Guanine-cytosine Base Pair Research Articles

Influence of Mg2+ on the Guanine–Cytosine Tautomeric Equilibrium: Simulations of the Induced Intermolecular Proton Transfer

Metallic ions are essential for stabilizing the nucleic acid structure, and are also involved in the majority of RNA and DNA biological functions. However, at large concentrations metals may play an opposite role by promoting alterations in the genetic code (mutagenicity). To contribute to the understanding of this effect, theoretical tools are used to investigate the influence of the magnesium dication on the guanine-cytosine (GC) base pair structure and stability. To this end, a fully hydrated Mg(2+) cation is inserted in two models: an isolated GC base pair, and a more realistic DNA model corresponding to a hydrated double-stranded trimer. Calculations performed with a hybrid ONIOM approach reveal that the Mg(2+) cation coordination to the GC base pair alters drastically the natural tautomeric equilibria in DNA by promoting single proton transfer. Nevertheless, the generated rare tautomer will have a limited impact on the total spontaneous mutation due to the low back-reaction barrier allowing a quick return to the canonical form. Additionally, it is demonstrated that the major effects of biological environment arise from the hydration and stacking influence, whereas the impact of phosphate groups is minor.

Electrical and optical characterization of DNA molecules as a function of concentration in aqueous solution

We present experimental data on the electrical and optical behavior of circular and linear plasmid DNA molecules embedded in an aqueous matrix. From the electrical point of view, the results indicate that the presence of water is essential when the DNA concentration is not sufficient to ensure conduction patterns, consistent with the conduction mechanisms proposed for DNA molecules. In fact, as droplets are layered on the substrate, a nonlinear behavior of the current-voltage curves is observed; when water evaporates, the conductivity decreases to a very low value that resembles the high resistivity of the substrate. As more droplets are added, the current increases giving higher conductivity, as expected, since more molecules participate into the conduction process. The conduction behavior of DNA could be due to a tunneling transport of charges inside the molecule, the tunneling barrier being the adenine-thymine bridge between consecutive guanine-cytosine base pairs. A hopping channel, activated by the water surrounding the molecules, could act as an additional mechanism between different molecules. Optical reflectance measurements, performed in the wavelength range 230–450 nm on dried samples, obtained by complete evaporation of the aqueous matrix containing plasmid DNA under UV-VIS light, reveal absorption in the wavelength range 230–300 nm, typical of DNA-based materials. Moreover, in correspondence of the absorption region, the higher the DNA concentration, the higher the reflectance reduction. This suggests that the DNA concentration strongly influences the spectral behavior of biological layers. Finally, we present preliminary results exploiting the possibility to control the morphological and optical features of DNA layers by means of proper lighting procedures. Both electrical and optical measurements indicate that the DNA concentration is a crucial parameter for technical applications. The results reported here provide a contribution for the possible use of DNA molecules in the field of electro-optical biosensors.

Effect of nucleobase sequence on the proton-transfer reaction and stability of the guanine–cytosine base pair radical anion

The formation of base pair radical anions is closely related to many fascinating research fields in biology and chemistry such as radiation damage to DNA and electron transport in DNA. However, the relevant knowledge so far mainly comes from studies on isolated base pair radical anions, and their behavior in the DNA environment is less understood. In this study, we focus on how the nucleobase sequence affects the properties of the guanine-cytosine (GC) base pair radical anion. The energetic barrier and reaction energy for the proton transfer along the N(1)(G)-H···N(3)(C) hydrogen bond and the stability of GC˙(-) (i.e., electron affinity of GC) embedded in different sequences of base-pair trimer were evaluated using density functional theory. The computational results demonstrated that the presence of neighboring base pairs has an important influence on the behavior of GC˙(-) in the gas phase. The excess electron was found to be localized on the embedded GC and the charge leakage to neighboring base pairs was very minor in all of the investigated sequences. Accordingly, the sequence behavior of the proton-transfer reaction and the stability of GC˙(-) is chiefly governed by electrostatic interactions with adjacent base pairs. However, the effect of base stacking, due to its electrostatic nature, is severely screened upon hydration, and thus, the sequence dependence of the properties of GC˙(-) in aqueous environment becomes relatively weak and less than that observed in the gas phase. The effect of geometry relaxation associated with neighboring base pairs as well as the possibility of proton transfer along the N(2)(G)-H···O(2)(C) channel have also been investigated. The implications of the present findings to the electron transport and radiation damage of DNA are discussed.

