DNA triple helix formation at homopurine sites interrupted by pyrimidine residues
DNA triple helix formation at homopurine sites interrupted by pyrimidine residues
Blocks of alternating G·TA and T·AT triplets can be stabilised when anchored to an adjacent block of eleven T·AT triplets. For example, the duplex A11(AT)6·(AT)6T11 can be recognised by the oligonucleotide T11(TG)6. These results have been extended to examine triplexes in which the alternating or anchoring regions have been made longer or shorter. An anchoring region of 11 X T·ATs allows formation of up to 11XT·AT/G·TA pairs, shorter stabilising tails generate less stable triplexes. The nature of the terminal triplet affects stability: T·AT is preferable to a G·TA. These triplexes are further stabilised by incorporating isolated numbers of C+·GC triplets in the anchoring region. For example, the triplex formed at AAAGAG(AT)6 is very stable in the absence of a triplex stabilising ligand, whereas a similar site without these 2 charged triplets does not form a triplex.
The effects of relocating a single G·TA at different positions within a 17mer triplex have been studied using quantitative footprinting. These reveal greatest triplex stability when G·TA occupies the central position. Lower stability is observed with G·TA at either the 5' or 3' ends, with the 3'-end complex being marginally more stable. The preferred triplets for flanking G·TA or T·CG show that T·AT on either side of these triplets is best; a single C+vGC on either side gives intermediate stability, and poorest stability is seen with 2 flanking C+·GCs.
Lastly, the charged base analogue propargylamino-dU (P) has been used to promote triplex formation at sites which otherwise require a stabilising ligand. The rank order of stability with P residues is TPTG > TC+GP > PC+GP > PC+GT. Incorporating C+ and P residues within one complex is most effective when these triplets are separated by uncharged triplets. The results with this base analogue extend stable triplex formation to sites in which 25% of the target sequence contains pyrimidines.
University of Southampton
1998
Gowers, Darren Matthew
(1998)
DNA triple helix formation at homopurine sites interrupted by pyrimidine residues.
University of Southampton, Doctoral Thesis.
Record type:
Thesis
(Doctoral)
Abstract
Blocks of alternating G·TA and T·AT triplets can be stabilised when anchored to an adjacent block of eleven T·AT triplets. For example, the duplex A11(AT)6·(AT)6T11 can be recognised by the oligonucleotide T11(TG)6. These results have been extended to examine triplexes in which the alternating or anchoring regions have been made longer or shorter. An anchoring region of 11 X T·ATs allows formation of up to 11XT·AT/G·TA pairs, shorter stabilising tails generate less stable triplexes. The nature of the terminal triplet affects stability: T·AT is preferable to a G·TA. These triplexes are further stabilised by incorporating isolated numbers of C+·GC triplets in the anchoring region. For example, the triplex formed at AAAGAG(AT)6 is very stable in the absence of a triplex stabilising ligand, whereas a similar site without these 2 charged triplets does not form a triplex.
The effects of relocating a single G·TA at different positions within a 17mer triplex have been studied using quantitative footprinting. These reveal greatest triplex stability when G·TA occupies the central position. Lower stability is observed with G·TA at either the 5' or 3' ends, with the 3'-end complex being marginally more stable. The preferred triplets for flanking G·TA or T·CG show that T·AT on either side of these triplets is best; a single C+vGC on either side gives intermediate stability, and poorest stability is seen with 2 flanking C+·GCs.
Lastly, the charged base analogue propargylamino-dU (P) has been used to promote triplex formation at sites which otherwise require a stabilising ligand. The rank order of stability with P residues is TPTG > TC+GP > PC+GP > PC+GT. Incorporating C+ and P residues within one complex is most effective when these triplets are separated by uncharged triplets. The results with this base analogue extend stable triplex formation to sites in which 25% of the target sequence contains pyrimidines.
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Published date: 1998
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Local EPrints ID: 463431
URI: http://eprints.soton.ac.uk/id/eprint/463431
PURE UUID: d67457ec-b0ae-4289-95e9-b43efb1bbe57
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Date deposited: 04 Jul 2022 20:51
Last modified: 04 Jul 2022 20:51
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Author:
Darren Matthew Gowers
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