SIMA phosphoramidite, 6-isomer | CAS 1411797-05-1

SIMA phosphoramidite, 6-isomer is a nucleic-acid building block designed for automated oligonucleotide synthesis, enabling the incorporation of a SIMA-derived functionality into DNA or RNA strands. This reagent format is commonly used in fluorescence labeling and nucleic-acid probe development workflows where a defined dye/handle is installed at a specific position during solid-phase synthesis, supporting downstream conjugation and imaging assay construction. Researchers typically select this phosphoramidite isomer to tune labeling placement and performance in nucleic-acid-based fluorescence experiments.

1. Oligonucleotide Fluorescent Labeling

SIMA phosphoramidite, 6-isomer is used by molecular biology and chemical biology groups to introduce a SIMA-related labeling handle directly into oligonucleotides during automated synthesis. This positional incorporation is particularly valuable when fluorescent readouts must be tied to a specific nucleotide location, such as in hybridization probes, strand displacement constructs, or labeled primers for fluorescence-based nucleic acid workflows. The resulting labeled oligonucleotides are then used in fluorescence microscopy, plate-based fluorescence assays, and other nucleic-acid imaging formats where controlled dye placement helps standardize probe behavior across batches.

2. Molecular Beacon Probe Construction

SIMA phosphoramidite, 6-isomer supports the development of fluorescence molecular beacons and related hairpin probes by allowing dye functionality to be built into the probe sequence during synthesis. In these designs, a labeled oligonucleotide can report target-dependent fluorescence changes upon hybridization, enabling real-time monitoring of nucleic acid interactions in assay development settings. Probe developers often rely on phosphoramidite incorporation to place the fluorophore/handle at a defined position relative to the stem and loop regions, improving reproducibility when screening beacon architectures for hybridization assays.

3. Fluorescent FRET Oligonucleotide Systems

SIMA phosphoramidite, 6-isomer is incorporated into donor/acceptor oligonucleotide constructs used for FRET-based nucleic acid sensing and reporting. Teams building FRET probe pairs for nucleic acid hybridization, strand displacement, or amplification-adjacent readouts benefit from the ability to install the SIMA-derived functionality at a predetermined site within the sequence. This enables systematic optimization of fluorophore spacing and labeling geometry, which is a key practical consideration when engineering FRET signal changes for fluorescence-based nucleic acid analysis platforms.

4. Labeled Primer And Probe Assay Development

SIMA phosphoramidite, 6-isomer is frequently used in assay development to generate fluorescently labeled primers and oligonucleotide probes for research-grade nucleic acid analysis workflows. In these applications, the reagent allows consistent incorporation of a SIMA-related labeling element into defined oligo reagents used for fluorescence readouts in hybridization assays, nucleic acid quantification experiments, and imaging-compatible probe panels. Oligonucleotide reagent developers value phosphoramidite-based synthesis control because it supports reproducible probe preparation for method development and comparative studies across different probe sequences.