutation detection, allele determination, and SNP detection.

Quenchers

FRET quenching depends on the ability of the fluorophore to transfer energy to the quencher. In order for this to happen, the emission spectrum of the fluorophore must overlap with the absorption spectrum of the quencher. In order for a quencher to quench fluorescence from several different fluorophores, it must therefore have a wide absorption spectrum and a high extinction coefficient.

Affinity Ligands

Oligonucletides can be labeled with biotin or digoxigenin or directly labeled with alkaline phosphatase. A variety of linker arms are available as spacers to minimize steric hindrance.

Spacers

Spacer modifcations C3, 9, C12 and 18 are used to insert a spacer arm in an oligonucleotide. These modifications can be added in multiple additions when a longer spacer is required.

Attachment moieties

A primary amino group or a thiol group can be used to attach a variety of modifiers (such as fluorescent dyes) to an oligonucleotide or used to attach an oligonucleotide to a solid surface.

TM increase

The stability of the DNA double helix depends on a fine balance of interactions including hydrogen bonds between bases, hydrogen bonds between bases and surrounding water molecules, and base-stacking interactions between adjacent bases. Slight variations in the DNA sequence can have profound implications on the stability of the DNA duplex.