Propargylamino modified bases for DNA duplex stabilisation
Propargylamino modified bases for DNA duplex stabilisation
Inherited diversity in the human genome leads to phenotypic variations that underlie an individual’s response to their environment. By typing these differences, referred to as single nucleotide polymorphisms, on a whole genome basis, it is hoped that the complex genetic basis of susceptibility to common diseases can be elucidated.
Herein is described the basis of a potential assay for the determination of single nucleotide polymorphisms on a whole genome basis. Initial studies were focused on the ability of a resin bead to support oligonucleotide and peptide synthesis, oligonucleotide duplex formation and identification of a peptide by mass spectrometry from a minimum number of beads. Poor hybridisation kinetics led to a synthetic investigation into the ability to modify the properties of the oligonucleotides to improve the kinetics and thermodynamics of duplex association. Hereinafter, it is shown that the propargylamino or 3-aminoprop-1-yne group stabilises DNA duplexes when placed at the C-5 position in pyrimidines and C-7 position in 7-deazapurines.
At physiological pH, the cationic propargylamine group, when introduced into an oliognucleotide, helps to reduce the repulsion between the anions on the phosphodiester backbone and therefore reduces the salt dependence of duplex formation. The alkyne moiety increases the geometrical overlap and therefore the dispersion forces in single and double stranded DNA. The novel heterocyclic base 7-amino-1-ynyl-7-deaza-2,6-diaminopurine, when base paired with dT, has a similar thermodynamic stability to a G.C base pair. This novel adenine analogue may therefore by useful in applications where Tm harmonisation would be an advantage.
University of Southampton
Booth, James Alexander
1e9bd35d-cc5b-4944-bd6c-b4eea0ff1b73
2004
Booth, James Alexander
1e9bd35d-cc5b-4944-bd6c-b4eea0ff1b73
Booth, James Alexander
(2004)
Propargylamino modified bases for DNA duplex stabilisation.
University of Southampton, Doctoral Thesis.
Record type:
Thesis
(Doctoral)
Abstract
Inherited diversity in the human genome leads to phenotypic variations that underlie an individual’s response to their environment. By typing these differences, referred to as single nucleotide polymorphisms, on a whole genome basis, it is hoped that the complex genetic basis of susceptibility to common diseases can be elucidated.
Herein is described the basis of a potential assay for the determination of single nucleotide polymorphisms on a whole genome basis. Initial studies were focused on the ability of a resin bead to support oligonucleotide and peptide synthesis, oligonucleotide duplex formation and identification of a peptide by mass spectrometry from a minimum number of beads. Poor hybridisation kinetics led to a synthetic investigation into the ability to modify the properties of the oligonucleotides to improve the kinetics and thermodynamics of duplex association. Hereinafter, it is shown that the propargylamino or 3-aminoprop-1-yne group stabilises DNA duplexes when placed at the C-5 position in pyrimidines and C-7 position in 7-deazapurines.
At physiological pH, the cationic propargylamine group, when introduced into an oliognucleotide, helps to reduce the repulsion between the anions on the phosphodiester backbone and therefore reduces the salt dependence of duplex formation. The alkyne moiety increases the geometrical overlap and therefore the dispersion forces in single and double stranded DNA. The novel heterocyclic base 7-amino-1-ynyl-7-deaza-2,6-diaminopurine, when base paired with dT, has a similar thermodynamic stability to a G.C base pair. This novel adenine analogue may therefore by useful in applications where Tm harmonisation would be an advantage.
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Published date: 2004
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Local EPrints ID: 466960
URI: http://eprints.soton.ac.uk/id/eprint/466960
PURE UUID: a1ff223b-3286-4d59-8e38-348fdacf5719
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Date deposited: 05 Jul 2022 08:04
Last modified: 16 Mar 2024 20:53
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Author:
James Alexander Booth
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