Hairpin and parallel quartet structures for telomeric sequences.
PDF (1.8M)
Journal: 1992/September - Nucleic Acids Research
ISSN: 0305-1048
PUBMED: 1508691
Abstract:
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(G4TnG4), with n = 1-4. Sequences d(G4T3G4) and d(G4T4G4) adopt a G-quartet structure formed by hairpin dimerization in 70 mM NaCl as judged by a characteristic circular dichroism signature with a 295 nm positive and 265 nm negative bands while d(G4TG4) 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(G4T2G4) 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(G4TnG4) with n = 2-4 in 70 mM NaCl. 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(T2G4)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 syn-anti-syn-anti 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.
Open in
PUBMED | PMC | Google Scholar | Wikipedia
Relations:
Content
Citations
(91)
References
(39)
Drugs
(2)
Chemicals
(1)
Organisms
(3)
Processes
(4)
Anatomy
(1)
Affiliates
(1)
Similar articles
Articles by the same authors
Discussion board
Nucleic Acids Res 20(15): 4061-4067
PMID: 1508691

Hairpin and parallel quartet structures for telomeric sequences.

Abstract

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(G4TnG4), with n = 1-4. Sequences d(G4T3G4) and d(G4T4G4) adopt a G-quartet structure formed by hairpin dimerization in 70 mM NaCl as judged by a characteristic circular dichroism signature with a 295 nm positive and 265 nm negative bands while d(G4TG4) 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(G4T2G4) 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(G4TnG4) with n = 2-4 in 70 mM NaCl. 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(T2G4)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 syn-anti-syn-anti 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.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.8M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.
icon of scanned page 4061
4061
icon of scanned page 4062
4062
icon of scanned page 4063
4063
icon of scanned page 4064
4064
icon of scanned page 4065
4065
icon of scanned page 4066
4066
icon of scanned page 4067
4067

