Classification of G-quadruplex DNA on the Basis of the Quadruplex Twist Angle and Planarity of G-quartets

Overview

Journal Acta Naturae

Specialty Biology

Date 2012 Jun 1

PMID 22649667

Citations 11

Authors

R V Reshetnikov

A M Kopylov

A V Golovin

Affiliations

Soon will be listed here.

Abstract

The present work is devoted to the analysis of the G-quadruplex DNA structure using the bioinformatics method. The interest towards quadruplex DNAs is determined by their involvement in the functioning of telomeres and onco-promoters as well as by the possibility to create on their basis aptamers and nanostructures. Here, we present an algorithm for a general analysis of the polymorphism of the G-quadruplex structure from the data bank PDB using original parameters. 74 structures were grouped according to the following parameters: the number of DNA strands, the number of G-quartets, and the location and orientation of the connecting loops. Two quantitative parameters were used to describe the quadruplex structure: the twist angle between two adjacent quartets (analogous to that for the complementary pair in the duplex DNA) and the quartet planarity (an original parameter). The distribution patterns of these values are specific for each group of quadruplex structures and are dependent upon the type of connecting loops used (diagonal, lateral or propeller). The tetramolecular loopless parallel quadruplex was used as a comparison template. The lateral loops introduce the strongest distortion into the structure of quadruplexes: the values of the twist angles are the lowest and are not typical for the other quadruplex groups. The loops of the diagonal type introduce much weaker deformation into quadruplexes; the structures with propeller loops are characterized by the optimum geometry of G-quartets. Hence, the correlation between the twist angle and the tension in the structure of quadruplex DNA is revealed.

Citing Articles

Nanoscale Interaction of Endonuclease APE1 with DNA.

Vemulapalli S, Hashemi M, Chen Y, Pramanik S, Bhakat K, Lyubchenko Y Int J Mol Sci. 2024; 25(10).

PMID: 38791183 PMC: 11121393. DOI: 10.3390/ijms25105145.

Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation.

Sahoo B, Kocman V, Clark N, Myers N, Deng X, Wong E Nucleic Acids Res. 2024; 52(8):4702-4722.

PMID: 38572746 PMC: 11077067. DOI: 10.1093/nar/gkae229.

Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation.

Sahoo B, Kocman V, Clark N, Myers N, Deng X, Wong E bioRxiv. 2023; .

PMID: 37790366 PMC: 10542165. DOI: 10.1101/2023.09.21.558871.

ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes.

Farag M, Messaoudi C, Mouawad L Nucleic Acids Res. 2023; 51(5):2087-2107.

PMID: 36794725 PMC: 10018348. DOI: 10.1093/nar/gkad060.

The first crystal structures of hybrid and parallel four-tetrad intramolecular G-quadruplexes.

Beseiso D, Chen E, McCarthy S, Martin K, Gallagher E, Miao J Nucleic Acids Res. 2022; 50(5):2959-2972.

PMID: 35212369 PMC: 8934647. DOI: 10.1093/nar/gkac091.

References

Arnott S, Chandrasekaran R, Marttila C . Structures for polyinosinic acid and polyguanylic acid. Biochem J. 1974; 141(2):537-43. PMC: 1168108. DOI: 10.1042/bj1410537. View

Mao X, Marky L, Gmeiner W . NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+. J Biomol Struct Dyn. 2004; 22(1):25-33. DOI: 10.1080/07391102.2004.10506977. View

Kettani A, Gorin A, Majumdar A, Hermann T, Skripkin E, Zhao H . A dimeric DNA interface stabilized by stacked A.(G.G.G.G).A hexads and coordinated monovalent cations. J Mol Biol. 2000; 297(3):627-44. DOI: 10.1006/jmbi.2000.3524. View

Lim K, Amrane S, Bouaziz S, Xu W, Mu Y, Patel D . Structure of the human telomere in K+ solution: a stable basket-type G-quadruplex with only two G-tetrad layers. J Am Chem Soc. 2009; 131(12):4301-9. PMC: 2662591. DOI: 10.1021/ja807503g. View

