Metal-mediated Base Pairs in Parallel-stranded DNA

Overview

Journal Beilstein J Org Chem

Specialty Chemistry

Date 2018 Mar 23

PMID 29564004

Citations 7

Authors

Jens Muller

Affiliations

Soon will be listed here.

Abstract

In nucleic acid chemistry, metal-mediated base pairs represent a versatile method for the site-specific introduction of metal-based functionality. In metal-mediated base pairs, the hydrogen bonds between complementary nucleobases are replaced by coordinate bonds to one or two transition metal ions located in the helical core. In recent years, the concept of metal-mediated base pairing has found a significant extension by applying it to parallel-stranded DNA duplexes. The antiparallel-stranded orientation of the complementary strands as found in natural B-DNA double helices enforces a cisoid orientation of the glycosidic bonds. To enable the formation of metal-mediated base pairs preferring a transoid orientation of the glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine-Ag(I)-cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated base pairs reported as yet in parallel-stranded DNA, compares them with their counterparts in regular DNA (where available), and explains the experimental conditions used to stabilize the respective parallel-stranded duplexes.

Citing Articles

Dynamic Structure and Stability of DNA Duplexes Bearing a Dinuclear Hg(II)-Mediated Base Pair.

Bachmann J, Schonrath I, Muller J, Doltsinis N Molecules. 2020; 25(21).

PMID: 33114568 PMC: 7663159. DOI: 10.3390/molecules25214942.

Stable Hg(II)-mediated base pairs with a phenanthroline-derived nucleobase surrogate in antiparallel-stranded DNA.

Jash B, Muller J J Biol Inorg Chem. 2020; 25(4):647-654.

PMID: 32277288 PMC: 7239801. DOI: 10.1007/s00775-020-01788-x.

Footprints of Nanoscale DNA-Silver Cluster Chromophores Activated-Electron Photodetachment Mass Spectrometry.

Blevins M, Kim D, Crittenden C, Hong S, Yeh H, Petty J ACS Nano. 2019; 13(12):14070-14079.

PMID: 31755695 PMC: 7047740. DOI: 10.1021/acsnano.9b06470.

Silver(I)-mediated base pairing in parallel-stranded DNA involving the luminescent cytosine analog 1,3-diaza-2-oxophenoxazine.

Schonrath I, Tsvetkov V, Zatsepin T, Aralov A, Muller J J Biol Inorg Chem. 2019; 24(5):693-702.

PMID: 31263954 DOI: 10.1007/s00775-019-01682-1.

Atomic Structure of a Fluorescent Ag Cluster Templated by a Multistranded DNA Scaffold.

Huard D, Demissie A, Kim D, Lewis D, Dickson R, Petty J J Am Chem Soc. 2018; 141(29):11465-11470.

PMID: 30562465 PMC: 6606393. DOI: 10.1021/jacs.8b12203.

References

Durland R, Kessler D, Gunnell S, Duvic M, Pettitt B, Hogan M . Binding of triple helix forming oligonucleotides to sites in gene promoters. Biochemistry. 1991; 30(38):9246-55. DOI: 10.1021/bi00102a017. View

Hensel S, Eckey K, Scharf P, Megger N, Karst U, Muller J . Excess Electron Transfer through DNA Duplexes Comprising a Metal-Mediated Base Pair. Chemistry. 2017; 23(43):10244-10248. DOI: 10.1002/chem.201702241. View

Sinha I, Kosters J, Hepp A, Muller J . 6-Substituted purines containing thienyl or furyl substituents as artificial nucleobases for metal-mediated base pairing. Dalton Trans. 2013; 42(45):16080-9. DOI: 10.1039/c3dt51691a. View

Lobana T, Kumari P, Sharma R, Castineiras A, Butcher R, Akitsu T . Thiosemicarbazone derivatives of nickel and copper: the unprecedented coordination of furan ring in octahedral nickel(II) and of triphenylphosphine in three-coordinate copper(I) complexes. Dalton Trans. 2011; 40(13):3219-28. DOI: 10.1039/c0dt01291b. View

Copp S, Schultz D, Swasey S, Gwinn E . Atomically precise arrays of fluorescent silver clusters: a modular approach for metal cluster photonics on DNA nanostructures. ACS Nano. 2015; 9(3):2303-10. DOI: 10.1021/nn506322q. View