Comprehensive evaluation of medium and long range correlated density functionals in TD-DFT investigation of DNA bases and base pairs: gas phase and water solution study

A comprehensive analysis of the performance of the TD-DFT method using different density functionals including recently developed medium and long-range correlation corrected density functionals have been carried out for lower-lying electronic singlet valence transitions of nucleic acid bases and the Watson–Crick base pairs in the gas phase and in the water solution. The standard 6-311++G(d,p) basis set was used. Ground state geometries of bases and base pairs were optimized at the M05-2X/6-311++G(d,p) level. The nature of potential energy surfaces (PES) was ascertained through the harmonic vibrational frequency analysis; all geometries were found to be minima at the respective PES. Electronic singlet vertical transition energies were also computed at the CC2/def2-TZVP level in the gas phase. The effect of state-specific water solvation on TD-DFT computed transition energies was considered using the PCM model. For the isolated bases the performance of the B3LYP functional was generally found to be superior among all functionals, but it measurably fails for charge-transfer states in the base pairs. The CC2/def2-TZVP computed transition energies were also revealed to be inferior compared with B3LYP results for the isolated bases. The performance of the ωB97XD, CAM-B3LYP and BMK functionals were found to be similar and comparable with the CC2 results for the isolated bases. However, for the Watson–Crick adenine–thymine and guanine–cytosine base pairs the performance of the ωB97XD functional was found to be the best among all the studied functionals in the present work in predicting the locally excited transitions as well as charge transfer states.

Theoretical Study of the Tautomerism in the One-Electron Oxidized Guanine−Cytosine Base Pair

Ionizing radiation on DNA mainly generates one-electron oxidized guanine-cytosine base pair (G(+·):C), and in the present paper we study all possible tautomers of G(+·):C by using ab initio approaches. Our calculations reveal that the tautomeric equilibrium follows a peculiar path, characterized by a stepwise mechanism: first the proton in the central hydrogen bond N1(G)-H1-N3(C) migrates from guanine to cytosine, and then the cytosine cation releases one proton from its amino group. During this second step, water acts as a proton acceptor, localizing the positive charge on one of the water molecules interacting with the guanine radical. In agreement with experimental findings, the computed energy barriers show that the deprotonation of the cytosine cation is the speed-limiting step in the tautomeric equilibrium. The influence of the number of water molecules incorporated in the theoretical model is analyzed in detail. The evolution of electronic properties along the reaction path is also discussed on the basis of partial atomic charges and spin density distributions. This work demonstrates that water indeed plays a crucial role in the tautomeric equilibra of base pairs.

ChemInform Abstract: Design of a Nonnatural Deoxyribonucleoside for Recognition of GC Base Pairs by Oligonucleotide-Directed Triple Helix Formation.

The deoxyribonucleoside 1-(2-deoxy-beta-D-ribofuranosyl)-3-methyl-5-amino-1H-pyrazolo4,3-d]py rimidin-7-one (P1) was designed such that two specific hydrogen bonds would form with guanine (G) of a Watson-Crick guanine-cytosine (GC) base pair in the major groove of double-helical DNA. One edge of the P1 heterocycle mimics N3-protonated cytosine, which would circumvent the pH dependence observed for the formation of triple helices containing C + GC base triplets. P1 was synthesized in five steps and incorporated by automated methods in pyrimidine oligodeoxyribonucleotides. From affinity cleaving analyses, the stabilities of base triplets decrease in the order P1.GC >> P1.CG >> P1.AT approximately P1.TA (pH 7.4, 35-degrees-C). P1 binds GC base pairs within a pyrimidinte triple-helix motif as selectively and strongly as C but over an extended pH range. Oligodeoxyribonucleotides containing P1 residues were shown to bind within plasmid DNA a single 15 base pair site containing five GC base pairs at pH 7.8 and a single 16 base pair site containing six contiguous GC base pairs at pH 7.4.

