The Experts below are selected from a list of 570 Experts worldwide ranked by ideXlab platform
Anthony T Yeung - One of the best experts on this subject based on the ideXlab platform.
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the reactivity of 4 5 8 Trimethylpsoralen with oligonucleotides containing at sites
Biochemistry, 1994Co-Authors: Muthukumar Ramaswamy, Anthony T YeungAbstract:Pyrimidine bases of duplex DNA, of appropriate sequence context, are photoreactive toward 4,5',8-Trimethylpsoralen in the presence of long-wavelength UV light. It is generally believed that a 5'-AT site is less photoreactive with psoralen than a 5'-TA site. We have compared the reactivities of these two sites using oligonucleotide duplexes of different sequence context and found that 5'-TA and 5'-AT sites are equally reactive in certain sequences. The presence of alternating pyrimidine and purine (5'-PyATPu-3') bases in oligonucleotide duplexes optimizes the reactivity of 4,5',8-Trimethylpsoralen in the 5'-AT sites.
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structure of the dna interstrand cross link of 4 5 8 Trimethylpsoralen
Biochemistry, 1992Co-Authors: Kandallu R Kumaresan, Muthukumar Ramaswamy, Anthony T YeungAbstract:4,5',8-Trimethylpsoralen (TMP) cross-links a 5' TpA or a 5' ApT site by photoreacting with one thymine moiety in each DNA strand. We are interested in whether psoralen interstrand cross-links all share one structure or whether there are significant differences. In this paper, we employed a rapid method for probing the structure of the cross-link by making a series of TMP cross-linked duplexes containing specific base-pair mismatches. The relative stability provided by a base pair can be correlated with neighboring base pairs by comparing the extents of gel retardation when base-pair mismatches happen in each position. From our studies, we infer that with respect to the furan-side strand, the 5'T.A base pair of the two T.A base pairs in the TpA site is not hydrogen bonded. Immediately on each side of the cross-linked TpA site is a highly stabilized base pair. Next, a region of decreased stability occurs in each arm of a cross-linked duplex and these base pairs of least stability are located farther away from the cross-linked thymines as the lengths of the arms of the cross-linked helix increase. Finally, even in 7 M urea at 49 degrees C the cross-linked helix is hydrogen bonded at both ends of a duplex of 22 base pairs. We propose that the structures of interstrand cross-links in DNA vary appreciably with the DNA sequence, the length of the DNA duplex, and the structures of the DNA cross-linking agents.
Muthukumar Ramaswamy - One of the best experts on this subject based on the ideXlab platform.
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the reactivity of 4 5 8 Trimethylpsoralen with oligonucleotides containing at sites
Biochemistry, 1994Co-Authors: Muthukumar Ramaswamy, Anthony T YeungAbstract:Pyrimidine bases of duplex DNA, of appropriate sequence context, are photoreactive toward 4,5',8-Trimethylpsoralen in the presence of long-wavelength UV light. It is generally believed that a 5'-AT site is less photoreactive with psoralen than a 5'-TA site. We have compared the reactivities of these two sites using oligonucleotide duplexes of different sequence context and found that 5'-TA and 5'-AT sites are equally reactive in certain sequences. The presence of alternating pyrimidine and purine (5'-PyATPu-3') bases in oligonucleotide duplexes optimizes the reactivity of 4,5',8-Trimethylpsoralen in the 5'-AT sites.
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structure of the dna interstrand cross link of 4 5 8 Trimethylpsoralen
Biochemistry, 1992Co-Authors: Kandallu R Kumaresan, Muthukumar Ramaswamy, Anthony T YeungAbstract:4,5',8-Trimethylpsoralen (TMP) cross-links a 5' TpA or a 5' ApT site by photoreacting with one thymine moiety in each DNA strand. We are interested in whether psoralen interstrand cross-links all share one structure or whether there are significant differences. In this paper, we employed a rapid method for probing the structure of the cross-link by making a series of TMP cross-linked duplexes containing specific base-pair mismatches. The relative stability provided by a base pair can be correlated with neighboring base pairs by comparing the extents of gel retardation when base-pair mismatches happen in each position. From our studies, we infer that with respect to the furan-side strand, the 5'T.A base pair of the two T.A base pairs in the TpA site is not hydrogen bonded. Immediately on each side of the cross-linked TpA site is a highly stabilized base pair. Next, a region of decreased stability occurs in each arm of a cross-linked duplex and these base pairs of least stability are located farther away from the cross-linked thymines as the lengths of the arms of the cross-linked helix increase. Finally, even in 7 M urea at 49 degrees C the cross-linked helix is hydrogen bonded at both ends of a duplex of 22 base pairs. We propose that the structures of interstrand cross-links in DNA vary appreciably with the DNA sequence, the length of the DNA duplex, and the structures of the DNA cross-linking agents.
