Enhanced Diagnostic Tools
The ability to cross link bases in double or triple stranded DNA or cross link bases in oligonucleotides with proteins or other types of molecules is essential for probing of nucleic acid secondary structure or the study of protein-nucleic acid complex. The example of using psoralen, an intercalator cross link bases into an oligonucleotide permits site-specific targeting of the cross-link into double-stranded and triple-stranded DNA. Halogenated bases is another class of UV cross linking modified bases used for probing the molecular structure of protein-DNA complexes. Bio-Synthesis offers cross-linker bases modifications which can be incorporated into 5’, 3’ or internally.
Contact Bio-Synthesis for oligonucleotide modification for cross linking.
Cross-linker base modifications generally fall into two categories, nucleic acid intercalators (for example, psoralen) and halogenated bases (for example, 5-Br-dC). Psoralen is one of the most commonly used intercalator cross-linkers used to probe nucleic acid secondary structure at specific sites with thymidine in both duplex and triplex DNA. Psoralen can form either monoadducts with one adjacent thymidine or diadducts with two thymidines when particular UV wavelength are used to cross-link in duplex DNA1. The Intercalation occurs on the same or complementary strands. For triplex DNA, psoralen C6-modified homopyrimidine oligos are used to bind to a complementary homopurine-homopyrimidine duplex, thereby forming a triplex that can be cross-linked together at the triplex-duplex junction point2. Psoralen-modified oligos have been used to demonstrate the existence of triple-helix-directed gene modification and nucleotide excision repair mechanism in DNA interstrand cross-link repair3-4.
Halogenated bases are another type of UV cross-linker bases used for probing molecular structure of protein-DNA complexes. 5-Br-dC and 5-Br-dG have been incorporated into dG-dC oligos capable of easily changing into the Z-conformation. This property allowed oligos to function as probes for detecting and studying Z-DNA binding proteins5. Substituting 5-Br-dU at several thymine positions of oligos allowed them to be used to characterize the binding of Nuclear Factor BA1 with DNA6.
Oligonucleotides are stable in solution at 4oC for up to 2 weeks. Properly reconstituted material stored at -20oC should be stable for at least 6 months. Dried DNA (when kept at -20oC) in a nuclease-free environment should be stable for years.