Oligo(2′-O-methyl)ribonucleotides Effective probes for duplex DNA

Miho Shimizu; Aritomo Konishi; Yasuaki Shimada; Hideo Inoue; Eiko Ohtsuka

doi:10.1016/0014-5793(92)80428-J

Oligo(2′-O-methyl)ribonucleotides Effective probes for duplex DNA

Miho Shimizu, Aritomo Konishi, Yasuaki Shimada, Hideo Inoue, Eiko Ohtsuka

Hokkaido University

Research output: Contribution to journal › Article › peer-review

108 Scopus citations

Abstract

To find novel probes for duplex DNA, we prepared four types of triplexes containing a homopurine-homopyrimidine 15-mer duplex DNA, and examined their thermal stabilities (T_m values). The single strands used for triplex formation were a DNA 15-mer having a defined C-T mixed sequence, and its sugar-modified analogs, namely 2′-fluoro DNA, RNA, and 2′-O-methyl RNA. The 2′-O-methyl RNA and the RNA-containing triplexes were similar in their enhanced stabilities at pH 6.1 and, amongst the four triplexes, the 2′-O-methyl was the most stable at pH 5.0. Furthermore, an experiment using a 34-mer duplex DNA suggested that the 2′-O-methyl RNA-triplex was destabilized, mostly as a result of the incorporation of a mismatched triplet, as compared to the DNA triplex counterpart. Thus, 2′-O-methyl RNA can serve as an effective probe for duplex DNA.

Original language	English
Pages (from-to)	155-158
Number of pages	4
Journal	FEBS Letters
Volume	302
Issue number	2
DOIs	https://doi.org/10.1016/0014-5793(92)80428-J
State	Published - 11 May 1992
Externally published	Yes

Keywords

2′-O-Methyl RNA probe
Duplex DNA
Native polyacrylamide gel electrophoresis
Sugar modification
T value
Triplex formation

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10.1016/0014-5793(92)80428-J

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title = "Oligo(2′-O-methyl)ribonucleotides Effective probes for duplex DNA",

abstract = "To find novel probes for duplex DNA, we prepared four types of triplexes containing a homopurine-homopyrimidine 15-mer duplex DNA, and examined their thermal stabilities (Tm values). The single strands used for triplex formation were a DNA 15-mer having a defined C-T mixed sequence, and its sugar-modified analogs, namely 2′-fluoro DNA, RNA, and 2′-O-methyl RNA. The 2′-O-methyl RNA and the RNA-containing triplexes were similar in their enhanced stabilities at pH 6.1 and, amongst the four triplexes, the 2′-O-methyl was the most stable at pH 5.0. Furthermore, an experiment using a 34-mer duplex DNA suggested that the 2′-O-methyl RNA-triplex was destabilized, mostly as a result of the incorporation of a mismatched triplet, as compared to the DNA triplex counterpart. Thus, 2′-O-methyl RNA can serve as an effective probe for duplex DNA.",

keywords = "2′-O-Methyl RNA probe, Duplex DNA, Native polyacrylamide gel electrophoresis, Sugar modification, T value, Triplex formation",

author = "Miho Shimizu and Aritomo Konishi and Yasuaki Shimada and Hideo Inoue and Eiko Ohtsuka",

year = "1992",

month = may,

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doi = "10.1016/0014-5793(92)80428-J",

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T1 - Oligo(2′-O-methyl)ribonucleotides Effective probes for duplex DNA

AU - Shimizu, Miho

AU - Konishi, Aritomo

AU - Shimada, Yasuaki

AU - Inoue, Hideo

AU - Ohtsuka, Eiko

PY - 1992/5/11

Y1 - 1992/5/11

N2 - To find novel probes for duplex DNA, we prepared four types of triplexes containing a homopurine-homopyrimidine 15-mer duplex DNA, and examined their thermal stabilities (Tm values). The single strands used for triplex formation were a DNA 15-mer having a defined C-T mixed sequence, and its sugar-modified analogs, namely 2′-fluoro DNA, RNA, and 2′-O-methyl RNA. The 2′-O-methyl RNA and the RNA-containing triplexes were similar in their enhanced stabilities at pH 6.1 and, amongst the four triplexes, the 2′-O-methyl was the most stable at pH 5.0. Furthermore, an experiment using a 34-mer duplex DNA suggested that the 2′-O-methyl RNA-triplex was destabilized, mostly as a result of the incorporation of a mismatched triplet, as compared to the DNA triplex counterpart. Thus, 2′-O-methyl RNA can serve as an effective probe for duplex DNA.

AB - To find novel probes for duplex DNA, we prepared four types of triplexes containing a homopurine-homopyrimidine 15-mer duplex DNA, and examined their thermal stabilities (Tm values). The single strands used for triplex formation were a DNA 15-mer having a defined C-T mixed sequence, and its sugar-modified analogs, namely 2′-fluoro DNA, RNA, and 2′-O-methyl RNA. The 2′-O-methyl RNA and the RNA-containing triplexes were similar in their enhanced stabilities at pH 6.1 and, amongst the four triplexes, the 2′-O-methyl was the most stable at pH 5.0. Furthermore, an experiment using a 34-mer duplex DNA suggested that the 2′-O-methyl RNA-triplex was destabilized, mostly as a result of the incorporation of a mismatched triplet, as compared to the DNA triplex counterpart. Thus, 2′-O-methyl RNA can serve as an effective probe for duplex DNA.

KW - 2′-O-Methyl RNA probe

KW - Duplex DNA

KW - Native polyacrylamide gel electrophoresis

KW - Sugar modification

KW - T value

KW - Triplex formation

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U2 - 10.1016/0014-5793(92)80428-J

DO - 10.1016/0014-5793(92)80428-J

M3 - 記事

C2 - 1633847

AN - SCOPUS:0026590969

SN - 0014-5793

VL - 302

SP - 155

EP - 158

JO - FEBS Letters

JF - FEBS Letters

IS - 2

ER -

Oligo(2′-O-methyl)ribonucleotides Effective probes for duplex DNA

Abstract

Keywords

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