Custom Minor Groove Binder (MGB) Probe Synthesis

BOC Sciences draws on our expertise and technology to offer a wide range of high-quality diagnostic probes to meet the needs of research and industry from R&D to production.

What are Minor Groove Binder (MGB) Probes?

MGB (Minor Groove Binder) probes are specialized probes for nucleic acid detection and are widely used in nucleic acid amplification techniques such as real-time polymerase chain reaction (real-time PCR). MGB probes are commonly used to detect and measure the presence of target DNA or RNA sequences and are useful for enhancing the specificity and sensitivity of PCR.

Fig 1. Structure and mechanism of action of MGB-probes. (Navarro et al., 2015)

Advantages of MGB Probes

• MGB-modified probes bind to target sequences with increased Tm values of 15-30°C, allowing for the design of shorter probe sequences.
• MGB probes utilize a non-fluorescent quenching group (NFQ), which greatly eliminates the background fluorescence generated by conventional quenching groups and improves the signal-to-noise ratio.
• MGB probes can be used to detect conserved sequences in short fragments, and can also be used to detect SNPs. Generally, the mutation site is designed in the middle 1/3 position of the probe, which can be used to distinguish single-base mutations.
• MGB binds to the minor groove of the DNA double-strand, which stabilizes the AT-rich sequence and reduces the impact of the Tm value of the target sequence on the experiment.

BOC Sciences' MGB Probe Customization Service

The design and synthesis of MGB probes are based on the DNA hybridization chain reaction (HCR), a signal amplification technique based on DNA's catalytic mechanism, in which two DNA single strands of a probe are designed and synthesized to hybridize with each other to form a stem-and-loop structure that triggers the subsequent amplification of the signal. MGB probes, on the other hand, are based on HCR, which adopts a four-stranded structure for the stem of the single strand of probe DNA, thus improving the stability and specificity of the probes.

• MGB Probe Design Services

  
  The design of MGB probes usually combines the dual functions of PCR primer and probe. One end has the function of a PCR primer and the other end contains the MGB structure. In the PCR amplification reaction, when the MGB probe binds to the target DNA or RNA sequence, the presence of MGB enhances the binding strength of the probe to the target sequence, thus improving the specificity and sensitivity of PCR detection.

However, the following factors need to be considered when performing the design process of MGB probes.

• Avoid G at the 5' end of the probe.
• Try to avoid repeated bases, especially G bases.
• The Tm value of the probe should be 8-10°C higher than the primer Tm value.
• Try to shorten the MGB probe to improve specificity.
• When performing SNP detection, in order to detect SNP sites, the SNP sites of the probe should be placed in the middle part as much as possible to avoid non-specific annealing caused by placing it at both ends.

• Custom Synthesis of MGB probes

  
  The custom synthesis service for MGB probes includes three types of MGB-TaqMan probes, MGB-Pleiades probes, and MGB-Eclipse probes.

• TaqMan-MGB Probe Customization

  
  BOC Sciences provides customized TaqMan-MGB probes, which are based on TaqMan probes with MGB attached to the 3' end to act as a hydrolysis probe that is hydrolyzed by Taq enzymes during amplification and releases fluorescent groups to generate signals.

• MGB-Pleiades Probe Customization

  
  BOC Sciences offers customization of MGB-Pleiades probes, which are labeled with a fluorescent group at the 5' end of the Pleiades-MGB probe and attached to MGB, and a quenching group at the 3' end of the Pleiades-MGB probe.

• MGB-Eclipse Probe Customization

  
  The Eclipse-MGB probe is labeled with a quencher group at its 5' end and attached to the MGB, 3' end-labeled with a fluorescent group. The MGB-Eclipse probe customization offered by BOC Sciences combines the MGB chemical cluster with the Eclipse Quencher technology, and is designed to provide high specificity and high signal-to-background ratio for nucleic acid detection.

With our unique supply capabilities, BOC Sciences' laboratories can provide oligonucleotide synthesis with consistent quality at every stage of development. By manufacturing our dye phosphoramidites, CPGs, linker phosphoramidites, etc., we can ensure that projects are scaled up from inception to commercial scale.

Reference

1. Navarro E, et al. Real-time PCR detection chemistry[J]. Clinica chimica acta, 2015, 439: 231-250.