Structure and Formation of Z-DNA and Z-RNA.

Publisher: MDPI Country of Publication: Switzerland NLM ID: 100964009 Publication Model: Electronic Cited Medium: Internet ISSN: 1420-3049 (Electronic) Linking ISSN: 14203049 NLM ISO Abbreviation: Molecules Subsets: MEDLINE

Original Publication: Basel, Switzerland : MDPI, c1995-

DNA, Z-Form* ; Nucleic Acids*; RNA ; Nucleic Acid Conformation ; DNA/chemistry

Despite structural differences between the right-handed conformations of A-RNA and B-DNA, both nucleic acids adopt very similar, left-handed Z-conformations. In contrast to their structural similarities and sequence preferences, RNA and DNA exhibit differences in their ability to adopt the Z-conformation regarding their hydration shells, the chemical modifications that promote the Z-conformation, and the structure of junctions connecting them to right-handed segments. In this review, we highlight the structural and chemical properties of both Z-DNA and Z-RNA and delve into the potential factors that contribute to both their similarities and differences. While Z-DNA has been extensively studied, there is a gap of knowledge when it comes to Z-RNA. Where such information is lacking, we try and extend the principles of Z-DNA stability and formation to Z-RNA, considering the inherent differences of the nucleic acids.

Molecules. 2018 Oct 09;23(10):. (PMID: 30304782)
Proc Natl Acad Sci U S A. 1986 Aug;83(15):5479-83. (PMID: 3461444)
Nucleic Acids Res. 2018 Nov 2;46(19):10504-10513. (PMID: 30184200)
J Am Chem Soc. 2003 Nov 5;125(44):13519-24. (PMID: 14583048)
Acc Chem Res. 1996 Sep;29(9):441-9. (PMID: 23618410)
J Biomol Struct Dyn. 1986 Oct;4(2):157-72. (PMID: 3271437)
Angew Chem Int Ed Engl. 2020 Sep 14;59(38):16553-16560. (PMID: 32516461)
Annu Rev Biophys Biophys Chem. 1988;17:125-44. (PMID: 2456073)
J Am Chem Soc. 1974 Sep 18;96(19):6023-6. (PMID: 4416770)
EMBO J. 1986 Oct;5(10):2737-44. (PMID: 3780676)
Nature. 1989 Nov 23;342(6248):456-60. (PMID: 2586615)
Science. 1991 Nov 15;254(5034):1003-6. (PMID: 1948069)
Front Biosci. 2007 May 01;12:4424-38. (PMID: 17485386)
Acta Crystallogr D Biol Crystallogr. 2001 Jul;57(Pt 7):990-5. (PMID: 11418767)
Proc Natl Acad Sci U S A. 1995 Jan 3;92(1):180-4. (PMID: 7816812)
J Mol Biol. 1986 Apr 20;188(4):707-19. (PMID: 3735433)
Proc Natl Acad Sci U S A. 2000 Dec 5;97(25):13532-6. (PMID: 11087828)
Nucleic Acids Res. 1993 Dec 25;21(25):5978-86. (PMID: 8290360)
Biophys J. 1993 Dec;65(6):2291-303. (PMID: 8312469)
J Chem Inf Model. 2021 Nov 22;61(11):5644-5657. (PMID: 34738826)
Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1514-8. (PMID: 14757814)
EMBO J. 1985 Dec 16;4(13A):3617-23. (PMID: 4092690)
Nature. 2005 Oct 20;437(7062):1183-6. (PMID: 16237447)
Science. 1999 Jun 11;284(5421):1841-5. (PMID: 10364558)
J Am Chem Soc. 2012 Mar 21;134(11):5276-83. (PMID: 22339354)
Biochemistry. 1993 Dec 14;32(49):13381-92. (PMID: 8257675)
Biochem Biophys Res Commun. 1972 Jun 28;47(6):1504-9. (PMID: 5040245)
Trends Genet. 2023 Feb;39(2):109-124. (PMID: 36604282)
Biophys J. 2000 Feb;78(2):1070-83. (PMID: 10653820)
Nucleic Acids Res. 1997 Nov 15;25(22):4589-98. (PMID: 9358170)
Biochemistry. 2006 Jan 31;45(4):1200-11. (PMID: 16430216)
Biochemistry. 1971 Nov 23;10(24):4426-33. (PMID: 5316837)
Biochem Biophys Res Commun. 2019 Jan 22;508(4):1215-1220. (PMID: 30558789)
