Solution structure of oligonucleotides covalently linked to a psoralen derivative

Bornet, Olivier; Prévost, Chantal; Vovelle, F.; Chassignol, Marcel; Thuong, Nguyen T.; Lancelot, G.

doi:10.1093/nar/23.5.788

Cited by 1 publication

(1 citation statement)

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“…Under the ligation conditions used in this paper (30°C-40°C), psoralen cross-linking was unnecessary for maintenance of duplex stability. However, for other applications, cross-linking can be accomplished by exposing the duplex-probe array ‫ן1(‬ SSPE buffer present, array sitting on ice) to long wavelength UV light, wherein the intercalated pso-ralen moiety cross-links the two thymidine bases located on opposing DNA strands (Bornet et al 1995). The optimal UV exposure was 6 J/cm 2 of 365 nm (long UV) applied to the outer glass surface of the DNA array.…”

Section: Synthesis Of Duplex-probe N-mer Dna Arraysmentioning

confidence: 99%

Mutation Detection by Ligation to Complete n-mer DNA Arrays

Gunderson¹,

Huang²,

Morris³

et al. 1998

Genome Res.

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A new approach to comparative nucleic acid sequence analysis is described that uses the ligation of DNA targets to high-density arrays containing complete sets of covalently attached oligonucleotides of length eight and nine. The combination of enzymatic or chemical ligation with a directed comparative analysis avoids many of the intrinsic difficulties associated with hybridization-based de novo sequence reconstruction methods described previously. Double-stranded DNA targets were fragmented and labeled to produce quasirandom populations of 5Ј termini suitable for ligation and detection on the arrays. Kilobase-size DNA targets were used to demonstrate that complete n-mer arrays can correctly verify known sequences and can determine the presence of sequence differences relative to a reference. By use of 9-mer arrays, sequences of 1.2-kb targets were verified with >99.9% accuracy. Mutations in target sequences were detected by directly comparing the intensity pattern obtained for an unknown with that obtained for a known reference sequence. For targets of moderate length (1.2 kb), 100% of the mutations in the queried sequences were detected with 9-mer arrays. For higher complexity targets (2.5 and 16.6 kb), a relatively high percentage of mutations (90% and 66%, respectively) were correctly identified with a low false-positive rate of <0.03 percent. The methods described provide a general approach to analyzing nucleic acid samples on the basis of the interpretation of sequence-specific patterns of hybridization and ligation on complete n-mer oligonucleotide arrays.

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Section: Synthesis Of Duplex-probe N-mer Dna Arraysmentioning

confidence: 99%