Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution

Human telomeric DNA consists of tandem repeats of the sequence d(TTAGGG). The formation and stabilization of DNA G-quadruplexes in the human telomeric sequence have been shown to inhibit the activity of telomerase, thus the telomeric DNA G-quadruplex has been considered as an attractive target for cancer therapeutic intervention. However, knowledge of the intact human telomeric G-quadruplex structure(s) formed under physiological conditions is a prerequisite for structure-based rational drug design. Here we report the folding structure of the human telomeric sequence in K+ solution determined by NMR. Our results demonstrate a novel, unprecedented intramolecular G-quadruplex folding topology with hybrid-type mixed parallel/antiparallel G-strands. This telomeric G-quadruplex structure contains three G-tetrads with mixed G-arrangements, which are connected consecutively with a double-chain-reversal side loop and two lateral loops, each consisting of three nucleotides TTA. This intramolecular hybrid-type telomeric G-quadruplex structure formed in K+ solution is distinct from those reported on the 22 nt Tel22 in Na+ solution and in crystalline state in the presence of K+, and appears to be the predominant conformation for the extended 26 nt telomeric sequence Tel26 in the presence of K+, regardless of the presence or absence of Na+. Furthermore, the addition of K+ readily converts the Na+-form conformation to the K+-form hybrid-type G-quadruplex. Our results explain all the reported experimental data on the human telomeric G-quadruplexes formed in the presence of K+, and provide important insights for understanding the polymorphism and interconversion of various G-quadruplex structures formed within the human telomeric sequence, as well as the effects of sequence and cations. This hybrid-type G-quadruplex topology suggests a straightforward pathway for the secondary structure formation with effective packing within the extended human telomeric DNA. The hybrid-type telomeric G-quadruplex is most likely to be of pharmacological relevance, and the distinct folding topology of this G-quadruplex suggests that it can be specifically targeted by G-quadruplex interactive small molecule drugs.

[1]  Roger A. Jones,et al.  An intramolecular G-quadruplex structure with mixed parallel/antiparallel G-strands formed in the human BCL-2 promoter region in solution. , 2006, Journal of the American Chemical Society.

[2]  A. Phan,et al.  (3 + 1) Assembly of three human telomeric repeats into an asymmetric dimeric G-quadruplex. , 2005, Journal of the American Chemical Society.

[3]  Daekyu Sun,et al.  Evidence for the presence of a guanine quadruplex forming region within a polypurine tract of the hypoxia inducible factor 1alpha promoter. , 2005, Biochemistry.

[4]  Laurence H. Hurley,et al.  Facilitation of a structural transition in the polypurine/polypyrimidine tract within the proximal promoter region of the human VEGF gene by the presence of potassium and G-quadruplex-interactive agents , 2005, Nucleic acids research.

[5]  J. Correia,et al.  Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal , 2005, Nucleic acids research.

[6]  Stephen Neidle,et al.  Putative DNA quadruplex formation within the human c-kit oncogene. , 2005, Journal of the American Chemical Society.

[7]  Samer Khateb,et al.  Homodimeric MyoD Preferentially Binds Tetraplex Structures of Regulatory Sequences of Muscle-specific Genes* , 2005, Journal of Biological Chemistry.

[8]  W. Wilson,et al.  Telomestatin and diseleno sapphyrin bind selectively to two different forms of the human telomeric G-quadruplex structure. , 2005, Journal of the American Chemical Society.

[9]  R. Shafer,et al.  Covalent ligation studies on the human telomere quadruplex , 2005, Nucleic acids research.

[10]  M. Fry,et al.  Formation and properties of hairpin and tetraplex structures of guanine-rich regulatory sequences of muscle-specific genes , 2005, Nucleic acids research.

[11]  A. Patkowski,et al.  Effect of ions on the polymorphism, effective charge, and stability of human telomeric DNA. Photon correlation spectroscopy and circular dichroism studies. , 2005, The journal of physical chemistry. B.