Biochemistry. 1984 Jan 3;23(1):54-62. (PMID: 6691966)
Nucleic Acids Symp Ser. 1985;(16):29-32. (PMID: 2418421)
Nucleic Acids Res. 1988 Sep 12;16(17):8695-705. (PMID: 3419929)
Biochemistry. 1995 Nov 7;34(44):14400-7. (PMID: 7578044)
Proc Natl Acad Sci U S A. 2007 Oct 16;104(42):16528-33. (PMID: 17925442)
J Inorg Biochem. 2013 Jul;124:15-25. (PMID: 23578858)
J Biomol Struct Dyn. 1983 Oct;1(1):21-57. (PMID: 6401113)
J Mol Biol. 1983 Jul 25;168(1):51-71. (PMID: 6308270)
Biopolymers. 1973;12(9):2075-82. (PMID: 4355395)
Nucleic Acids Res. 2017 Apr 7;45(6):3537-3546. (PMID: 28034958)
J Am Chem Soc. 2004 Feb 25;126(7):1958-61. (PMID: 14971928)
J Biol Chem. 1989 May 15;264(14):7921-35. (PMID: 2722771)
Nucleic Acids Res. 1986 Feb 25;14(4):1801-9. (PMID: 3951996)
Cell. 1984 May;37(1):321-31. (PMID: 6722876)
J Phys Chem B. 2013 Nov 7;117(44):13866-71. (PMID: 24111542)
Proc Natl Acad Sci U S A. 1996 Oct 29;93(22):12116-21. (PMID: 8901542)
Nucleic Acids Res. 1993 May 25;21(10):2343-8. (PMID: 8506132)
Science. 1985 Aug 9;229(4713):571-2. (PMID: 3839596)
Cell Host Microbe. 2021 Aug 11;29(8):1266-1276.e5. (PMID: 34192517)
Biopolymers. 1990 Jan;29(1):109-22. (PMID: 1691662)
Nucleic Acids Res. 1999 Feb 15;27(4):949-55. (PMID: 9927725)
Nature. 1984 Oct 11-17;311(5986):584-6. (PMID: 6482970)
J Mol Biol. 1972 Jun 28;67(3):375-96. (PMID: 5045303)
Proc Natl Acad Sci U S A. 1988 Apr;85(8):2579-83. (PMID: 3357884)
Biochemistry. 1982 Jul 6;21(14):3400-8. (PMID: 7115677)
Cold Spring Harb Symp Quant Biol. 1987;52:135-46. (PMID: 2456875)
Biochem Biophys Res Commun. 2003 Mar 28;303(1):81-90. (PMID: 12646170)
Proc Natl Acad Sci U S A. 1985 Jun;82(11):3611-5. (PMID: 3858839)
Phys Chem Chem Phys. 2013 Oct 14;15(38):15829-32. (PMID: 23995025)
Commun Biol. 2019 Jan 7;2:7. (PMID: 30729177)
Acta Crystallogr D Biol Crystallogr. 2014 Jul;70(Pt 7):1790-800. (PMID: 25004957)
J Biomol Struct Dyn. 1988 Oct;6(2):299-309. (PMID: 2482766)
Biochem Biophys Res Commun. 1972 Sep 26;48(6):1392-9. (PMID: 5077825)
Biochem Biophys Res Commun. 1969 Nov 6;37(4):623-9. (PMID: 5353893)
J Biomol Struct Dyn. 1984 Jun;1(6):1347-71. (PMID: 6400825)
J Am Chem Soc. 1972 Nov 1;94(22):7903-11. (PMID: 4342597)
Biochemistry. 1989 Jun 13;28(12):4923-8. (PMID: 2475172)
Science. 1983 Mar 25;219(4591):1434-6. (PMID: 6402818)
Eur J Biochem. 1999 Mar;260(2):293-307. (PMID: 10095763)
Nucleic Acids Res. 2021 May 7;49(8):4782-4792. (PMID: 33872377)
J Mol Biol. 2001 Feb 2;305(5):1057-72. (PMID: 11162114)
Science. 1985 Oct 4;230(4721):82-4. (PMID: 4035359)
Science. 1982 Apr 30;216(4545):475-85. (PMID: 7071593)
RNA. 2023 Jan 3;:. (PMID: 36596670)
J Mol Biol. 2000 Jul 28;300(5):1113-31. (PMID: 10903858)
Nucleic Acids Res. 2004 Nov 08;32(19):5945-53. (PMID: 15534365)
Proc Natl Acad Sci U S A. 1981 Mar;78(3):1619-23. (PMID: 6262820)
J Mol Biol. 1984 May 25;175(3):419-23. (PMID: 6726815)
Biochemistry. 1994 Feb 8;33(5):1073-86. (PMID: 8110738)
J Biomol Struct Dyn. 1987 Oct;5(2):249-74. (PMID: 3271473)
Nat Commun. 2021 Feb 4;12(1):793. (PMID: 33542240)
Biochem Biophys Res Commun. 2021 Oct 30;583:142-145. (PMID: 34735876)
Biochemistry. 1997 Oct 28;36(43):13241-7. (PMID: 9341213)
Biophys J. 2002 Mar;82(3):1554-69. (PMID: 11867468)
Biochemistry. 1985 Jan 15;24(2):237-40. (PMID: 3978072)
Eur Biophys J. 1990;19(2):87-92. (PMID: 2073893)