Images in this article

Image
Image
on p.4065
Image
Image
on p.4065
Image
Image
on p.4066
Image
Image
on p.4066
Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Blackburn EH, Gall JG. A tandemly repeated sequence at the termini of the extrachromosomal ribosomal RNA genes in Tetrahymena. J Mol Biol. 1978 Mar 25;120(1):33–53. [PubMed] [Google Scholar]
  • Klobutcher LA, Swanton MT, Donini P, Prescott DM. All gene-sized DNA molecules in four species of hypotrichs have the same terminal sequence and an unusual 3' terminus. Proc Natl Acad Sci U S A. 1981 May;78(5):3015–3019.[PMC free article] [PubMed] [Google Scholar]
  • Oka Y, Shiota S, Nakai S, Nishida Y, Okubo S. Inverted terminal repeat sequence in the macronuclear DNA of Stylonychia pustulata. Gene. 1980 Sep;10(4):301–306. [PubMed] [Google Scholar]
  • Kipling D, Cooke HJ. Hypervariable ultra-long telomeres in mice. Nature. 1990 Sep 27;347(6291):400–402. [PubMed] [Google Scholar]
  • Moyzis RK, Buckingham JM, Cram LS, Dani M, Deaven LL, Jones MD, Meyne J, Ratliff RL, Wu JR. A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes. Proc Natl Acad Sci U S A. 1988 Sep;85(18):6622–6626.[PMC free article] [PubMed] [Google Scholar]
  • Richards EJ, Ausubel FM. Isolation of a higher eukaryotic telomere from Arabidopsis thaliana. Cell. 1988 Apr 8;53(1):127–136. [PubMed] [Google Scholar]
  • Henderson ER, Blackburn EH. An overhanging 3' terminus is a conserved feature of telomeres. Mol Cell Biol. 1989 Jan;9(1):345–348.[PMC free article] [PubMed] [Google Scholar]
  • Blackburn EH. Telomeres: structure and synthesis. J Biol Chem. 1990 Apr 15;265(11):5919–5921. [PubMed] [Google Scholar]
  • Sen D, Gilbert W. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature. 1988 Jul 28;334(6180):364–366. [PubMed] [Google Scholar]
  • Sen D, Gilbert W. A sodium-potassium switch in the formation of four-stranded G4-DNA. Nature. 1990 Mar 29;344(6265):410–414. [PubMed] [Google Scholar]
  • Sundquist WI, Klug A. Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops. Nature. 1989 Dec 14;342(6251):825–829. [PubMed] [Google Scholar]
  • Williamson JR, Raghuraman MK, Cech TR. Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell. 1989 Dec 1;59(5):871–880. [PubMed] [Google Scholar]
  • Guschlbauer W, Chantot JF, Thiele D. Four-stranded nucleic acid structures 25 years later: from guanosine gels to telomer DNA. J Biomol Struct Dyn. 1990 Dec;8(3):491–511. [PubMed] [Google Scholar]
  • Sasisekharan V, Zimmerman S, Davies DR. The structure of helical 5'-guanosine monophosphate. J Mol Biol. 1975 Feb 25;92(2):171–179. [PubMed] [Google Scholar]
  • Pinnavaia TJ, Miles HT, Becker ED. Letter: Self-assembled 5'-guanosine monophosphate. Nuclear magnetic resonance evidence for a regular, ordered structure and slow chemical exchange. J Am Chem Soc. 1975 Nov 26;97(24):7198–7200. [PubMed] [Google Scholar]
  • Arnott S, Chandrasekaran R, Marttila CM. Structures for polyinosinic acid and polyguanylic acid. Biochem J. 1974 Aug;141(2):537–543.[PMC free article] [PubMed] [Google Scholar]
  • Zimmerman SB, Cohen GH, Davies DR. X-ray fiber diffraction and model-building study of polyguanylic acid and polyinosinic acid. J Mol Biol. 1975 Feb 25;92(2):181–192. [PubMed] [Google Scholar]
  • Jin RZ, Breslauer KJ, Jones RA, Gaffney BL. Tetraplex formation of a guanine-containing nonameric DNA fragment. Science. 1990 Oct 26;250(4980):543–546. [PubMed] [Google Scholar]
  • Panyutin IG, Kovalsky OI, Budowsky EI, Dickerson RE, Rikhirev ME, Lipanov AA. G-DNA: a twice-folded DNA structure adopted by single-stranded oligo(dG) and its implications for telomeres. Proc Natl Acad Sci U S A. 1990 Feb;87(3):867–870.[PMC free article] [PubMed] [Google Scholar]
  • Albergo DD, Marky LA, Breslauer KJ, Turner DH. Thermodynamics of (dG--dC)3 double-helix formation in water and deuterium oxide. Biochemistry. 1981 Mar 17;20(6):1409–1413. [PubMed] [Google Scholar]
  • Mishra RK, Latha PK, Brahmachari SK. Interruptions of (CG)n sequences by GG, TG and CA need not prevent B to Z transition in solution. Nucleic Acids Res. 1988 May 25;16(10):4651–4665.[PMC free article] [PubMed] [Google Scholar]
  • Gray DM. A circular dichroism study of poly dG, poly dC, and poly dG:dC. Biopolymers. 1974;13(10):2087–2102. [PubMed] [Google Scholar]
