Metal Cations in G-Quadruplex Folding and Stability.
This review is focused on the structural and physicochemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location, and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy, and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in the presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.
Department of Chemistry and Biochemistry, Kent State University Kent, OH, USA.
Debmalya
D
Bhattacharyya
Department of Chemistry and Biochemistry, Kent State University Kent, OH, USA.
Gayan
G
Mirihana Arachchilage
Department of Chemistry and Biochemistry, Kent State University Kent, OH, USA.
Soumitra
S
Basu
DNA; G-quadruplex; RNA; metal ion coordination; polymorphism; stability; structure
Biochemistry. 2015 Mar 17;54(10):1879-85
25730526
Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11593-8
12195017
Metallomics. 2015 Nov;7(11):1508-14
26381587
J Mol Biol. 1996 Jan 26;255(3):476-83
8568891
Biochimie. 2008 May;90(5):686-96
18294461
Nucleic Acids Res. 2012 Jun;40(11):4727-41
22351747
Biochim Biophys Acta. 2014 Dec;1840(12):3503-10
25234228
J Am Chem Soc. 2012 Dec 12;134(49):19953-6
23190255
J Am Chem Soc. 2015 Jan 14;137(1):210-8
25495387
Chemphyschem. 2015 Jul 20;16(10):2099-105
25917128
Biochemistry. 1999 Apr 6;38(14):4355-64
10194354
Nucleic Acid Ther. 2011 Jun;21(3):185-200
21749296
Curr Opin Struct Biol. 2009 Jun;19(3):239-50
19487118
Nucleic Acids Res. 1998 Mar 1;26(5):1167-72
9469822
Org Lett. 2000 Oct 19;2(21):3277-80
11029189
Biochem J. 2015 Apr 1;467(1):91-102
25793418
Nucleic Acids Res. 2006;34(16):4506-14
16945956
J Am Chem Soc. 2008 Oct 29;130(43):14287-93
18834130
Biochemistry. 2010 Sep 28;49(38):8300-6
20726580
J Am Chem Soc. 2007 Jul 18;129(28):8794-800
17580943
Nucleic Acids Res. 2005 May 24;33(9):2901-7
15914666
Biopolymers. 2000-2001;56(3):147-94
11745110
Nucleic Acids Res. 2008 Nov;36(19):6260-8
18832370
Nucleic Acids Res. 2007;35(8):2554-63
17412708
Nucleic Acids Res. 2010 Sep;38(16):5569-80
20413582
Structure. 1993 Dec 15;1(4):263-82
8081740
RNA. 2008 Jul;14(7):1290-6
18515550
Nucleic Acids Res. 2004 May 11;32(8):2598-606
15141030
Biophys J. 1998 Aug;75(2):968-81
9675197
Nucleic Acids Res. 2010 Nov;38(20):7022-36
20571090
Science. 1994 Jul 22;265(5171):520-4
8036494
Nucleic Acids Res Suppl. 2001;(1):259-60
12836363
J Am Chem Soc. 2010 Dec 22;132(50):17831-9
21105704
Chemistry. 2005 Oct 7;11(20):6064-79
16052652
Dalton Trans. 2015 Feb 28;44(8):3701-7
25573281
Nucleic Acids Res. 2000 May 1;28(9):1969-77
10756199
Biochemistry. 2007 Mar 20;46(11):3036-44
17311417
Biochemistry. 2015 Dec 8;54(48):7067-78
26554903
Biochemistry. 2014 Aug 26;53(33):5461-70
25072107
Biochemistry. 2000 Feb 15;39(6):1462-8
