Inosine Can Increase DNA′s Susceptibility to Photo‐oxidation by a Ru^II Complex due to Structural Change in the Minor Groove

Abstract

Key to the development of DNA-targeting phototherapeutic drugs is determining the interplay between the photoactivity of the drug and its binding preference for a target sequence. For the photo-oxidising lambda-[Ru(TAP) (dppz)] (Λ-1) (dppz=dipyridophenazine) complex bound to either d{T C G G C G C C G A } (G9) or d{TCGGCGCCIA} (I9), the X-ray crystal structures show the dppz intercalated at the terminal T C ;G A step or T C ;I A step. Thus substitution of the G nucleobase by inosine does not affect intercalation in the solid state although with I9 the dppz is more deeply inserted. In solution it is found that the extent of guanine photo-oxidation, and the rate of back electron-transfer, as determined by pico- and nanosecond time-resolved infrared and transient visible absorption spectroscopy, is enhanced in I9, despite it containing the less oxidisable inosine. This is attributed to the nature of the binding in the minor groove due to the absence of an NH group. Similar behaviour and the same binding site in the crystal are found for d{TTGGCGCCAA} (A9). In solution, we propose that intercalation occurs at the C G ;C I or T G ;C A steps, respectively, with G the likely target for photo-oxidation. This demonstrates how changes in the minor groove (in this case removal of an NH group) can facilitate binding of Ru dppz complexes and hence influence any sensitised reactions occurring at these sites. No similar enhancement of photooxidation on binding to I9 is found for the delta enantiomer.

Polypyridyl‐Based Copper Phenanthrene Complexes: A New Type of Stabilized Artificial Chemical Nuclease

“…Enzyme hAAG enhanced the cleavage activity of [Cu(TPMA)( N , N ′)] 2+ complexes but not of [Cu(TPMA)] 2+ and, when combined with observations of additional DNA damage with Endo V, it seems reasonable to suggest that deoxyinosine (dI) or free‐base hypoxanthine was generated by these ternary compounds. The base dI is a naturally occurring noncanonical base that arises from deamination of adenine; however, it can be formed from radical generation of Ade‐N6‐yl . The Ade‐N6‐yl radical may also be generated by Cu 2+ /H 2 O 2 with elegantly designed immuno‐spin trapping experiments establishing its formation via a 5,5′‐dimethyl‐1‐pyrroline N ‐oxide (DMPO) nucleoside adduct .…”

X‐ray Crystal Structures Show DNA Stacking Advantage of Terminal Nitrile Substitution in Ru‐dppz Complexes

“…dppz chromophorei sd etermined by the cytosine C2 sugar ring face contacts to the deoxyribose hydrogen atoms of C1', C2' and C4' with the TAP2 ligand, as described in our previous paper concerning the effect of the orientationo fi nosine substitutiona tt his position. [27] The major orientation of the nitrile substituent is on the G9ÀA10 (the "purines ide") of the complete intercalation cavity.…”

“…[26] The primary stabilising interactionw as shown to be the stacking betweent he DNA bases and the dppz ligand.T he angle of the (canted) intercalation wass ubsequently shown to be determinedb yasecondary stacking interaction between the phen or TAPa ncillary ligand and the 2'-deoxyribose sugaro fo ne of the four bases forming the intercalation cavity,t hus altering the photophysical properties of the bound complexes. [27] This binding modei sn ow seen to be the dominant binding mode for both enantiomerso f[ Ru(L) 2 (dppz)] 2 + (where L = bidentate N-heterocycle). The only exception recorded so far is the symmetricalb inding of the lambda enantiomer to ac entral TA/TA step, which we now believe can only be seen at this site.…”

“…We have previously observed with different derivatives of L-[Ru(TAP) 2 (dppz)] 2 + that intercalation into the terminal TC/GA base step can force the terminal adenine (A10) to flip out and form ar everse Watson-Crick base pair with as ymmetry-related strand. [27] Therefore, as illustrated in Figure 2, the "purines ide" of the intercalation cavity was incomplete, even for an unsubstituteddppz. Perhapsmost strikingly,wefound that reversible dehydration of our original crystal exhibited ar emarkable reversal, with the dehydrated form showingt hat the "purine side" of the intercalationc avity was now intact,b ut the "pyrimidines ide" instead was the one which had flippedo ut.…”

Spectro-electrochemical Studies on [Ru(TAP)2(dppz)]2+—Insights into the Mechanism of its Photosensitized Oxidation of Oligonucleotides

“…[19][20][21][22][23][24][25] Photoinduced reactions sensitized by such complexes are conveniently monitored by transient visible absorption (TA) and by time-resolved infra-red (TRIR) spectroscopy. [25][26][27][28][29][30] Initial experiments, which were carried out with racemic samples and double-stranded polydGdC, demonstrated modest isotope effects for both the excited state and subsequent reverse reactions. 26 This was interpreted as a possible PCET process but in this case with the isotope effect being as a result of proton-transfer within the G-C base pair, and not to formation of [Ru(TAP)(TAPH)(dppz)] 2+ as expected for 5′-GMP.…”