FREQUENTLY ASKED TECHNICAL QUESTION
QUESTION: What is the sequence requirement for psoralen mediated cross-linking in double stranded DNA?
RESPONSE:Psoralens are a class of naturally occurring heterocyclic compounds which intercalates between bases in double-stranded or triple stranded DNA. Upon exposure to long wavelength light (350 nm) Psoralen forms covalent linkages to Thymidine (cyclobutane linkage). Psoralen is a bifunctional reagent and can form either a monoadduct, linking one adjacent thymidine on the same or complimentary strand, or a diadduct, linking adjacent thymidines on the same or complimentary strands. Diadducts formed between adjacent thymidines are photoreversable with short wavelength UV light (254 nm).
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Type of Adduct
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Optimal Sequence
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Cross-linking
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Reversing
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Wavelength
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Wavelength
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Monoadduct
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5’-Psoralen-XAX-XXX-
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350 nm
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NA
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Diadduct
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5’-Psoralen-TAX-XXX-
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350 nm
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254 nm
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Note: For adducts between double-stranded DNA use Psoralen C210-1982.
For adducts between triple-stranded DNA use Psoralen C6 which has a longer linker arm 10-1983.
REFERENCE(S):
1. U. Pieles and U. Englisch, Nucleic Acids Res., 1989, 17, 285.
QUESTION: What are the relative extinction coefficients of 5'-Fluorescein, Hex and Tet etc.. at 260 nm and their Lambda max?
RESPONSE:Please see http://www.glenresearch.com/Technical/Extinctions.html
REFERENCE(S):
Oligonucleotide Properties Calculator; http://www.basic.northwestern.edu/biotools/oligocalc.html
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