Probing Nucleic Acid Structure with Shape‐Selective Rhodium and Ruthenium Complexes

Abstract

In this unit, transition metal complexes are used as photochemical probes for the structure of RNA and DNA. The transition metal ion provides a rigid substitutionally inert framework and an octahedral geometry for ligand coordination. The complexes can be constructed to define shapes, symmetries, and functionalities that complement those of the nucleic acid target. Complex formation is easily detected by light-induced nucleic acid cleavage. The modular construction of the complexes makes it possible to generate probes to examine a wide variety of structural characteristics of nucleic acids.

Probing a Major DNA Weakness: Resolving the Groove and Sequence Selectivity of the Diimine Complex Λ‐[Ru(phen)2phi]2+

“…It is possible that this sequence permits a different binding mode such as semiintercalation (kinking) or insertion, or a combination of these, which would be highly stabilising. [32,49]…”

Solid-Phase Chemical Synthesis of Stable Isotope-Labeled RNA to Aid Structure and Dynamics Studies by NMR Spectroscopy

“…The latter technique is complicated by the acid-labile nature of the phosphoramidites, which requires specialized electro-spray ionization techniques in non-aqueous buffers with lithium chloride for accurate mass determination [63,64]. Several groups have developed synthetic strategies to obtain 13 C/ 15 N-labeled RNA phosphoramidites with a variety of 2′-OH protecting groups [38,39,55,56,59,60,61,62,65,66,67,68]. This section will highlight the many efforts employed to synthesize labeled RNA phosphoramidites.…”

“…Jones and colleagues developed a chemo-enzymatic synthetic strategy to prepare 2′-O-tBDMS phosphoramidites from isotope labeled nucleosides prepared by de novo biosynthesis [69,70,71,72,73,74]. Starting from labeled adenosine or guanosine, the phosphoramidites were prepared in 7 steps with overall yields of 60% [66,74]. Furthermore, 85%–90% regioselective 2′-silylation was achieved by concomitant treatment of N -Pac-,5′-DMTr-adenosine or -guanosine with a mixture of phenyl- H -phosphonate, tert -butyldimethylsilyl chloride (tBDMS-Cl), and 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) [66,74].…”

“…Starting from labeled adenosine or guanosine, the phosphoramidites were prepared in 7 steps with overall yields of 60% [66,74]. Furthermore, 85%–90% regioselective 2′-silylation was achieved by concomitant treatment of N -Pac-,5′-DMTr-adenosine or -guanosine with a mixture of phenyl- H -phosphonate, tert -butyldimethylsilyl chloride (tBDMS-Cl), and 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) [66,74]. The [7,NH 2 - 15 N 2 ]-adenosine was prepared in 7 steps with 45% yield starting from an inexpensive pyrimidine, 6-amino-2-thioxo-1,2-dhydro-4(3 H )-pyrimidone, and [ 15 N]-NaNO 2 and [ 15 N]-NH 4 Cl as 15 N sources for N7 and NH 2 , respectively [69].…”

Research Progress on the Biological Activities of Metal Complexes Bearing Polycyclic Aromatic Hydrazones

“…In addition, the metal complexes of polycyclic aromatics can also be used as DNA probes for medical applications. For example, J. K. Barton et al previously carried out the probe identification and reaction of the corresponding transition metal complexes applied to double-helix DNA, focusing on the role of DNA charge-transfer chemistry in DNA repair [ 6 , 7 , 8 ]. They explored the different properties of DNA and RNA by pairing different central metal ions such as Ru and Rh with various commercially available or custom-made ligands to form metal complexes of different structures as probes and using the photochemical properties of these metal ions to induce nucleic acid cleavage.…”