[12]  Roger A. Jones,et al.  Solution structure of the biologically relevant G-quadruplex element in the human c-MYC promoter. Implications for G-quadruplex stabilization. , 2005, Biochemistry.

[13]  Stephen Neidle,et al.  Loop-length-dependent folding of G-quadruplexes. , 2004, Journal of the American Chemical Society.

[14]  Danzhou Yang,et al.  Novel DNA Bis-intercalation by MLN944, a Potent Clinical Bisphenazine Anticancer Drug* , 2004, Journal of Biological Chemistry.

[15]  L. Hurley,et al.  The dynamic character of the G-quadruplex element in the c-MYC promoter and modification by TMPyP4. , 2004, Journal of the American Chemical Society.

[16]  A. Phan,et al.  Propeller-type parallel-stranded G-quadruplexes in the human c-myc promoter. , 2004, Journal of the American Chemical Society.

[17]  F. Quadrifoglio,et al.  G-rich oligonucleotide inhibits the binding of a nuclear protein to the Ki-ras promoter and strongly reduces cell growth in human carcinoma pancreatic cells. , 2004, Biochemistry.

[18]  A. Phan,et al.  Two-repeat human telomeric d(TAGGGTTAGGGT) sequence forms interconverting parallel and antiparallel G-quadruplexes in solution: distinct topologies, thermodynamic properties, and folding/unfolding kinetics. , 2003, Journal of the American Chemical Society.

[19]  S. Balasubramanian,et al.  Studies on the structure and dynamics of the human telomeric G quadruplex by single-molecule fluorescence resonance energy transfer , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[20]  M. Katahira,et al.  Intramolecular Higher Order Packing of Parallel Quadruplexes Comprising a G:G:G:G Tetrad and a G(:A):G(:A):G(:A):G Heptad of GGA Triplet Repeat DNA* , 2003, Journal of Biological Chemistry.

[21]  P. Bates,et al.  Biophysical and biological properties of quadruplex oligodeoxyribonucleotides. , 2003, Nucleic acids research.

[22]  S. Bombard,et al.  Platinum cross-linking of adenines and guanines on the quadruplex structures of the AG3(T2AG3)3 and (T2AG3)4 human telomere sequences in Na+ and K+ solutions. , 2003, Nucleic acids research.

[23]  D. Bearss,et al.  Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Stephen Neidle,et al.  Crystal structure of parallel quadruplexes from human telomeric DNA , 2002, Nature.

[25]  Gary Parkinson,et al.  Telomere maintenance as a target for anticancer drug discovery , 2002, Nature Reviews Drug Discovery.

[26]  Laurence H. Hurley,et al.  DNA and its associated processes as targets for cancer therapy , 2002, Nature Reviews Cancer.

[27]  J. Kypr,et al.  Conserved guanine-guanine stacking in tetraplex and duplex DNA , 2001, European Biophysics Journal.

[28]  L. Hurley,et al.  Secondary DNA structures as molecular targets for cancer therapeutics. , 2001, Biochemical Society transactions.

[29]  M. Katahira,et al.  An intramolecular quadruplex of (GGA)(4) triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction. , 2001, Journal of molecular biology.

[30]  Carol W. Greider,et al.  Telomere Dysfunction Increases Mutation Rate and Genomic Instability , 2001, Cell.

[31]  J. Kypr,et al.  Conformational properties of DNA fragments containing GAC trinucleotide repeats associated with skeletal displasias , 2001, European Biophysics Journal.

[32]  W. Rutter,et al.  Unusual DNA structure of the diabetes susceptibility locus IDDM2 and its effect on transcription by the insulin promoter factor Pur-1/MAZ. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[33]  E. Blackburn,et al.  Telomere states and cell fates , 2000, Nature.

[34]  Roger A. Jones,et al.  A dimeric DNA interface stabilized by stacked A.(G.G.G.G).A hexads and coordinated monovalent cations. , 2000, Journal of molecular biology.

