Triplex formation by a psoralen-conjugated oligodeoxyribonucleotide containing the base analog 8-oxo-adenine

Paul S. Miller, Guixia Bi, Sarah A. Kipp, Victor Fok, Robert K. DeLong

Research output: Contribution to journalArticle

Abstract

Oligodeoxyribonucleotides containing thymidine and 8-oxo-2'-deoxyadenosine can form pyr·pur·pyr type triplexes with double-stranded DNA. Unlike triplexes whose third strands contain thymidine and deoxycytidine, the stability of these triplexes is independent of pH. We have prepared d-ps-TAAATAAATTTTTAT-L [I(A)], where A is 8-oxo-2'-deoxyadenosine, ps is 4'-hydroxymethyl-4,5),8-trimethylpsorale and L is a 6-amino-2-(hydroxymethyl)hexyl linker. The oligomer is designed to interact with a homopurine sequence in the promoter region of the human gene coding for the 92 kDa form of collagenase type IV. Oligomer I(A) and oligomer I(C), which contains 2'-deoxycytidine in place of 8-oxo-2'-deoxycytidine, both form stable triplexes at pH 6.2, but only I(A) forms a stable triplex with a model duplex DNA target at pH 7.5, as determined by UV melting experiments. Triplex formation is stabilized by the presence of the psoralen group. Upon irradiation both I(A) and I(C) form photoadducts with the DNA target at pH 6.2, but only I(A) forms a photoadduct at pH 7.5. In these photoreactions oligomer I(A) appears to selectively form a photoadduct with a C in the purine-rich strand of the duplex target. Although a T residue is present in the pyrimidine-rich strand of the target at the duplex/triplex junction, essentially no adduct formation takes place with this strand, nor is interstrand cross-linking observed. The extent of photoadduct formation decreases with increasing temperature, behavior which is consistent with the UV melting curve of the triplex. A tetramethylrhodamine derivative of I(A) was prepared and found to cross-link less extensively than I(A) itself. Oligomer I(A) is completely resistant to hydrolysis when incubated for 24 h in the presence of 10% fetal bovine serum at 37°C, although it is hydrolyzed by S1 nuclease. The properties of oligomer I(A) suggest that 8-oxo-containing oligomers may find utility as antigene oligonucleotide reagents.

Original languageEnglish (US)
Pages (from-to)730-736
Number of pages7
JournalNucleic Acids Research
Volume24
Issue number4
DOIs
StatePublished - 1996

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Ficusin
Oligodeoxyribonucleotides
Adenine
Deoxycytidine
Thymidine
Freezing
DNA
Matrix Metalloproteinase 9
Genetic Promoter Regions
Oligonucleotides
Hydrolysis
Temperature
Serum
Genes

ASJC Scopus subject areas

  • Genetics

Cite this

Triplex formation by a psoralen-conjugated oligodeoxyribonucleotide containing the base analog 8-oxo-adenine. / Miller, Paul S.; Bi, Guixia; Kipp, Sarah A.; Fok, Victor; DeLong, Robert K.

In: Nucleic Acids Research, Vol. 24, No. 4, 1996, p. 730-736.

Research output: Contribution to journalArticle

Miller, Paul S. ; Bi, Guixia ; Kipp, Sarah A. ; Fok, Victor ; DeLong, Robert K. / Triplex formation by a psoralen-conjugated oligodeoxyribonucleotide containing the base analog 8-oxo-adenine. In: Nucleic Acids Research. 1996 ; Vol. 24, No. 4. pp. 730-736.
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abstract = "Oligodeoxyribonucleotides containing thymidine and 8-oxo-2'-deoxyadenosine can form pyr·pur·pyr type triplexes with double-stranded DNA. Unlike triplexes whose third strands contain thymidine and deoxycytidine, the stability of these triplexes is independent of pH. We have prepared d-ps-TAAATAAATTTTTAT-L [I(A)], where A is 8-oxo-2'-deoxyadenosine, ps is 4'-hydroxymethyl-4,5),8-trimethylpsorale and L is a 6-amino-2-(hydroxymethyl)hexyl linker. The oligomer is designed to interact with a homopurine sequence in the promoter region of the human gene coding for the 92 kDa form of collagenase type IV. Oligomer I(A) and oligomer I(C), which contains 2'-deoxycytidine in place of 8-oxo-2'-deoxycytidine, both form stable triplexes at pH 6.2, but only I(A) forms a stable triplex with a model duplex DNA target at pH 7.5, as determined by UV melting experiments. Triplex formation is stabilized by the presence of the psoralen group. Upon irradiation both I(A) and I(C) form photoadducts with the DNA target at pH 6.2, but only I(A) forms a photoadduct at pH 7.5. In these photoreactions oligomer I(A) appears to selectively form a photoadduct with a C in the purine-rich strand of the duplex target. Although a T residue is present in the pyrimidine-rich strand of the target at the duplex/triplex junction, essentially no adduct formation takes place with this strand, nor is interstrand cross-linking observed. The extent of photoadduct formation decreases with increasing temperature, behavior which is consistent with the UV melting curve of the triplex. A tetramethylrhodamine derivative of I(A) was prepared and found to cross-link less extensively than I(A) itself. Oligomer I(A) is completely resistant to hydrolysis when incubated for 24 h in the presence of 10{\%} fetal bovine serum at 37°C, although it is hydrolyzed by S1 nuclease. The properties of oligomer I(A) suggest that 8-oxo-containing oligomers may find utility as antigene oligonucleotide reagents.",
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AU - DeLong, Robert K.

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N2 - Oligodeoxyribonucleotides containing thymidine and 8-oxo-2'-deoxyadenosine can form pyr·pur·pyr type triplexes with double-stranded DNA. Unlike triplexes whose third strands contain thymidine and deoxycytidine, the stability of these triplexes is independent of pH. We have prepared d-ps-TAAATAAATTTTTAT-L [I(A)], where A is 8-oxo-2'-deoxyadenosine, ps is 4'-hydroxymethyl-4,5),8-trimethylpsorale and L is a 6-amino-2-(hydroxymethyl)hexyl linker. The oligomer is designed to interact with a homopurine sequence in the promoter region of the human gene coding for the 92 kDa form of collagenase type IV. Oligomer I(A) and oligomer I(C), which contains 2'-deoxycytidine in place of 8-oxo-2'-deoxycytidine, both form stable triplexes at pH 6.2, but only I(A) forms a stable triplex with a model duplex DNA target at pH 7.5, as determined by UV melting experiments. Triplex formation is stabilized by the presence of the psoralen group. Upon irradiation both I(A) and I(C) form photoadducts with the DNA target at pH 6.2, but only I(A) forms a photoadduct at pH 7.5. In these photoreactions oligomer I(A) appears to selectively form a photoadduct with a C in the purine-rich strand of the duplex target. Although a T residue is present in the pyrimidine-rich strand of the target at the duplex/triplex junction, essentially no adduct formation takes place with this strand, nor is interstrand cross-linking observed. The extent of photoadduct formation decreases with increasing temperature, behavior which is consistent with the UV melting curve of the triplex. A tetramethylrhodamine derivative of I(A) was prepared and found to cross-link less extensively than I(A) itself. Oligomer I(A) is completely resistant to hydrolysis when incubated for 24 h in the presence of 10% fetal bovine serum at 37°C, although it is hydrolyzed by S1 nuclease. The properties of oligomer I(A) suggest that 8-oxo-containing oligomers may find utility as antigene oligonucleotide reagents.

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