Electronic and molecular structure of M-DNA fragments

To study M-DNA molecular structure (such DNA with transition metal ions placed between the nucleic bases is able to conduct the electric current) and its conductivity mechanisms, we carried out ab initio quantum-mechanical calculations of electronic and spatial structures, thermodynamic characteristics of adenine-thymine (АТ) and guanine-cytosine (GC) base pair complexes with Zn(2+) and Ni(2+). To take into account the influence of the alkaline environment, calculations for these complexes were also carried out with hydroxyl and two water molecules. Computations were performed at MP2 level of theory using 6-31+G* basis set. Analogous calculations were carried out for (AC)(TG) stacking dimer of nucleic acid base pairs with two Zn(2+). The calculation of the interaction energy in complexes has shown the preference of locating the metal ion (instead of the imino proton) between bases in M-DNA. The electronic transition energy calculation has revealed the reduction of the first singlet transition energy in АТ and GC complexes with Ni(2+) from 4.5eV to 0.4 - 0.6eV. Ni(2+) orbitals take part in the formation of HOMO and LUMO on the complexes investigated. It was shown that charges of metal ions incorporated into complexes with nucleic bases and in dimer decrease significantly.

Theoretical Investigation of Hydrogen Atom Transfer in the Cytosine-Guanine Base Pair and Its Coupling with Electronic Rearrangement. Concerted vs Stepwise Mechanism

The transformation of the DNA base pairs from the Watson-Crick (WC) structures to its tautomers having imino-enol form can be achieved via two types of hydrogen atom transfer processes: (i) concerted, and/or (ii) stepwise (step by step). Here, we have studied and compared these two mechanisms in the cytosine-guanine (C-G) system. In the first mechanism there is the concerted movement of two hydrogen atoms along two of the three H-bridges that bond the bases, one from the cytosine to guanine and the other in the opposite direction. This movement must be coupled to an electronic reorganization, with some bond orders that pass from single to double and vice versa, in order to preserve the neutrality of these new structures. In the stepwise mechanism the movement of the hydrogen atoms and the electronic reorganization are not concerted, and it implicates the movement of a hydrogen atom at a time with the identification of two or more steps in this reaction. There are two possible neutral imino-enol structures in the C-G system, and both have been considered here. The principal result from this paper is that a different behavior is observed if the hydrogen transfer begins with a H of the guanine or of the cytosine and that a concerted (synchronic in the N-N and asynchronic in the N-O) double-hydrogen transfer can be activated only when the first H atom to move is that of the guanine, in particular. This is different from the A-T system(1) studied previously where the movement in a N-N bridge produces a zwitterionic structure and that in the N-O the concerted double-hydrogen transfer. In both cases a general conclusion can be given: the concerted double-hydrogen process begins with a hydrogen atom of a purinic base.

A theoretical study of Ru(II) polypyridyl DNA intercalators: Structure and electronic absorption spectroscopy of [Ru(phen) 2(dppz)] 2+ and [Ru(tap) 2(dppz)] 2+ complexes intercalated in guanine–cytosine base pairs

The structural and spectroscopic properties of [Ru(phen) 2(dppz)] 2+ and [Ru(tap) 2(dppz)] 2+ (phen = 1,10-phenanthroline; tap = 1,4,5,8-tetraazaphenanthrene; dppz = dipyridophenazine ) have been investigated by means of density functional theory (DFT), time-dependent DFT (TD–DFT) within the polarized continuum model (IEF–PCM) and quantum mechanics/molecular mechanics (QM/MM) calculations. The model of the Δ and Λ enantiomers of Ru(II) intercalated in DNA in the minor and major grooves is limited to the metal complexes intercalated in two guanine–cytosine base pairs. The main experimental spectral features of these complexes reported in DNA or synthetic polynucleotides are better reproduced by the theoretical absorption spectra of the Δ enantiomers regardless of intercalation mode (major or minor groove). This is especially true for [Ru(phen) 2(dppz)] 2+. The visible absorption of [Ru(tap) 2(dppz)] 2+ is governed by the MLCT tap transitions regardless of the environment (water, acetonitrile or bases pair), the visible absorption of [Ru(phen) 2(dppz)] 2+ is characterized by transitions to metal-to-ligand-charge-transfer MLCT dppz in water and acetonitrile and to MLCT phen when intercalated in DNA. The response of the IL dppz state to the environment is very sensitive. In vacuum, water and acetonitrile these transitions are characterized by significant oscillator strengths and their positions depend significantly on the medium with blue shifts of about 80 nm when going from vacuum to solvent. When the complex is intercalated in the guanine–cytosine base pairs the 1IL dppz transition contributes mainly to the band at 370 nm observed in the spectrum of [Ru(phen) 2(dppz)] 2+ and to the band at 362 nm observed in the spectrum of [Ru(tap) 2(dppz)] 2+.