  • Marck C, Thiele D. Poly(dG).poly(dC) at neutral and alkaline pH: the formation of triple stranded poly(dG).poly(dG).poly(dC). Nucleic Acids Res. 1978 Mar;5(3):1017–1028.[PMC free article] [PubMed] [Google Scholar]
  • Xodo LE, Manzini G, Quadrifoglio F, van der Marel GA, van Boom JH. Oligodeoxynucleotide folding in solution: loop size and stability of B-hairpins. Biochemistry. 1988 Aug 23;27(17):6321–6326. [PubMed] [Google Scholar]
  • Hardin CC, Henderson E, Watson T, Prosser JK. Monovalent cation induced structural transitions in telomeric DNAs: G-DNA folding intermediates. Biochemistry. 1991 May 7;30(18):4460–4472. [PubMed] [Google Scholar]
  • Hilbers CW, Haasnoot CA, de Bruin SH, Joordens JJ, van der Marel GA, van Boom JH. Hairpin formation in synthetic oligonucleotides. Biochimie. 1985 Jul-Aug;67(7-8):685–695. [PubMed] [Google Scholar]
  • Hare DR, Reid BR. Three-dimensional structure of a DNA hairpin in solution: two-dimensional NMR studies and distance geometry calculations on d(CGCGTTTTCGCG). Biochemistry. 1986 Sep 9;25(18):5341–5350. [PubMed] [Google Scholar]
  • Henderson E, Hardin CC, Walk SK, Tinoco I, Jr, Blackburn EH. Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs. Cell. 1987 Dec 24;51(6):899–908. [PubMed] [Google Scholar]
  • Friedmann T, Brown DM. Base-specific reactions useful for DNA sequencing: methylene blue--sensitized photooxidation of guanine and osmium tetraoxide modification of thymine. Nucleic Acids Res. 1978 Feb;5(2):615–622.[PMC free article] [PubMed] [Google Scholar]
  • Burton K, Riley WT. Selective degradation of thymidine and thymine deoxynucleotides. Biochem J. 1966 Jan;98(1):70–77.[PMC free article] [PubMed] [Google Scholar]
  • Hayatsu H, Ukita T. The selective degradation of pyrimidines in nucleic acids by permanganate oxidation. Biochem Biophys Res Commun. 1967 Nov 30;29(4):556–561. [PubMed] [Google Scholar]
  • Rich A, Nordheim A, Wang AH. The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem. 1984;53:791–846. [PubMed] [Google Scholar]
  • Wang Y, Jin R, Gaffney B, Jones RA, Breslauer KJ. Characterization by 1H NMR of glycosidic conformations in the tetramolecular complex formed by d(GGTTTTTGG). Nucleic Acids Res. 1991 Sep 11;19(17):4619–4622.[PMC free article] [PubMed] [Google Scholar]
  • Wang Y, de los Santos C, Gao XO, Greene K, Live D, Patel DJ. Multinuclear nuclear magnetic resonance studies of Na cation-stabilized complex formed by d(G-G-T-T-T-T-C-G-G) in solution. Implications for G-tetrad structures. J Mol Biol. 1991 Dec 5;222(3):819–832. [PubMed] [Google Scholar]
  • Kang C, Zhang X, Ratliff R, Moyzis R, Rich A. Crystal structure of four-stranded Oxytricha telomeric DNA. Nature. 1992 Mar 12;356(6365):126–131. [PubMed] [Google Scholar]
  • Smith FW, Feigon J. Quadruplex structure of Oxytricha telomeric DNA oligonucleotides. Nature. 1992 Mar 12;356(6365):164–168. [PubMed] [Google Scholar]
  • Pluta AF, Zakian VA. Recombination occurs during telomere formation in yeast. Nature. 1989 Feb 2;337(6206):429–433. [PubMed] [Google Scholar]
  • Cherry JM, Blackburn EH. The internally located telomeric sequences in the germ-line chromosomes of Tetrahymena are at the ends of transposon-like elements. Cell. 1985 Dec;43(3 Pt 2):747–758. [PubMed] [Google Scholar]
  • Herrick G, Cartinhour S, Dawson D, Ang D, Sheets R, Lee A, Williams K. Mobile elements bounded by C4A4 telomeric repeats in Oxytricha fallax. Cell. 1985 Dec;43(3 Pt 2):759–768. [PubMed] [Google Scholar]
Molecular Biophysics Unit, Indian Institute of Science, Bangalore.
Molecular Biophysics Unit, Indian Institute of Science, Bangalore.
Copyright notice
Abstract
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(G4TnG4), with n = 1-4. Sequences d(G4T3G4) and d(G4T4G4) adopt a G-quartet structure formed by hairpin dimerization in 70 mM NaCl as judged by a characteristic circular dichroism signature with a 295 nm positive and 265 nm negative bands while d(G4TG4) 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(G4T2G4) 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(G4TnG4) with n = 2-4 in 70 mM NaCl. 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(T2G4)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 syn-anti-syn-anti 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.
Collaboration tool especially designed for Life Science professionals.Drag-and-drop any entity to your messages.