[35]  D. V. Von Hoff,et al.  G-quadruplexes as targets for drug design. , 2000, Pharmacology & therapeutics.

[36]  A. Phan.  Long-range imino proton-13C J-couplings and the through-bond correlation of imino and non-exchangeable protons in unlabeled DNA , 2000, Journal of biomolecular NMR.

[37]  D. Patel,et al.  A diamond-shaped zipper-like DNA architecture containing triads sandwiched between mismatches and tetrads. , 2000, Journal of molecular biology.

[38]  N. Maizels,et al.  The Saccharomyces cerevisiae Sgs1 helicase efficiently unwinds G-G paired DNAs. , 1999, Nucleic acids research.

[39]  Jean-Louis Mergny,et al.  G-quadruplex DNA: A target for drug design , 1998, Nature Medicine.

[40]  N. Maizels,et al.  The Bloom’s Syndrome Helicase Unwinds G4 DNA* , 1998, The Journal of Biological Chemistry.

[41]  P. Pečinka,et al.  DNA tetraplex formation in the control region of c-myc. , 1998, Nucleic acids research.

[42]  Bas van Steensel,et al.  TRF2 Protects Human Telomeres from End-to-End Fusions , 1998, Cell.

[43]  C. Harley,et al.  Extension of life-span by introduction of telomerase into normal human cells. , 1998, Science.

[44]  Roger A. Jones,et al.  Use of a 13C Atom To Differentiate Two 15N-Labeled Nucleosides. Syntheses of [15NH2]-Adenosine, [1,NH2-15N2]- and [2-13C-1,NH2-15N2]-Guanosine, and [1,7,NH2-15N3]- and [2-13C-1,7,NH2-15N3]-2‘-Deoxyguanosine , 1997 .

[45]  R. Wellinger,et al.  The terminal DNA structure of mammalian chromosomes , 1997, The EMBO journal.

[46]  J. Langmore,et al.  Long G Tails at Both Ends of Human Chromosomes Suggest a C Strand Degradation Mechanism for Telomere Shortening , 1997, Cell.

[47]  K. Usdin,et al.  The Chicken -Globin Gene Promoter Forms a Novel Cinched Tetrahelical Structure (*) , 1996, The Journal of Biological Chemistry.

[48]  D. Patel,et al.  Solution structure of the Oxytricha telomeric repeat d[G4(T4G4)3] G-tetraplex. , 1995, Journal of molecular biology.

[49]  D. Patel,et al.  Solution structure of the Tetrahymena telomeric repeat d(T2G4)4 G-tetraplex. , 1994, Structure.

[50]  P. Balagurumoorthy,et al.  Structure and stability of human telomeric sequence. , 1994, The Journal of biological chemistry.

[51]  J. Feigon,et al.  Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG). , 1994, Journal of molecular biology.

[52]  D. Patel,et al.  Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. , 1993, Structure.

[53]  K. Docherty,et al.  The human insulin gene linked polymorphic region exhibits an altered DNA structure. , 1992, Nucleic acids research.

[54]  C B Harley,et al.  Telomere loss: mitotic clock or genetic time bomb? , 1991, Mutation research.

[55]  C. Harley,et al.  Telomeres shorten during ageing of human fibroblasts , 1990, Nature.

[56]  Pierre Plateau,et al.  Exchangeable proton NMR without base-line distorsion, using new strong-pulse sequences , 1982 .

[57]  M. Maksimovic,et al.  Solution , 1902, The Mathematical Gazette.

[58]  Jean-Louis Mergny,et al.  Targeting telomeres and telomerase. , 2008, Biochimie.

[59]  Yujian He,et al.  Intramolecular quadruplex conformation of human telomeric DNA assessed with 125I-radioprobing. , 2004, Nucleic acids research.

[60]  S. Neidle,et al.  G‐quadruplexes as therapeutic targets , 2000, Biopolymers.

[61]  Healy Kc.  Telomere dynamics and telomerase activation in tumor progression: prospects for prognosis and therapy. , 1995, Oncology research.