The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine–thymine and guanine–cytosine base pairs

The substituent effects on the geometrical parameters and the individual hydrogen bond (HB) energies of base pairs such as X-adenine-thymine (X-A-T), X-thymine-adenine (X-T-A), X-guanine-cytosine (X-G-C), and X-cytosine-guanine (X-C-G) have been studied by the quantum mechanical calculations at the B3LYP and MP2 levels with the 6-311++G(d,p) basis set. The electron withdrawing (EW) substituents (F and NO(2)) increase the total binding energy (DeltaE) of X-G-C derivatives and the electron donating (ED) substituent (CH(3)) decreases it when they are introduced in the 8 and 9 positions of G. The effects of substituents are reversed when they are located in the 1, 5, and 6 positions of C, with exception of CH(3) in the 1 position and F in the 5 position, which in both cases the DeltaE value decreases negligibly small. With minor exceptions (X=8-CH(3), 8-F, and 9-NO(2)), both ED and EW substituents increase slightly the DeltaE values of X-A-T derivatives. The individual HB energies (E (HB)s) have been estimated using electron densities that calculated at the hydrogen bond critical points (HBCPs) by the atoms in molecules (AIM) method. Most of changes of individual HBs are in consistent with the ED/EW nature of substituents and the role of atoms entered H-bonding. The remarkable change is observed for NO(2) substituted derivative in each case.

The Protonated Guanine–Cytosine Base Pair

Protonated base pairs were recently implicated in the context of DNA proton transfer and charge migration. The effects of protonating different sites of the guanine-cytosine (GC) base pair are studied here by using the DZP++ B3LYP density functional method. Optimized structures for the protonated GC base pair are compared with those of parent GC and the neutral hydrogenated GC radical (GCH). Proton and hydrogen-atom additions significantly disturb the structure of the GC base pair. However, the structural perturbations arising from protonation are often less than those arising from hydrogenation of GC. Protonation of the GC base pair causes significant strengthening of the interstrand hydrogen bonds and a concomitant increase in the base dissociation energies. The adiabatic ionization potentials (AIPs), vertical ionization potentials (VIPs), and proton affinities (PAs) for the different protonation sites of the GC base pair are predicted. The N7 site of guanine is the preferred site for protonation of the GC base pair.

Ab Initio Study of Alkylation of Guanine-Cytosine Base Pair by Sulfur and Nitrogen Mustards

Quantum modeling of the N7(G) alkylation of guanine-cytosine (G-C) base pair by sulfur (HD) and nitrogen mustard (HN2) was performed by using the Density Functional Theory (DFT) BPW91/6–31G++DP procedure. The vibrational IR and Raman spectra are discussed with regard to the N7 position of guanine when electrophilic HD+ episulfonium and HN2+ aziridinium attack the G-C base pair. Thermodynamic and polarizability considerations are also presented. The computed electronic chemical potential and the electrophilicity of the studied species indicate that an electronic transfer is produced from the nucleophile (G-C) base pair to the electrophile HD+ episulfonium or HN2+ aziridinium during the alkylation process.

DFT calculations on the deprotonation site of the one-electron oxidised guanine–cytosine base pair

As calculated by the density functional theory (DFT), the acidity of cytosine's exocyclic amine group (C-N(4)H2) in the base pair G-C is considerably increased upon its one-electron oxidation. The proton affinity (PA) of the amine moiety is lowered by ionisation of G-C (which yields G(*+)-C) from -348.1 to -269.1 kcal mol(-1). The PA is further decreased by 7.6 kcal mol(-1) as a result of the ensuing proton transfer from G(*+) to C to yield the spin-charge separated base pair G(-H)(*)-C(+H)(+). Under these conditions and taking the hydration energy of H(+) into account, the overall proton transfer from the C-N(4)H2 group to the aqueous phase in the major groove is exothermic by -2.4 kcal mol(-1). This proton transfer to water from the initially present DNA radical cation constitutes separation of charge from spin and thus reduces positive charge transfer in double stranded DNA.