10684628
J Mol Biol. 2000 Mar 31;297(3):627-44
10731417
Nat Chem Biol. 2007 Apr;3(4):218-21
17322877
Nucleic Acids Res. 2012 Nov;40(21):11047-57
22977177
J Mol Biol. 2000 Feb 11;296(1):1-5
10656813
Angew Chem Int Ed Engl. 2001 Aug 3;40(15):2827-2831
29711994
Rapid Commun Mass Spectrom. 2011 Jul 30;25(14):2095-8
21698693
Eur J Biochem. 1995 Oct 15;233(2):631-43
7588810
FEBS Lett. 2007 Apr 17;581(8):1657-60
17399710
Biochemistry. 2005 Dec 13;44(49):16341-50
16331995
Nucleic Acids Res. 1992 Aug 11;20(15):4061-7
1508691
Nucleic Acids Res. 2004 Feb 11;32(3):1097-102
14960719
RNA Biol. 2012 Aug;9(8):1099-109
22858673
J Phys Chem B. 2008 Jul 10;112(27):8151-9
18553964
Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10546-50
7937991
Nucleic Acids Res. 2012 Feb;40(3):1033-49
21993297
Nature. 1991 Apr 25;350(6320):718-20
2023635
J Am Chem Soc. 2004 Dec 22;126(50):16405-15
15600342
Biochemistry. 2009 Jun 16;48(23):5313-9
19397366
Biochemistry. 2013 Apr 2;52(13):2176-83
23445442
Biochemistry. 1993 Jun 22;32(24):6220-8
8512932
Nucleic Acids Res. 1997 Feb 1;25(3):617-25
9016604
Nature. 1991 May 23;351(6324):331-2
1709723
Biopolymers. 2006 Aug 15;82(6):558-69
16538665
Nucleic Acids Res. 2005 Oct 20;33(18):6070-80
16239639
J Mol Biol. 2001 Jul 6;310(2):367-77
11428895
Nucleic Acids Res. 2008 Jan;36(Database issue):D381-5
17962308
J Am Chem Soc. 2005 Nov 30;127(47):16723-32
16305263
Biochemistry. 2013 Mar 5;52(9):1528-38
23387555
Nucleic Acids Res. 1990 Oct 25;18(20):6057-60
2235488
Anal Chem. 2011 Jan 1;83(1):225-30
21141923
Nucleic Acids Res. 2006 Apr 26;34(7):2117-27
16641317
J Mol Biol. 2002 Jul 5;320(2):189-200
12079378
Curr Opin Chem Biol. 2009 Jun;13(3):345-53
19515602
Biopolymers. 2000-2001;56(3):123-46
11745109
Nucleic Acids Res. 2010 Nov;38(20):7187-98
20571083
Biochemistry. 1992 Jan 28;31(3):833-41
1731941
J Am Chem Soc. 2003 Jan 8;125(1):42-3
12515502
J Biochem Biophys Methods. 1995 Feb;30(1):1-8
7608467
Curr Med Chem. 2010;17(29):3438-48
20712562
Chem Biol. 2015 Feb 19;22(2):262-72
25641166
Nucleic Acids Res. 2005 May 24;33(9):2908-16
15914667
Biochimie. 2013 Feb;95(2):117-23
23084930
Nature. 2002 Jun 20;417(6891):876-80
12050675
Org Biomol Chem. 2009 Nov 21;7(22):4677-84
19865704
Nucleic Acids Res. 2005 Apr 07;33(6):2022-31
15817566
Biochemistry. 2006 Jun 27;45(25):7854-60
16784237
J Mol Biol. 1999 Jan 8;285(1):233-43
9878402
J Am Chem Soc. 2010 Sep 15;132(36):12724-32
20735000
Nucleic Acids Res. 2007;35(12):4214-22
17576685
J Mol Biol. 1998 Aug 14;281(2):261-70
9698547
Org Biomol Chem. 2004 Jul 21;2(14):1970-3
15254621
FEBS Lett. 2001 May 11;496(2-3):128-33
11356196
ChemMedChem. 2014 May;9(5):899-911
24729465
Nucleic Acids Res. 2013 Jul;41(12):6222-31
23620292
