Dipeptides Containing Pyrene and Modified Photochemically Reactive Tyrosine: Noncovalent and Covalent Binding to Polynucleotides.

Dipeptides 1 and 2 were synthesized from unnatural amino acids containing pyrene as a fluorescent label and polynucleotide binding unit, and modified tyrosine as a photochemically reactive unit. Photophysical properties of the peptides were investigated by steady-state and time-resolved fluorescence. Both peptides are fluorescent (Φf = 0.3-0.4) and do not show a tendency to form pyrene excimers in the concentration range < 10-5 M, which is important for their application in the fluorescent labeling of polynucleotides. Furthermore, both peptides are photochemically reactive and undergo deamination delivering quinone methides (QMs) (ΦR = 0.01-0.02), as indicated from the preparative photomethanolysis study of the corresponding N-Boc protected derivatives 7 and 8. Both peptides form stable complexes with polynucleotides (log Ka > 6) by noncovalent interactions and similar affinities, binding to minor grooves, preferably to the AT reach regions. Peptide 2 with a longer spacer between the fluorophore and the photo-activable unit undergoes a more efficient deamination reaction, based on the comparison with the N-Boc protected derivatives. Upon light excitation of the complex 2·oligoAT10, the photo-generation of QM initiates the alkylation, which results in the fluorescent labeling of the oligonucleotide. This study demonstrated, as a proof of principle, that small molecules can combine dual forms of fluorescent labeling of polynucleotides, whereby initial addition of the dye rapidly forms a reversible high-affinity noncovalent complex with ds-DNA/RNA, which can be, upon irradiation by light, converted to the irreversible (covalent) form. Such a dual labeling ability of a dye could have many applications in biomedicinal sciences.

Kinetics of chain reaction driven by proton-coupled electron transfer: α-hydroxyethyl radical and bromoacetate in buffered aqueous solutions.

We measured and computed the rate constants of the reaction between the α-hydroxyethyl radical (˙CH(CH3)OH) and bromoacetate (BrCH2CO2-) in the non-buffered (NB), as well as in the bicarbonate (HCO3-) and hydrogen phosphate (HPO42-) buffered aqueous solutions in the presence of ethanol. These complex multistep reactions are initiated by the proton-coupled electron transfer (PCET) which reduces BrCH2CO2- and incites its debromination. The PCET is followed by the step in which the resulting carboxymethyl radical propagates a radical chain reaction thus recovering ˙CH(CH3)OH and enhancing the debromination yields. It is found that the rate constants for the initial PCET step (k1) are raised by ca. an order of magnitude in the presence of the buffers (k1(NB) = 1.4 × 105 dm3 mol-1 s-1; k1(HCO3-) = 1.4 × 106 dm3 mol-1 s-1; k1(HPO42-) = 1.1 × 106 dm3 mol-1 s-1). To rationalize this, we used density functional theory at the M06-2X-D3/6-311+G(2d,p) level in conjunction with the polarizable continuum model (PCM) for an implicit description of the aqueous environment. To acceptably reproduce the measured rate constants, the minimal solute, consisting of ˙CH(CH3)OH, BrCH2CO2- and the buffer anion, has to be expanded by at least 2-3 explicit molecules of the water solvent. The used kinetic model consisting of a set of coupled differential equations indicates the sigmoid dependence of yields vs. k1 thereby confirming the autocatalytic trait of these reactions. The computations unravel the profound influence of the presence of buffers on these reaction systems. On the one hand, the buffer anions promote the PCET by accelerating the proton transfer; on the other hand, they slow down the propagation step by forming the strong hydrogen bonds with the carboxymethyl radical. The two opposing effects cancel out and cause the Br- yields to remain approximately comparable in the non-buffered and buffered media.

Non-Covalent Binding of Tripeptides-Containing Tryptophan to Polynucleotides and Photochemical Deamination of Modified Tyrosine to Quinone Methide Leading to Covalent Attachment.

A series of tripeptides TrpTrpPhe (1), TrpTrpTyr (2), and TrpTrpTyr[CH2N(CH3)2] (3) were synthesized, and their photophysical properties and non-covalent binding to polynucleotides were investigated. Fluorescent Trp residues (quantum yield in aqueous solvent ΦF = 0.03-0.06), allowed for the fluorometric study of non-covalent binding to DNA and RNA. Moreover, high and similar affinities of 2×HCl and 3×HCl to all studied double stranded (ds)-polynucleotides were found (logKa = 6.0-6.8). However, the fluorescence spectral responses were strongly dependent on base pair composition: the GC-containing polynucleotides efficiently quenched Trp emission, at variance to AT- or AU-polynucleotides, which induced bisignate response. Namely, addition of AT(U) polynucleotides at excess over studied peptide induced the quenching (attributed to aggregation in the grooves of polynucleotides), whereas at excess of DNA/RNA over peptide the fluorescence increase of Trp was observed. The thermal denaturation and circular dichroism (CD) experiments supported peptides binding within the grooves of polynucleotides. The photogenerated quinone methide (QM) reacts with nucleophiles giving adducts, as demonstrated by the photomethanolysis (quantum yield ΦR = 0.11-0.13). Furthermore, we have demonstrated photoalkylation of AT oligonucleotides by QM, at variance to previous reports describing the highest reactivity of QMs with the GC reach regions of polynucleotides. Our investigations show a proof of principle that QM precursor can be imbedded into a peptide and used as a photochemical switch to enable alkylation of polynucleotides, enabling further applications in chemistry and biology.