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Hairpin and parallel quartet structures for telomeric sequences

Balagurumoorthy, P and Brahmachari, Samir K and Mohanty, Debasisa and Bansal, Manju and Sasisekharan, V (1992) Hairpin and parallel quartet structures for telomeric sequences. In: Nucleic Acids Research, 20 (15). pp. 4061-4067.

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The role of thymine residues in the formation of G-quartet structures for telomeric sequences has been investigated using model oligonucleotides of the type d$(G_4T_nG_44)$, with n = 1–4. Sequences d$(G_4T_3G_4)$ and d$(G_4T_4G_4)$ adopt a G-quartet structure formed by hairpin dimerization in 70 mM NaCI as judged by a characteristic circular dichrolsm signature with a 295 nm positive and 265 nm negative bands while d$(G_4T G_4)$ adopts a parallel G-quartet structure like d(G12) which exhibits a strong positive band at 260 nm and a negative band at 240 nm. The sequence d$(G_4T_2G_4)$ exhibits a mixture of both conformations. The stability of hairpin G-quartet structures decreases with decrease in the number of Intervening thymine residues. Potassium permanganate, a single strand specific probe has been used to establish the presence of loops composed of T residues in the hairpin G quartet structures formed by the oligonucleotides d$(G_4T_nG_4)$ with n = 2 – 4 in 70 mM NaCI. The formation of hairpin G quartet structure for the above sequences is further supported by the enhanced electrophoretic mobility observed on non-denaturing polyacrylamide gels. Human telomeric sequence d$(TTAGGG)_4$ which showed enhanced electrophoretic mobility like Tetrahymena telomeric sequence d$(T_2G_4)4 also exhibited a characteristic CD spectrum for a folded-back G-quartet structure. A detailed model for G-quartet structure involving hairpin dimer with alternating synanti-synanti conformation for the guanine residues both along the chain as well as around the G tetrad with at least two thymine residues in the loop is proposed. Intermolecular association of short telomeric sequences reported here provides a possible model for chromosomal pairing.

Item Type: Journal Article
Publication: Nucleic Acids Research
Publisher: Oxford University Press
Additional Information: Copyright of this article belongs to Oxford University Press
Keywords: Hairpin;parallel quartet structures;telomeric sequences
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 23 Feb 2008
Last Modified: 27 Aug 2008 13:09
URI: http://eprints.iisc.ac.in/id/eprint/12852

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