Synthesis of DNA Oligomers Possessing a Covalently Cross‐Linked Watson–Crick Base Pair Model

Li, Hongyu; Qiu, Yao-Ling; Moyroud, Elisabeth; Kishi, Yoshito

doi:10.1002/1521-3757(20010417)113:8<1519::aid-ange1519>3.0.co;2-#

Cited by 9 publications

(4 citation statements)

References 26 publications

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Section: Introductionmentioning

confidence: 92%

“…[1] In this paper, using n-type DNA oligomers as examples, we present experimental results demonstrating that these oligomers indeed exhibit conformational properties close to those of corresponding native DNA duplexes.For the current studies, we used DNA oligomers I and II, containing an arbitrarily chosen base sequence. [2] To compare the global conformations of I and II with that of the corresponding native DNA duplex III, we first measured their circular dichroism (CD) spectra (Figure 1).…”

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confidence: 89%

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Solution Structure ofn-Type DNA Oligomers Possessing a Covalently Cross-Linked Watson-Crick Base Pair Model

Qiu

Kishi

2001

ChemBioChem

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KEYWORDS:DNA structures´nucleosides´nucleotides´oligonucleotidesẂ atson ± Crick base pairsWe have recently reported a general synthetic route to DNA oligomers containing a covalently cross-linked Watson ± Crick base pair model. [1] In this paper, using n-type DNA oligomers as examples, we present experimental results demonstrating that these oligomers indeed exhibit conformational properties close to those of corresponding native DNA duplexes.For the current studies, we used DNA oligomers I and II, containing an arbitrarily chosen base sequence. [2] To compare the global conformations of I and II with that of the corresponding native DNA duplex III, we first measured their circular dichroism (CD) spectra (Figure 1). [3] These exhibited the distinct characteristics of B-form DNA. [4] Figure 2 summarizes the temperature-dependent CD spectra, yielding the melting temperature (T m ) curves and thermodynamic parameters (Table 1) for Figure 1. CD spectra (10 mM Na 2 HPO 4 (pH 6.8), 0.1 M NaCl; DNA concentration: 40 ± 80 mM) of I and II, in reference to III. Figures A and B show the CD spectra of I and II (solid lines), respectively, in reference to III (broken line). Figure 2.Temperature-dependent CD spectra and melting curves of I ± III (10 mM Na 2 HPO 4 (pH 6.8), 0.1 M NaCl; DNA concentration: 40 ± 80 mM). Figures A ± C show the CD spectra of I ± III, respectively, at the temperatures indicated in Figure A. Figure D presents the melting curves of I ± III at 267 nm. No concentration dependency of T m was detected at 50 versus 150 mM of I.[a] Prof.

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Section: Introductionmentioning

confidence: 92%

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confidence: 89%

Solution Structure ofn-Type DNA Oligomers Possessing a Covalently Cross-Linked Watson-Crick Base Pair Model

Qiu

Kishi

2001

ChemBioChem

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“…In an effort to investigate how repair proteins distinguish interstrand cross-link lesions, the synthesis of clinically relevant interstrand cross-linked duplexes remains important in the armamentarium of DNA repair. Two general approaches have emerged to produce these DNA lesions including the de novo synthesis of unique site-specific ICLs – and the production of hybridization triggered ICLs whereby two complementary oligonucleotides are annealed, one of which contains a reactive cross-linked precursor that covalently links the two strands at a unique site after annealing , .…”

Section: Introductionmentioning

confidence: 99%

Synthesis and Characterization of DNA Containing anN¹-2′-Deoxyinosine-ethyl-N³-thymidine Interstrand Cross-Link: A Structural Mimic of the Cross-Link Formed by 1,3-Bis-(2-chloroethyl)-1-nitrosourea

Wilds

Noronha

2008

Chem. Res. Toxicol.