Nucleic Acids Res. 2016 Jul 8;44(12):5944-56. (PMID: 27151194)
Biochemistry. 1992 Oct 13;31(40):9622-8. (PMID: 1390739)
Annu Rev Biochem. 1984;53:791-846. (PMID: 6383204)
Nat Chem. 2019 Nov;11(11):963-965. (PMID: 31654047)
Proc Natl Acad Sci U S A. 2010 May 18;107(20):9088-92. (PMID: 20439751)
Nature. 1979 Dec 13;282(5740):680-6. (PMID: 514347)
Nature. 1982 Sep 23;299(5881):312-6. (PMID: 6287292)
J Mol Biol. 1987 Sep 5;197(1):141-5. (PMID: 3681991)
Nucleic Acids Res. 2009 Jul;37(13):4353-9. (PMID: 19465399)
J Mol Biol. 1967 Jul 28;27(2):369-84. (PMID: 6048986)
J Mol Biol. 1995 May 19;248(5):918-30. (PMID: 7760333)
Biopolymers. 1989 Nov;28(11):1939-57. (PMID: 2480822)
J Mol Biol. 1970 Feb 28;48(1):109-23. (PMID: 5448585)
Nature. 1983 Jul 7-13;304(5921):83-6. (PMID: 6866095)
Biophys Rev. 2019 Jun;11(3):383-387. (PMID: 31119604)
Proc Natl Acad Sci U S A. 1997 Aug 5;94(16):8421-6. (PMID: 9237992)
J Mol Biol. 1993 May 20;231(2):475-88. (PMID: 8510158)
Nucleic Acids Res. 1999 Jan 15;27(2):543-50. (PMID: 9862978)
Nucleic Acids Res. 1982 Dec 11;10(23):7879-92. (PMID: 7155900)
Annu Rev Phys Chem. 2010;61:63-83. (PMID: 20055667)
Methods. 2004 Nov;34(3):300-11. (PMID: 15325648)
J Phys Chem B. 2008 Aug 7;112(31):9428-36. (PMID: 18630860)
Science. 2003 Jul 18;301(5631):347-9. (PMID: 12869755)
Biopolymers. 1997;14(1):65-90. (PMID: 19174848)
J Am Chem Soc. 2004 Sep 1;126(34):10522-3. (PMID: 15327293)
Curr Opin Virol. 2021 Dec;51:134-140. (PMID: 34688984)
Nucleic Acids Res. 2014 Dec 16;42(22):13981-96. (PMID: 25428372)
Biopolymers. 1973;12(8):1787-814. (PMID: 4733709)
Nat Struct Mol Biol. 2022 Nov;29(11):1113-1121. (PMID: 36352138)
Structure. 2007 Apr;15(4):395-404. (PMID: 17437712)
Nature. 1953 Apr 25;171(4356):737-8. (PMID: 13054692)
Biopolymers. 1998;48(4):234-52. (PMID: 10699842)
Biophys J. 1997 Sep;73(3):1553-61. (PMID: 9284322)
Molecules. 2018 Jul 21;23(7):. (PMID: 30037061)
Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:113-7. (PMID: 6574834)
Genetica. 1999;106(1-2):37-47. (PMID: 10710708)
Nucleic Acids Res. 2004 Aug 03;32(13):4044-54. (PMID: 15292450)
Biophys J. 1996 Sep;71(3):1215-21. (PMID: 8873995)
Biochemistry. 1987 Aug 11;26(16):5186-90. (PMID: 2822105)
Nature. 2022 Jun;606(7914):594-602. (PMID: 35614224)
Biochemistry. 1986 Jun 17;25(12):3648-55. (PMID: 3718951)
J Mol Biol. 1973 Dec 5;81(2):93-105. (PMID: 4777309)
Nature. 1986 Nov 27-Dec 3;324(6095):385-8. (PMID: 3785407)
ChemMedChem. 2014 Sep;9(9):2052-8. (PMID: 25044630)
Am J Psychiatry. 2003 Apr;160(4):623-4. (PMID: 12668347)
Biochemistry. 1990 Aug 7;29(31):7229-36. (PMID: 2207101)
Nature. 1980 Feb 21;283(5749):743-5. (PMID: 7354864)
Proc Natl Acad Sci U S A. 1990 Jun;87(12):4630-4. (PMID: 2352940)
Nucleic Acids Res. 2004 Jan 09;32(1):248-54. (PMID: 14715922)
Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7716-21. (PMID: 20385834)
Biophys J. 1998 Nov;75(5):2422-34. (PMID: 9788937)
Chem Rev. 2006 Jun;106(6):2045-64. (PMID: 16771442)

F31 AI167396 United States AI NIAID NIH HHS; R21 AI171827 United States AI NIAID NIH HHS

Keywords: Z-DNA; Z-RNA; chemical modifications; hydration; junctions; sequence preference

0 (DNA, Z-Form)
63231-63-0 (RNA)
9007-49-2 (DNA)
0 (Nucleic Acids)

Date Created: 20230121 Date Completed: 20230124 Latest Revision: 20230831

20250114

PMC9867160

10.3390/molecules28020843

36677900