Use of a thiol tether for the site-specific attachment of reporter groups to DNA

Control of A Double Helix DNA Assembly by Use of Cross-Linked Oligonucleotides

“…Because the linker of each diastereomer orients in a different direction during duplex formation, the modified duplexes having the different diastereochemistry of the phosphorus atoms show different duplex forming activities. 5,6 In this experiment, the similar stereochemical effect in the formation of the DNA assemblies was observed, and all the assemblies containing the B-diastereomer were thermally more stable than those with the A-diastereomer. These results indicate that the B-diastereomers are advantageous for connecting two double helixes with less steric hindrance than the A-counterparts.…”

Control of A Double Helix DNA Assembly by Use of Cross-Linked Oligonucleotides

“…Because the linker of each diastereomer orients in a different direction during duplex formation, the modified duplexes having the different diastereochemistry of the phosphorus atoms show different duplex forming activities. 5,6 In this experiment, the similar stereochemical effect in the formation of the DNA assemblies was observed, and all the assemblies containing the B-diastereomer were thermally more stable than those with the A-diastereomer. These results indicate that the B-diastereomers are advantageous for connecting two double helixes with less steric hindrance than the A-counterparts.…”

Novel Phosphoramidite Monomer for the Site-Selective Incorporation of a Diastereochemically Pure Phosphoramidate to Oligonucleotide

“…The smaller stabilization in the present case is associated with the restricted rotation of the tethers around the phosphoramidate linkage. A similar argument has been made for the modified oligonucleotides, in which a pyrene is attached to an internal phosphorothioate …”

“…A similar argument has been made for the modified oligonucleotides, in which a pyrene is attached to an internal phosphorothioate. 19 The hypochromicity of the oligonucleotide-Acr(A) on duplex formation (31% at 424 nm when the ratio of the two DNAs is 1:1) is larger than the value of the Bdiastereomer (22%). The red shift (5 nm) of the former is also larger than that (2 nm) for the latter (see Figure 5).…”

Four-Way-Branched DNA−Porphyrin Conjugates for Construction of Four Double-Helix-DNA Assembled Structures

“…Because the spacing of 10 bases between the two linkers of the porphyrin connectors corresponds to one helical turn, the linkers can be placed on the same side of the duplex for alignment. A cystamine tether was introduced via a phosphoramidate linkage according to the reported method. 7b-d, Two adjacent diastereomer peaks appeared on HPLC, and the faster and slower eluting diastereomers are denoted as diastereomers A and B, respectively (Figure S2, Supporting Information). 7b-d The sequences of the synthetic oligonucleotides are CGGCTpACTCC ( 1 ) and GTGCTpAGCGG ( 2 ), with p denoting the position of a phosphoramidate where a linker of the porphyrin derivative is attached.…”

Control of A Double Helix DNA Assembly by Use of Cross-Linked Oligonucleotides

“…Because the linker of each diastereomer orients in a different direction during duplex formation, the modified duplexes having the different diastereochemistry of the phosphorus atoms show different duplex forming activities. 5,6 In this experiment, the similar stereochemical effect in the formation of the DNA assemblies was observed, and all the assemblies containing the B-diastereomer were thermally more stable than those with the A-diastereomer. These results indicate that the B-diastereomers are advantageous for connecting two double helixes with less steric hindrance than the A-counterparts.…”

Novel Phosphoramidite Monomer for the Site-Selective Incorporation of a Diastereochemically Pure Phosphoramidate to Oligonucleotide

“…The smaller stabilization in the present case is associated with the restricted rotation of the tethers around the phosphoramidate linkage. A similar argument has been made for the modified oligonucleotides, in which a pyrene is attached to an internal phosphorothioate …”

“…A similar argument has been made for the modified oligonucleotides, in which a pyrene is attached to an internal phosphorothioate. 19 The hypochromicity of the oligonucleotide-Acr(A) on duplex formation (31% at 424 nm when the ratio of the two DNAs is 1:1) is larger than the value of the Bdiastereomer (22%). The red shift (5 nm) of the former is also larger than that (2 nm) for the latter (see Figure 5).…”

Four-Way-Branched DNA−Porphyrin Conjugates for Construction of Four Double-Helix-DNA Assembled Structures

“…Because the spacing of 10 bases between the two linkers of the porphyrin connectors corresponds to one helical turn, the linkers can be placed on the same side of the duplex for alignment. A cystamine tether was introduced via a phosphoramidate linkage according to the reported method. 7b-d, Two adjacent diastereomer peaks appeared on HPLC, and the faster and slower eluting diastereomers are denoted as diastereomers A and B, respectively (Figure S2, Supporting Information). 7b-d The sequences of the synthetic oligonucleotides are CGGCTpACTCC ( 1 ) and GTGCTpAGCGG ( 2 ), with p denoting the position of a phosphoramidate where a linker of the porphyrin derivative is attached.…”

Control of A Double Helix DNA Assembly by Use of Cross-Linked Oligonucleotides

“…Because the linker of each diastereomer orients in a different direction during duplex formation, the modified duplexes having the different diastereochemistry of the phosphorus atoms show different duplex forming activities. 5,6 In this experiment, the similar stereochemical effect in the formation of the DNA assemblies was observed, and all the assemblies containing the B-diastereomer were thermally more stable than those with the A-diastereomer. These results indicate that the B-diastereomers are advantageous for connecting two double helixes with less steric hindrance than the A-counterparts.…”

Novel Phosphoramidite Monomer for the Site-Selective Incorporation of a Diastereochemically Pure Phosphoramidate to Oligonucleotide

“…The smaller stabilization in the present case is associated with the restricted rotation of the tethers around the phosphoramidate linkage. A similar argument has been made for the modified oligonucleotides, in which a pyrene is attached to an internal phosphorothioate …”

“…A similar argument has been made for the modified oligonucleotides, in which a pyrene is attached to an internal phosphorothioate. 19 The hypochromicity of the oligonucleotide-Acr(A) on duplex formation (31% at 424 nm when the ratio of the two DNAs is 1:1) is larger than the value of the Bdiastereomer (22%). The red shift (5 nm) of the former is also larger than that (2 nm) for the latter (see Figure 5).…”

Four-Way-Branched DNA−Porphyrin Conjugates for Construction of Four Double-Helix-DNA Assembled Structures

“…Because the spacing of 10 bases between the two linkers of the porphyrin connectors corresponds to one helical turn, the linkers can be placed on the same side of the duplex for alignment. A cystamine tether was introduced via a phosphoramidate linkage according to the reported method. 7b-d, Two adjacent diastereomer peaks appeared on HPLC, and the faster and slower eluting diastereomers are denoted as diastereomers A and B, respectively (Figure S2, Supporting Information). 7b-d The sequences of the synthetic oligonucleotides are CGGCTpACTCC ( 1 ) and GTGCTpAGCGG ( 2 ), with p denoting the position of a phosphoramidate where a linker of the porphyrin derivative is attached.…”