Proton Transfer in Guanine−Cytosine Radical Anion Embedded in B-Form DNA

The electron-attachment-induced proton transfer in the guanine-cytosine (G:C) base pair is thought to be relevant to the issues of charge transport and radiation damage in DNA. However, our understanding on the reaction mainly comes from the data of isolated bases and base pairs, and the behavior of the reaction in the DNA duplex is not clear. In the present study, the proton-transfer reaction in reduced G:C stacks is investigated by quantum mechanical calculations with the aim to clarify how each environmental factor affects the proton transfer in G:C(*-). The calculations show that while the proton transfer in isolated G:C(*-) is exothermic with a small energetic barrier, it becomes endothermic with a considerably enhanced energetic barrier in G:C stacks. The substantial effect of G:C stacking is proved to originate from the electrostatic interactions between the dipole moments of outer G:C base pairs and the middle G:C(*-) base-pair radical anion; the extent of charge delocalization is very small and plays little role in affecting the proton transfer in G:C(*-). On the basis of the electrostatic model, the sequence dependence of the proton transfer in the ionized G:C base pair is predicted. In addition, the water molecules in the first hydration shell around G:C(*-) display a pronounced effect that facilitates the proton-transfer reaction; further consideration of bulk hydration only slightly lowers the energetic barrier and reaction energy. We also notice that the water arrangement around an embedded G:C(*-) is different from that around an isolated G:C(*-), which could result in a very different solvent effect on the energetics of the proton transfer. In contrast to the important influences of base stacking and hydration, the effects of sugar-phosphate backbone and counterions are found to be minor. Our calculations also reveal that a G:C base pair embedded in DNA is capable of accommodating two excess electrons only in bulk hydration; the resultant G(N1-H)(-):C(N3+H)(-) dianion is stable and exists long enough to lead to DNA damage. The combination of the present results with the previous findings in literature suggests that the behaviors of charge transport and low-energy electron-induced damage in DNA are highly susceptible to the hydration level.

Reply to “Comment on ‘Excited States of DNA Base Pairs Using Long-Range Corrected Time-Dependent Density Functional Theory’”

In this work we present a study of the excitation energies of adenine, cytosine, guanine, thymine and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC-functionals, BNL, CAM-B3LYP and LC-PBE0 with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement a smaller attenuation parameter was needed which leads to non-optimum performance for ground state properties. B3LYP, on the other hand, severely underestimates the charge transfer (CT) transitions in the base pairs. Surprisingly we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair, but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance was obtained with the LC-PBE0 functional which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange.

Intermolecular Proton Transfer in Microhydrated Guanine−Cytosine Base Pairs: a New Mechanism for Spontaneous Mutation in DNA

Accurate calculations of the double proton transfer (DPT) in the adenine-thymine base pair (AT) were presented in a previous work [J. Phys. Chem. A 2009, 113, 7892.] where we demonstrated that the mechanism of the reaction in solution is strongly affected by surrounding water. Here we extend our methodology to the guanine-cytosine base pair (GC), for which it turns out that the proton transfer in the gas phase is a synchronous concerted mechanism. The O(G)-H-N(C) hydrogen bond strength emerges as the key parameter in this process, to the extent that complete transfer takes place by means of this hydrogen bond. Since the main effect of the molecular environment is precisely to weaken this bond, the direct proton transfer is not possible in solution, and thus the tautomeric equilibrium must be assisted by surrounding water molecules in an asynchronous concerted mechanism. This result demonstrates that water plays a crucial role in proton reactions. It does not act as a passive element but actually catalyzes the DPT.

Excited States of DNA Base Pairs Using Long-Range Corrected Time-Dependent Density Functional Theory

In this work, we present a study of the excitation energies of adenine, cytosine, guanine, thymine, and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC functionals, BNL, CAM-B3LYP, and LC-PBE0, with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement, a smaller attenuation parameter is needed, which leads to nonoptimum performance for ground-state properties. B3LYP, on the other hand, severely underestimates the charge-transfer (CT) transitions in the base pairs. Surprisingly, we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance is obtained with the LC-PBE0 functional, which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange. Thus, this work highlights the difficulties in obtained LC functionals, which provides a good description of both ground- and excited-state properties.

