Combining nucleoside analogues to achieve recognition of oligopurine tracts by triplex-forming oligonucleotides at physiological pH

David A. Rusling; Loic Le Strat; Vicki E. C. Powers; Victoria J. Broughton-Head; James Booth; Oliver Lack; Tom Brown; Keith R. Fox

doi:10.1016/j.febslet.2005.10.056

Combining nucleoside analogues to achieve recognition of oligopurine tracts by triplex-forming oligonucleotides at physiological pH

David A. Rusling, Loic Le Strat, Vicki E. C. Powers, Victoria J. Broughton-Head, James Booth, Oliver Lack, Tom Brown, Keith R. Fox

University Hospital Southampton NHS Foundation Trust

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

Abstract

We have used DNase I footprinting to examine DNA triple helix formation at a 12 base pair oligopurine.oligopyrimidine sequence, using oligonucleotides that contain combinations of 2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine (bis-amino-U, BAU) and 3-methyl-2-aminopyridine (MeP) in place of T and C, respectively. This combination acts cooperatively to enable high affinity triple helix formation at physiological pH. The affinity depends on the number of substitutions and their arrangement; oligonucleotides in which these analogues are evenly distributed throughout the third strand bind much better than those in which they are clustered together.

Original language	English
Pages (from-to)	6616-6620
Number of pages	5
Journal	FEBS Letters
Volume	579
Issue number	29
Early online date	9 Nov 2005
DOIs	https://doi.org/10.1016/j.febslet.2005.10.056
Publication status	Published - 5 Dec 2005

Keywords

Aminopyridines
Base Sequence
DNA/chemistry
DNA Footprinting
Deoxyribonuclease I
Hydrogen-Ion Concentration
Nucleic Acid Conformation
Nucleosides/chemistry
Oligonucleotides/chemistry
Purines/chemistry
Uridine/analogs & derivatives

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10.1016/j.febslet.2005.10.056

Cite this

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title = "Combining nucleoside analogues to achieve recognition of oligopurine tracts by triplex-forming oligonucleotides at physiological pH",

abstract = "We have used DNase I footprinting to examine DNA triple helix formation at a 12 base pair oligopurine.oligopyrimidine sequence, using oligonucleotides that contain combinations of 2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine (bis-amino-U, BAU) and 3-methyl-2-aminopyridine (MeP) in place of T and C, respectively. This combination acts cooperatively to enable high affinity triple helix formation at physiological pH. The affinity depends on the number of substitutions and their arrangement; oligonucleotides in which these analogues are evenly distributed throughout the third strand bind much better than those in which they are clustered together.",

keywords = "Aminopyridines, Base Sequence, DNA/chemistry, DNA Footprinting, Deoxyribonuclease I, Hydrogen-Ion Concentration, Nucleic Acid Conformation, Nucleosides/chemistry, Oligonucleotides/chemistry, Purines/chemistry, Uridine/analogs & derivatives",

author = "Rusling, {David A.} and {Le Strat}, Loic and Powers, {Vicki E. C.} and Broughton-Head, {Victoria J.} and James Booth and Oliver Lack and Tom Brown and Fox, {Keith R.}",

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doi = "10.1016/j.febslet.2005.10.056",

language = "English",

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T1 - Combining nucleoside analogues to achieve recognition of oligopurine tracts by triplex-forming oligonucleotides at physiological pH

AU - Rusling, David A.

AU - Le Strat, Loic

AU - Powers, Vicki E. C.

AU - Broughton-Head, Victoria J.

AU - Booth, James

AU - Lack, Oliver

AU - Brown, Tom

AU - Fox, Keith R.

PY - 2005/12/5

Y1 - 2005/12/5

N2 - We have used DNase I footprinting to examine DNA triple helix formation at a 12 base pair oligopurine.oligopyrimidine sequence, using oligonucleotides that contain combinations of 2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine (bis-amino-U, BAU) and 3-methyl-2-aminopyridine (MeP) in place of T and C, respectively. This combination acts cooperatively to enable high affinity triple helix formation at physiological pH. The affinity depends on the number of substitutions and their arrangement; oligonucleotides in which these analogues are evenly distributed throughout the third strand bind much better than those in which they are clustered together.

AB - We have used DNase I footprinting to examine DNA triple helix formation at a 12 base pair oligopurine.oligopyrimidine sequence, using oligonucleotides that contain combinations of 2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine (bis-amino-U, BAU) and 3-methyl-2-aminopyridine (MeP) in place of T and C, respectively. This combination acts cooperatively to enable high affinity triple helix formation at physiological pH. The affinity depends on the number of substitutions and their arrangement; oligonucleotides in which these analogues are evenly distributed throughout the third strand bind much better than those in which they are clustered together.

KW - Aminopyridines

KW - Base Sequence

KW - DNA/chemistry

KW - DNA Footprinting

KW - Deoxyribonuclease I

KW - Hydrogen-Ion Concentration

KW - Nucleic Acid Conformation

KW - Nucleosides/chemistry

KW - Oligonucleotides/chemistry

KW - Purines/chemistry

KW - Uridine/analogs & derivatives

U2 - 10.1016/j.febslet.2005.10.056

DO - 10.1016/j.febslet.2005.10.056

M3 - Article

C2 - 16293248

SN - 0014-5793

VL - 579

SP - 6616

EP - 6620

JO - FEBS Letters

JF - FEBS Letters

IS - 29

ER -

Combining nucleoside analogues to achieve recognition of oligopurine tracts by triplex-forming oligonucleotides at physiological pH

Abstract

Keywords

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