Chem Soc Rev. 2008 Jul;37(7):1375-84
18568163
Nucleic Acids Res. 2012 May;40(9):4229-36
22241774
Nature. 2014 Sep 4;513(7516):65-70
25079319
Biochemistry. 1992 Sep 15;31(36):8406-14
1382577
J Mol Biol. 2002 Oct 4;322(5):955-70
12367521
Biochemistry. 2005 Nov 22;44(46):15238-46
16285727
Biochemistry. 2002 Oct 8;41(40):12133-9
12356314
J Am Chem Soc. 2005 Jul 20;127(28):9980-1
16011344
Biochemistry. 2011 Aug 23;50(33):7251-8
21744844
Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13665-70
11707581
Nature. 1992 Mar 12;356(6365):164-8
1545871
Biochemistry. 1992 Apr 21;31(15):3769-76
1567831
Methods Enzymol. 2001;338:400-20
11460560
Structure. 1999 Jul 15;7(7):803-15
10425682
Biochemistry. 2009 Dec 8;48(48):11487-95
19860473
Analyst. 2012 Feb 7;137(3):704-9
22143190
J Mol Biol. 1996 Jul 19;260(3):378-94
8757801
Biol Chem. 2001 Apr;382(4):621-8
11405224
Biochemistry. 1991 May 7;30(18):4460-72
2021636
J Mol Biol. 1997 Oct 17;273(1):171-82
9367755
Org Biomol Chem. 2008 Feb 21;6(4):627-36
18264563
J Biol Chem. 2003 Oct 10;278(41):39330-6
12857733
RNA Biol. 2011 Sep-Oct;8(5):802-5
21734463
Biochemistry. 1993 Aug 24;32(33):8682-92
8357810
Nucleic Acids Res. 2013 Jun;41(11):5898-911
23609544
Anal Chim Acta. 2014 Feb 17;812:161-7
24491777
Nature. 1953 Apr 25;171(4356):737-8
13054692
PLoS One. 2013;8(3):e58529
23516498
RNA Biol. 2012 Jan;9(1):81-6
22258148
Nucleic Acids Res. 2007;35(22):7429-55
17913750
Inorg Chem. 2010 Sep 20;49(18):8371-80
20795697
Proc Natl Acad Sci U S A. 1962 Dec 15;48:2013-8
13947099
Curr Opin Struct Biol. 1999 Jun;9(3):305-14
10361092
Biochimie. 2011 Aug;93(8):1297-309
21679743
Biopolymers. 2015 Jul;103(7):376-86
25807937
Biochem Biophys Res Commun. 2000 Nov 30;278(3):833-8
11095993
Nucleosides Nucleotides Nucleic Acids. 2007;26(8-9):1155-9
18058556
Biochemistry. 1996 Dec 3;35(48):15383-90
8952490
Nucleic Acids Res. 2010 Nov;38(21):7858-68
20660477
J Mol Biol. 2002 Jul 26;320(5):911-24
12126614
J Am Chem Soc. 2007 Aug 22;129(33):10106-7
17661470
Biochimie. 2008 Jan;90(1):131-55
17822826
Nucleic Acids Res. 2006;34(18):5133-44
16998187
Nucleic Acids Res. 2008 Mar;36(4):1321-33
18187510
J Biol Chem. 1994 Aug 26;269(34):21858-69
8063830
Nucleic Acids Res. 2005 Feb 24;33(4):1182-92
15731338
Nucleic Acids Res. 2005 Jun 28;33(11):3691-7
15985684
Nucleic Acids Res. 2007;35(2):406-13
17169996
Nucleic Acids Res. 2006 May 10;34(9):2536-49
16687659
RNA Biol. 2015;12(3):320-9
25826664
J Phys Chem B. 2013 Jun 13;117(23):6896-905
23683360
J Phys Chem B. 2009 Jun 25;113(25):8784-92
19480441
J Am Chem Soc. 2001 Nov 7;123(44):10799-804
11686680
Chem Commun (Camb). 2007 Nov 7;(41):4286-8
18217607
PLoS One. 2009;4(2):e4399
19198658
J Am Chem Soc. 2006 Apr 26;128(16):5404-15
16620112