Quinoline alkaloids as intercalative topoisomerase inhibitors

Quinoline alkaloids are abundant in the Rutaceae, and many have exhibited cytotoxic activity. Because structurally related antitumor alkaloids such as camptothecin and fagaronine are known to function as intercalative topoisomerase poisons, it is hypothesized that cytotoxic Stauranthus alkaloids may also serve as intercalative topoisomerase inhibitors. To test this hypothesis theoretically, ten Stauranthus quinoline alkaloids were examined for potential intercalation into DNA using a molecular docking approach. Four of the alkaloids (stauranthine, skimmianine, 3',6'-dihydroxy-3',6'-dihydrostauranthine, and trans-3',4'-dihydroxy-3',4'-dihydrostauranthine) were able to intercalatively dock consistently into DNA. In order to probe the intermolecular interactions that may be responsible for intercalation of these quinoline alkaloids, density functional calculations have been carried out using both the B3LYP and M06 functionals. M06 calculations indicated favorable pi-pi interactions between either skimmianine or stauranthine and the guanine-cytosine base pair. Furthermore, the lowest-energy face-to-face orientation of stauranthine with guanine is consistent with favorable dipole-dipole orientations, favorable electrostatic interactions, and favorable frontier molecular orbital interactions. Likewise, the lowest-energy face-to-face orientation of stauranthine with the guanine-cytosine base pair reveals favorable electrostatic interactions as well as frontier molecular orbital interactions. Thus, not only can quinoline alkaloids dock intercalatively into DNA, but the docked orientations are also electronically favorable.

Ionization potential and structure relaxation of adenine, thymine, guanine and cytosine bases and their base pairs: A quantification of reactive sites

We present density functional theory (DFT) calculations using B3LYP/6-31++G∗∗ method to show relaxation in geometry of base pairs on cation radical formation. The changes in hydrogen bond length and angles show that in the cationic radical form the structure of the base pairs relaxes due to the distribution of charge. According to a recent study, it has been found that, upon excitation hole transfer from base to sugar occurs which results in sugar radical formation and leads to strand breakage [45] [A. Kumar, M.D. Sevilla, J. Phys. Chem. B 110 (2006) 24181]. One hydrogen bond increases, while the other decreases in Adenine–Thymine (AT) base pair and in case of Guanine–Cytosine (GC) base pair, one bond increases and other two decrease. Same is the case with bond angles for both the base pairs. Analysis of the electron density map of Singly Occupied Molecular Orbital (SOMO) reveals that electron is transferred mainly from adenine and guanine bases in the cationic radical formation of AT and GC base pair, respectively. The reactive sites of bases have been analyzed using condensed Fukui functions in a relaxed and frozen core approximation. The effects of relaxation on the reactivity indices are also analyzed.

Excited State, Charge Transfer, and Spin Dynamics in DNA Hairpin Conjugates with Perylenediimide Hairpin Linkers

A series of short DNA hairpins (nG) using perylene-3,4:9,10-bis(dicarboximide) (PDI) as the hairpin linker was synthesized in which the distance between the PDI and a guanine-cytosine (G-C) base pair is systematically varied by changing the number (n - 1) of adenine-thymine (A-T) base pairs between them. Due to the relatively large hydrophobic surface of PDI, the nG hairpins dimerize in buffer solutions. The photophysics and photochemistry of these hairpins were investigated using femtosecond transient absorption and time-resolved electron paramagnetic resonance (TREPR) spectroscopy. Photoexcitation of the self-assembled PDI dimer within each nG hairpin results in subpicosecond formation of its lower exciton state ((1*)PDI(2)) followed by formation of an excimer-like state ((1*X)PDI(2)) with tau = 10-28 ps. Both of these states are lower in energy than (1*)PDI, so that neither can oxidize A, C, and T. Electron transfer from G to (1*)PDI(2) is faster than formation of (1*X)PDI(2) only for 1G. Electron transfer from G to (1*X)PDI(2) for 2G-8G, occurs by the superexchange mechanism and, thus, becomes exponentially less efficient as the G-PDI(2) distance increases. Nevertheless, TREPR studies show that photoexcitation of 2G and 4G produce spin-correlated radical ion pairs having electron spin polarization patterns indicating that a low yield of charge separation proceeds from (1*X)PDI(2) by the radical pair intersystem crossing (RP-ISC) mechanism to initially yield a singlet radical ion pair. The strong spin-polarization of the radical ion pairs makes it possible to observe them, even though their concentration is low. As expected, the hairpin lacking G (0G) and that having the longest G-PDI(2) distance (8G) display no TREPR radical ion pair signals. Hairpins 0G, 2G, 4G, and 8G all exhibit triplet EPR spectra at 85 K. Simulations of the spectra show that (3*)PDI is produced mainly by a spin-orbit-induced intersystem crossing mechanism, while the spectra of 2G and 4G have 5% and 21% contributions, respectively, from (3*)PDI produced by charge recombination of radical ion pairs that originate from RP-ISC. These low percentages of RP-ISC derived (3*)PDI result mainly from the low yield of radical ion pairs in 2G and 4G.