Grunenberg J . The Interstitial Carbon of the Nitrogenase FeMo Cofactor is Far Better Stabilized than Previously Assumed. Angew Chem Int Ed Engl. 2017; 56(25):7288-7291. DOI: 10.1002/anie.201701790. View

Kaul C, Muller M, Wagner M, Schneider S, Carell T . Reversible bond formation enables the replication and amplification of a crosslinking salen complex as an orthogonal base pair. Nat Chem. 2011; 3(10):794-800. DOI: 10.1038/nchem.1117. View

Engelhard D, Nowack J, Clever G . Copper-Induced Topology Switching and Thrombin Inhibition with Telomeric DNA G-Quadruplexes. Angew Chem Int Ed Engl. 2017; 56(38):11640-11644. DOI: 10.1002/anie.201705724. View

Germann M, Zhou N, van de Sande J, Vogel H . Parallel-stranded duplex DNA: an NMR perspective. Methods Enzymol. 1995; 261:207-25. DOI: 10.1016/s0076-6879(95)61011-1. View

10.

Schmidbaur H, Schier A . Argentophilic interactions. Angew Chem Int Ed Engl. 2014; 54(3):746-84. DOI: 10.1002/anie.201405936. View

11.

Mandal S, Hebenbrock M, Muller J . A Dinuclear Mercury(II)-Mediated Base Pair in DNA. Angew Chem Int Ed Engl. 2016; 55(50):15520-15523. DOI: 10.1002/anie.201608354. View

12.

Takezawa Y, Yoneda S, Duprey J, Nakama T, Shionoya M . Metal-responsive structural transformation between artificial DNA duplexes and three-way junctions. Chem Sci. 2018; 7(5):3006-3010. PMC: 6004775. DOI: 10.1039/c6sc00383d. View

13.

Ono T, Yoshida K, Saotome Y, Sakabe R, Okamoto I, Ono A . Synthesis of covalently linked parallel and antiparallel DNA duplexes containing the metal-mediated base pairs T-Hg(II)-T and C-Ag(I)-C. Chem Commun (Camb). 2010; 47(5):1542-4. DOI: 10.1039/c0cc02028a. View

14.

Ensslen P, Wagenknecht H . One-Dimensional Multichromophor Arrays Based on DNA: From Self-Assembly to Light-Harvesting. Acc Chem Res. 2015; 48(10):2724-33. DOI: 10.1021/acs.accounts.5b00314. View

15.

Jash B, Scharf P, Sandmann N, Fonseca Guerra C, Megger D, Muller J . A metal-mediated base pair that discriminates between the canonical pyrimidine nucleobases. Chem Sci. 2017; 8(2):1337-1343. PMC: 5360170. DOI: 10.1039/c6sc03482a. View

16.

Morvan F, Debart F, Vasseur J . From anionic to cationic alpha-anomeric oligodeoxynucleotides. Chem Biodivers. 2010; 7(3):494-535. DOI: 10.1002/cbdv.200900220. View

17.

Guo X, Seela F . Anomeric 2'-Deoxycytidines and Silver Ions: Hybrid Base Pairs with Greatly Enhanced Stability and Efficient DNA Mismatch Detection with α-dC. Chemistry. 2017; 23(49):11776-11779. DOI: 10.1002/chem.201703017. View

18.

Dominguez-Martin A, Johannsen S, Sigel A, Operschall B, Song B, Sigel H . Intrinsic acid-base properties of a hexa-2'-deoxynucleoside pentaphosphate, d(ApGpGpCpCpT): neighboring effects and isomeric equilibria. Chemistry. 2013; 19(25):8163-81. DOI: 10.1002/chem.201203330. View

19.

Liu S, Clever G, Takezawa Y, Kaneko M, Tanaka K, Guo X . Direct conductance measurement of individual metallo-DNA duplexes within single-molecule break junctions. Angew Chem Int Ed Engl. 2011; 50(38):8886-90. DOI: 10.1002/anie.201102980. View

20.

Aramini J, Kalisch B, Pon R, van de Sande J, Germann M . Structure of a DNA duplex that contains alpha-anomeric nucleotides and 3'-3' and 5'-5' phosphodiester linkages: coexistence of parallel and antiparallel DNA. Biochemistry. 1996; 35(29):9355-65. DOI: 10.1021/bi960612p. View