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Interstrand cross-links, which are generated by chemotherapeutic treatment with bis-alkylating agents, exert their therapeutic effect by connecting the nucleobases of adjacent DNA strands together and represent some of the most threatening forms of damage suffered by genomic DNA. However, one of the reasons for treatment failure using these agents is due to enhanced repair of this DNA damage. The pursuit of understanding the repair of interstrand cross-links by repair systems has necessitated the synthesis of sufficient quantities of such damaged DNA. We report the synthesis of a site-specific interstrand cross-linked duplex containing an ethylene-bridged N (1)-2'-deoxyinosine- N (3)-thymidine base pair prepared by solution and solid-phase synthesis as a mimic for the lesion formed by the therapeutic agent 1,3-bis-(2-chloroethyl)-1-nitrosourea using both a phosphoramidite and a bis-phosphoramidite approach. UV thermal denaturation experiments revealed that this cross-linked duplex was stabilized by 52 degrees C relative to the noncross-linked control, and circular dichroism studies indicated little deviation from a B-form structure compared to a duplex that contained a G-C base pair at the same position. Molecular models of the cross-linked duplex that were geometry optimized using the AMBER forcefield also suggest that this lesion induces minimal distortion in B-form DNA. This modified oligonucleotide will be useful for studies related to the investigation of interstrand cross-linked DNA repair.

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“… Deprotection of the 3′-position of uridine was performed. The support was washed and reinstalled on the synthesizer, and a final DNA-chain elongation was performed in the 5′- to 3′-direction by using reverse nucleoside phosphoramidites (3′-DMTr, 5′-phosphoramidite) ( 19 ) (Scheme 1 , step C). …”

Section: Resultsmentioning

confidence: 99%

Linking two DNA duplexes with a rigid linker for DNA nanotechnology

et al. 2015

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DNA has recently emerged as a promising material for the construction of nanosized architectures. Chemically modified DNA has been suggested to be an important component of such architectural building blocks. We have designed and synthesized a novel H-shaped DNA oligonucleotide dimer that is cross-linked with a structurally rigid linker composed of phenylene and ethynylene groups. A rotatable DNA unit was constructed through the self-assembly of this H-shaped DNA component and two complementary DNA oligonucleotides. In addition to the rotatable unit, a locked DNA unit containing two H-shaped DNA components was also constructed. As an example of an extended locked structure, a hexagonal DNA origami dimer and oligomer were constructed by using H-shaped DNA as linkers.

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Synthesis of DNA Oligomers Possessing a Covalently Cross‐Linked Watson–Crick Base Pair Model

Cited by 9 publications

References 26 publications

Solution Structure ofn-Type DNA Oligomers Possessing a Covalently Cross-Linked Watson-Crick Base Pair Model

Solution Structure ofn-Type DNA Oligomers Possessing a Covalently Cross-Linked Watson-Crick Base Pair Model

Synthesis and Characterization of DNA Containing anN¹-2′-Deoxyinosine-ethyl-N³-thymidine Interstrand Cross-Link: A Structural Mimic of the Cross-Link Formed by 1,3-Bis-(2-chloroethyl)-1-nitrosourea

Linking two DNA duplexes with a rigid linker for DNA nanotechnology

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Synthesis of DNA Oligomers Possessing a Covalently Cross‐Linked Watson–Crick Base Pair Model

Cited by 9 publications

References 26 publications

Solution Structure ofn-Type DNA Oligomers Possessing a Covalently Cross-Linked Watson-Crick Base Pair Model

Solution Structure ofn-Type DNA Oligomers Possessing a Covalently Cross-Linked Watson-Crick Base Pair Model

Synthesis and Characterization of DNA Containing anN1-2′-Deoxyinosine-ethyl-N3-thymidine Interstrand Cross-Link: A Structural Mimic of the Cross-Link Formed by 1,3-Bis-(2-chloroethyl)-1-nitrosourea

Linking two DNA duplexes with a rigid linker for DNA nanotechnology

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Product

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About

Synthesis and Characterization of DNA Containing anN¹-2′-Deoxyinosine-ethyl-N³-thymidine Interstrand Cross-Link: A Structural Mimic of the Cross-Link Formed by 1,3-Bis-(2-chloroethyl)-1-nitrosourea