Kandallu R Kumaresan - One of the best experts on this subject based on the ideXlab platform.
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structure of the dna interstrand cross link of 4 5 8 Trimethylpsoralen
Biochemistry, 1992Co-Authors: Kandallu R Kumaresan, Muthukumar Ramaswamy, Anthony T YeungAbstract:4,5',8-Trimethylpsoralen (TMP) cross-links a 5' TpA or a 5' ApT site by photoreacting with one thymine moiety in each DNA strand. We are interested in whether psoralen interstrand cross-links all share one structure or whether there are significant differences. In this paper, we employed a rapid method for probing the structure of the cross-link by making a series of TMP cross-linked duplexes containing specific base-pair mismatches. The relative stability provided by a base pair can be correlated with neighboring base pairs by comparing the extents of gel retardation when base-pair mismatches happen in each position. From our studies, we infer that with respect to the furan-side strand, the 5'T.A base pair of the two T.A base pairs in the TpA site is not hydrogen bonded. Immediately on each side of the cross-linked TpA site is a highly stabilized base pair. Next, a region of decreased stability occurs in each arm of a cross-linked duplex and these base pairs of least stability are located farther away from the cross-linked thymines as the lengths of the arms of the cross-linked helix increase. Finally, even in 7 M urea at 49 degrees C the cross-linked helix is hydrogen bonded at both ends of a duplex of 22 base pairs. We propose that the structures of interstrand cross-links in DNA vary appreciably with the DNA sequence, the length of the DNA duplex, and the structures of the DNA cross-linking agents.
Yinsheng Wang - One of the best experts on this subject based on the ideXlab platform.
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structure elucidation of dna interstrand cross link by a combination of nuclease p1 digestion with mass spectrometry
Analytical Chemistry, 2003Co-Authors: Yuesong Wang, Yinsheng WangAbstract:DNA interstrand cross-link reagents are among the most powerful agents for cancer treatment. Here we report a combined nuclease P1 digestion/mass spectrometry method for the structure elucidation of duplex oligodeoxynucleotides (ODNs) containing an interstrand cross-link. Our results demonstrate that nuclease P1 digestion of a double-stranded ODN containing an interstrand cross-link (ICL) of 4,5',8-Trimethylpsoralen or mitomycin C gives a tetranucleotide bearing the cross-linked nucleobase moiety. Product ion spectra of the deprotonated ions of the tetranucleotides provide information about the structure of the cross-link. Furthermore, product-ion spectra of tetranucleotides containing two orientation isomers of mitomycin C interstrand cross-link are distinctive. We believe that the method described in this paper can be generally applicable for investigating the structures of other DNA ICLs.
Akira Murakami - One of the best experts on this subject based on the ideXlab platform.
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synthesis of oligonucleotides containing 4 5 8 Trimethylpsoralen at the 2 o position and their cross linking properties with rnas
Current protocols in human genetics, 2014Co-Authors: Akio Kobori, Asako Yamayoshi, Akira MurakamiAbstract:4,5',8-Trimethylpsoralen-conjugated oligonucleotides have been used in the study of photo-cross-linking with target oligonucleotides and in the field of the photodynamic therapy. This unit describes synthetic procedures for oligonucleotides using 2'-O-methylphosphoramidite units and an adenosine phosphoramidite unit containing a 4,5',8-Trimethylpsoralen derivative attached at the 2' position of an adenosine sugar moiety via an ethoxymethylene linkage. Procedures for obtaining the photo-cross-linking efficiency of 2'-O-methyloligonucleotides containing a 4,5',8-Trimethylpsoralen derivative with a target oligonucleotide under UV irradiation conditions are also described, together with the procedure for preparation of (32)P-radiolabeled RNA.
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synthesis and crosslinking activity of 4 n 4 5 8 Trimethylpsoralen 4 ylmethyl 2 deoxycytidine containing oligodeoxyribonucleotides
Chemistry Letters, 2012Co-Authors: Akio Kobori, Asako Yamayoshi, Tomita Kohji, Yuko Nagae, Akira MurakamiAbstract:Photocrosslinking oligonucleotides have been developed to investigate and control gene functions without damaging living systems. Here, 4-N-(4,5′,8-Trimethylpsoralen-4′-ylmethyl)-2′-deoxycytidine-c...
