Targeting of nucleic acid junctions: addressing to a branch point an oligodeoxynucleotide conjugated with an intercalator

OM Ali; T Franch; K Gerdes; EB Pedersen

doi:10.1093/nar/26.21.4919

Targeting of nucleic acid junctions: addressing to a branch point an oligodeoxynucleotide conjugated with an intercalator

OM Ali, T Franch, K Gerdes, EB Pedersen

8 Citations (Scopus)

Abstract

It is possible to enhance targeting of a DNA stem flank domain with a complementary DNA when it is conjugated with diphenyl ether at the branch point, The nucleoside 2'-deoxy-5-methyl-N-4-(4-phenoxyphenyl)cytidine (5) was synthesized from thymidine by tritylation, acetylation, amination via 2,4,6-trimethylbenzenesulfonyl activation and subsequent de-protection. When a three-way junction is formed with a bulged nucleoside 5 at the branch point, the thermal melting temperature was increased by 9 degrees C when compared with wild-type DNA, When hybridizing to one of the flanks at a stem allowing coaxial stacking to the stem, modification at the branch point resulted in Delta T-m = 5,8 degrees C, For targeting to RNA the results were more ambiguous. RNase H activity was observed in some cases when an intercalating aromatic ring was addressed at the branch point. RNase H activity was observed even for a short 7mer ODN.

Original language	English
Journal	Nucleic Acids Research
Volume	26
Issue number	21
Pages (from-to)	4919-4924
Number of pages	6
ISSN	0305-1048
DOIs	https://doi.org/10.1093/nar/26.21.4919
Publication status	Published - 1998
Externally published	Yes

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10.1093/nar/26.21.4919

Cite this

@article{e57da9bacc9943b494e347e1ac460441,

title = "Targeting of nucleic acid junctions: addressing to a branch point an oligodeoxynucleotide conjugated with an intercalator",

abstract = "It is possible to enhance targeting of a DNA stem flank domain with a complementary DNA when it is conjugated with diphenyl ether at the branch point, The nucleoside 2'-deoxy-5-methyl-N-4-(4-phenoxyphenyl)cytidine (5) was synthesized from thymidine by tritylation, acetylation, amination via 2,4,6-trimethylbenzenesulfonyl activation and subsequent de-protection. When a three-way junction is formed with a bulged nucleoside 5 at the branch point, the thermal melting temperature was increased by 9 degrees C when compared with wild-type DNA, When hybridizing to one of the flanks at a stem allowing coaxial stacking to the stem, modification at the branch point resulted in Delta T-m = 5,8 degrees C, For targeting to RNA the results were more ambiguous. RNase H activity was observed in some cases when an intercalating aromatic ring was addressed at the branch point. RNase H activity was observed even for a short 7mer ODN.",

author = "OM Ali and T Franch and K Gerdes and EB Pedersen",

year = "1998",

doi = "10.1093/nar/26.21.4919",

language = "English",

volume = "26",

pages = "4919--4924",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "21",

}

TY - JOUR

T1 - Targeting of nucleic acid junctions: addressing to a branch point an oligodeoxynucleotide conjugated with an intercalator

AU - Ali, OM

AU - Franch, T

AU - Gerdes, K

AU - Pedersen, EB

PY - 1998

Y1 - 1998

N2 - It is possible to enhance targeting of a DNA stem flank domain with a complementary DNA when it is conjugated with diphenyl ether at the branch point, The nucleoside 2'-deoxy-5-methyl-N-4-(4-phenoxyphenyl)cytidine (5) was synthesized from thymidine by tritylation, acetylation, amination via 2,4,6-trimethylbenzenesulfonyl activation and subsequent de-protection. When a three-way junction is formed with a bulged nucleoside 5 at the branch point, the thermal melting temperature was increased by 9 degrees C when compared with wild-type DNA, When hybridizing to one of the flanks at a stem allowing coaxial stacking to the stem, modification at the branch point resulted in Delta T-m = 5,8 degrees C, For targeting to RNA the results were more ambiguous. RNase H activity was observed in some cases when an intercalating aromatic ring was addressed at the branch point. RNase H activity was observed even for a short 7mer ODN.

AB - It is possible to enhance targeting of a DNA stem flank domain with a complementary DNA when it is conjugated with diphenyl ether at the branch point, The nucleoside 2'-deoxy-5-methyl-N-4-(4-phenoxyphenyl)cytidine (5) was synthesized from thymidine by tritylation, acetylation, amination via 2,4,6-trimethylbenzenesulfonyl activation and subsequent de-protection. When a three-way junction is formed with a bulged nucleoside 5 at the branch point, the thermal melting temperature was increased by 9 degrees C when compared with wild-type DNA, When hybridizing to one of the flanks at a stem allowing coaxial stacking to the stem, modification at the branch point resulted in Delta T-m = 5,8 degrees C, For targeting to RNA the results were more ambiguous. RNase H activity was observed in some cases when an intercalating aromatic ring was addressed at the branch point. RNase H activity was observed even for a short 7mer ODN.

U2 - 10.1093/nar/26.21.4919

DO - 10.1093/nar/26.21.4919

M3 - Journal article

SN - 0305-1048

VL - 26

SP - 4919

EP - 4924

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 21

ER -