Patel P, Hosur R . NMR observation of T-tetrads in a parallel stranded DNA quadruplex formed by Saccharomyces cerevisiae telomere repeats. Nucleic Acids Res. 1999; 27(12):2457-64. PMC: 148448. DOI: 10.1093/nar/27.12.2457. View

Webba Da Silva M . Association of DNA quadruplexes through G:C:G:C tetrads. Solution structure of d(GCGGTGGAT). Biochemistry. 2003; 42(49):14356-65. DOI: 10.1021/bi0355185. View

Campbell N, Parkinson G, Reszka A, Neidle S . Structural basis of DNA quadruplex recognition by an acridine drug. J Am Chem Soc. 2008; 130(21):6722-4. DOI: 10.1021/ja8016973. View

crnugelj M, Hud N, Plavec J . The solution structure of d(G(4)T(4)G(3))(2): a bimolecular G-quadruplex with a novel fold. J Mol Biol. 2002; 320(5):911-24. DOI: 10.1016/s0022-2836(02)00569-7. View

Hu L, Lim K, Bouaziz S, Phan A . Giardia telomeric sequence d(TAGGG)4 forms two intramolecular G-quadruplexes in K+ solution: effect of loop length and sequence on the folding topology. J Am Chem Soc. 2009; 131(46):16824-31. DOI: 10.1021/ja905611c. View

10.

Phan A, Kuryavyi V, Luu K, Patel D . Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution. Nucleic Acids Res. 2007; 35(19):6517-25. PMC: 2095816. DOI: 10.1093/nar/gkm706. View

11.

Dai J, Carver M, Punchihewa C, Jones R, Yang D . Structure of the Hybrid-2 type intramolecular human telomeric G-quadruplex in K+ solution: insights into structure polymorphism of the human telomeric sequence. Nucleic Acids Res. 2007; 35(15):4927-40. PMC: 1976458. DOI: 10.1093/nar/gkm522. View

12.

Nimjee S, Rusconi C, Sullenger B . Aptamers: an emerging class of therapeutics. Annu Rev Med. 2005; 56:555-83. DOI: 10.1146/annurev.med.56.062904.144915. View

13.

Sket P, crnugelj M, Plavec J . d(G3T4G4) forms unusual dimeric G-quadruplex structure with the same general fold in the presence of K+, Na+ or NH4+ ions. Bioorg Med Chem. 2004; 12(22):5735-44. DOI: 10.1016/j.bmc.2004.08.009. View

14.

Wang Y, Patel D . Guanine residues in d(T2AG3) and d(T2G4) form parallel-stranded potassium cation stabilized G-quadruplexes with anti glycosidic torsion angles in solution. Biochemistry. 1992; 31(35):8112-9. DOI: 10.1021/bi00150a002. View

15.

Sundquist W, Klug A . Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops. Nature. 1989; 342(6251):825-9. DOI: 10.1038/342825a0. View

16.

Gill M, Strobel S, Loria J . Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex. Nucleic Acids Res. 2006; 34(16):4506-14. PMC: 1636370. DOI: 10.1093/nar/gkl616. View

17.

Phan A, Kuryavyi V, Gaw H, Patel D . Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter. Nat Chem Biol. 2006; 1(3):167-73. PMC: 4690526. DOI: 10.1038/nchembio723. View

18.

Gavathiotis E, Heald R, Stevens M, Searle M . Drug recognition and stabilisation of the parallel-stranded DNA quadruplex d(TTAGGGT)4 containing the human telomeric repeat. J Mol Biol. 2003; 334(1):25-36. DOI: 10.1016/j.jmb.2003.09.018. View

19.

Jing N, Zhu Q, Yuan P, Li Y, Mao L, Tweardy D . Targeting signal transducer and activator of transcription 3 with G-quartet oligonucleotides: a potential novel therapy for head and neck cancer. Mol Cancer Ther. 2006; 5(2):279-86. DOI: 10.1158/1535-7163.MCT-05-0302. View

20.

Wang Y, Patel D . Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. Structure. 1993; 1(4):263-82. DOI: 10.1016/0969-2126(93)90015-9. View