Sequence-specific recognition of double helical RNA and RNA·DNA by triple helix formation

Hogyu Han, P. B. Dervan

Research output: Contribution to journalArticle

156 Citations (Scopus)

Abstract

The stabilities of eight triple helical pyrimidine · purine · pyrimidine structures comprised of identical sequence but different RNA (R) or DNA (D) strand combinations were measured by quantitative affinity cleavage titration. The differences in equilibrium binding affinities reveal the importance of strand composition. For the sequences studied here, the stabilities of complexes containing a pyrimidine third strand D or R and purine·pyrimidine double helical DD, DR, RD, and RR decrease in order: D + DD, R + DD, R + DR, D + DR > R + RD, R + RR >> D + RR, D + RD (pH 7.0, 25°C, 100 mM NaCl/1 mM spermine). These findings suggest that RNA and DNA oligonucleotides will be useful for targeting (i) double helical DNA and (ii) RNA·DNA hybrids if the purine Watson-Crick strand is DNA. However, RNA, but not DNA, oligonucleotides will be useful for sequence-specific binding of (i) double helical RNA and (ii) RNA·DNA hybrids if the purine Watson-Crick strand is RNA. This has implications for the design of artificial ligands targeted to specific sequences of double helical RNA and RNA·DNA hybrids.

Original languageEnglish
Pages (from-to)3806-3810
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Volume90
Issue number9
Publication statusPublished - 1993 Jan 1
Externally publishedYes

Fingerprint

RNA
DNA
Oligonucleotides
Spermine
Ligands
pyrimidine
purine

ASJC Scopus subject areas

  • General
  • Genetics

Cite this

@article{7e3cf1db09ca42c79b5bdf22add68835,
title = "Sequence-specific recognition of double helical RNA and RNA·DNA by triple helix formation",
abstract = "The stabilities of eight triple helical pyrimidine · purine · pyrimidine structures comprised of identical sequence but different RNA (R) or DNA (D) strand combinations were measured by quantitative affinity cleavage titration. The differences in equilibrium binding affinities reveal the importance of strand composition. For the sequences studied here, the stabilities of complexes containing a pyrimidine third strand D or R and purine·pyrimidine double helical DD, DR, RD, and RR decrease in order: D + DD, R + DD, R + DR, D + DR > R + RD, R + RR >> D + RR, D + RD (pH 7.0, 25°C, 100 mM NaCl/1 mM spermine). These findings suggest that RNA and DNA oligonucleotides will be useful for targeting (i) double helical DNA and (ii) RNA·DNA hybrids if the purine Watson-Crick strand is DNA. However, RNA, but not DNA, oligonucleotides will be useful for sequence-specific binding of (i) double helical RNA and (ii) RNA·DNA hybrids if the purine Watson-Crick strand is RNA. This has implications for the design of artificial ligands targeted to specific sequences of double helical RNA and RNA·DNA hybrids.",
author = "Hogyu Han and Dervan, {P. B.}",
year = "1993",
month = "1",
day = "1",
language = "English",
volume = "90",
pages = "3806--3810",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
number = "9",

}

TY - JOUR

T1 - Sequence-specific recognition of double helical RNA and RNA·DNA by triple helix formation

AU - Han, Hogyu

AU - Dervan, P. B.

PY - 1993/1/1

Y1 - 1993/1/1

N2 - The stabilities of eight triple helical pyrimidine · purine · pyrimidine structures comprised of identical sequence but different RNA (R) or DNA (D) strand combinations were measured by quantitative affinity cleavage titration. The differences in equilibrium binding affinities reveal the importance of strand composition. For the sequences studied here, the stabilities of complexes containing a pyrimidine third strand D or R and purine·pyrimidine double helical DD, DR, RD, and RR decrease in order: D + DD, R + DD, R + DR, D + DR > R + RD, R + RR >> D + RR, D + RD (pH 7.0, 25°C, 100 mM NaCl/1 mM spermine). These findings suggest that RNA and DNA oligonucleotides will be useful for targeting (i) double helical DNA and (ii) RNA·DNA hybrids if the purine Watson-Crick strand is DNA. However, RNA, but not DNA, oligonucleotides will be useful for sequence-specific binding of (i) double helical RNA and (ii) RNA·DNA hybrids if the purine Watson-Crick strand is RNA. This has implications for the design of artificial ligands targeted to specific sequences of double helical RNA and RNA·DNA hybrids.

AB - The stabilities of eight triple helical pyrimidine · purine · pyrimidine structures comprised of identical sequence but different RNA (R) or DNA (D) strand combinations were measured by quantitative affinity cleavage titration. The differences in equilibrium binding affinities reveal the importance of strand composition. For the sequences studied here, the stabilities of complexes containing a pyrimidine third strand D or R and purine·pyrimidine double helical DD, DR, RD, and RR decrease in order: D + DD, R + DD, R + DR, D + DR > R + RD, R + RR >> D + RR, D + RD (pH 7.0, 25°C, 100 mM NaCl/1 mM spermine). These findings suggest that RNA and DNA oligonucleotides will be useful for targeting (i) double helical DNA and (ii) RNA·DNA hybrids if the purine Watson-Crick strand is DNA. However, RNA, but not DNA, oligonucleotides will be useful for sequence-specific binding of (i) double helical RNA and (ii) RNA·DNA hybrids if the purine Watson-Crick strand is RNA. This has implications for the design of artificial ligands targeted to specific sequences of double helical RNA and RNA·DNA hybrids.

UR - http://www.scopus.com/inward/record.url?scp=0027168393&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0027168393&partnerID=8YFLogxK

M3 - Article

C2 - 7683407

AN - SCOPUS:0027168393

VL - 90

SP - 3806

EP - 3810

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 9

ER -