Spacer modifications in oligonucleotides involve the introduction of non-nucleotide linkers between nucleotides or at specific positions within the oligo sequence. These spacers serve various functions and confer several advantages in oligonucleotide design and applications. Here are some key functions of spacer modifications:

1.Enhanced flexibility: Spacer modifications can increase the flexibility of oligonucleotides by introducing flexible linker molecules between nucleotides. This increased flexibility can improve the accessibility of oligos to their target molecules and enhance binding kinetics.

2.Reduced steric hindrance: Spacers can alleviate steric hindrance between adjacent functional groups or molecules, particularly in complex hybridization reactions involving bulky molecules or secondary structures. By providing additional space between nucleotides, spacers can improve hybridization efficiency and specificity.

3.Prevention of steric clashes: Spacers can prevent steric clashes between functional groups within the oligonucleotide sequence or between the oligo and other biomolecules. This is particularly important in applications such as molecular beacon probes or aptamer-based sensors, where structural integrity is crucial for proper function.

4.Modulation of backbone flexibility: Spacer modifications can alter the backbone flexibility of oligonucleotides, affecting their conformational dynamics and interactions with target molecules. This modulation can influence the stability, specificity, and binding kinetics of oligonucleotide-target complexes.

5.Facilitation of conjugation: Spacers can provide attachment points for conjugation of various functional moieties, such as fluorophores, quenchers, affinity tags, or therapeutic payloads. By introducing spacers at specific positions within the oligonucleotide sequence, conjugation sites can be strategically placed to minimize interference with hybridization or biological activity.

6.Improvement of nuclease resistance: Certain spacer modifications can enhance the nuclease resistance of oligonucleotides by sterically hindering access of nucleases to the phosphodiester backbone. This can prolong the half-life of oligos in biological environments and improve their stability for therapeutic or diagnostic applications.

7.Regulation of oligonucleotide properties: Spacer modifications allow for fine-tuning of oligonucleotide properties such as solubility, charge, hydrophobicity, and conformational flexibility. By selecting appropriate spacer molecules and incorporating them at specific positions within the oligo sequence, researchers can tailor oligonucleotide characteristics to suit particular applications.

Overall, spacer modifications play a crucial role in oligonucleotide design and optimization, enabling improved performance and expanded functionality in a wide range of biotechnological and biomedical applications.

GenCefe provides customized DNA oligo modification/labeling services, including more than 100 modifications such as biotin, digoxigenin, phosphate, thiol, sulfhydryl, amino, special bases, and a variety of fluorescent groups. 100% of the delivered modified probes/primers have passed mass spectrometry detection to ensure accuracy and purity, meeting the needs of scientific research and industrial-grade modified primers/probes.