Selection of G-quadruplex folding topology with LNA-modified human telomeric sequences in K+ solution

G-rich nucleic acid oligomers can form G-quadruplexes built by G-tetrads stacked upon each other. Depending on the nucleotide sequence, G-quadruplexes fold mainly with two topologies: parallel, in which all G-tracts are oriented parallel to each other, or antiparallel, in which one or more G-tracts are oriented antiparallel to the other G-tracts. In the former topology, all glycosidic bond angles conform to anti conformations, while in the latter topology they adopt both syn and anti conformations. It is of interest to understand the molecular forces that govern G-quadruplex folding. Here, we approach this problem by examining the impact of LNA (locked nucleic acid) modifications on the folding topology of the dimeric model system of the human telomere sequence. In solution, this DNA G-quadruplex forms a mixture of G-quadruplexes with antiparallel and parallel topologies. Using CD and NMR spectroscopies, we show that LNA incorporations can modulate this equilibrium in a rational manner and we establish a relationship between incorporation of LNA nucleotides in syn and/or anti positions and the shift of the equilibrium to obtain exclusively the parallel G-quadruplex. The change in topology is driven by a combination of the C3'-endo puckering of LNA nucleotides and their preference for the anti glycosidic conformation. In addition, the parallel LNA-modified G-quadruplexes are thermally stabilised by about 11 °C relative to their DNA counterparts.     

The mutual relationship between H-bonding and π-stacking interactions: the estimation of individual binding energies in the phenylalanine:G ··· C ternary complex

The mutual relationship between stacked interaction and the individual hydrogen bonds in the phenylalanine:guanine?···?cytosine (Ph:G-C) and phenylalanine:cytosine?···?guanine (Ph:C-G) complexes have been studied at the MPWB1K/6-311++G** and M05-2X/cc-pVDZ levels of theory. The interplay of π-stacking and H-bonding results in the weakening of both interactions. The effect of π-stacking on the geometries and individual hydrogen bond (HB) energies of guanine–cytosine (G-C) base pair have been investigated using electron densities calculated by the atoms in molecules (AIM) method at the hydrogen bond critical points (BCP). The results of AIM analysis are in good agreement with the calculated individual hydrogen bond energies. The π-stacking interactions strengths the HB1 and weakens HB2 and HB3 in the Ph:G-C complexes, while the opposite is true in the Ph:C-G complex. With the increase in the distance between phenylalanine ring and the groups involved in H-bond interactions the change in the H-bond energy increases and the changes in the individual H-bond and π-stacking energies decrease in the ternary complexes.     

Theoretical Study of Hydrated Cd~（2＋） Interactions with Guanine

Theoretical study was performed to investigate how the hydration of cadmium ca-tion influences the structure and properties of guanine.The aqueous environment was simulated by both explicit solvent(1-5 water molecules) model and implicit solvent model.For complexes in which Cd2+ attached to the N(7) and O(6) sites of guanine,energy analysis together with the Natural Bonding Orbital(NBO) analysis were performed to elucidate the bonding characteristics in detail.The most stable structures are penta-coordinate complexes without aqua ligand located at the guanine site.Higher number of water ligands corresponds to higher stabilization energies.Average bonding energies of G-Cd increase with the number of water molecules.Bonding energies of water ligands depend on its position in the complexes.The charge distribution of guanine changed with increasing the number of water ligands,which may also influence the base-pairing pattern of guanine.There is positive charge transfer from guanine to aqua ligand as the number of the hydration waters increases.IEFPCM optimization has results comparable to the [CdG(H2O)5]2+ structure 5a.     

鸟嘌呤质子互变反应机理的DFT研究

在密度泛函B3LYP/6-311G++**理论水平上,对气相和水相鸟嘌呤的两种形式(烯醇式与酮式)之间的质子转移(Path A:分子内和Path B:水助质子转移)互变异构体及其过渡态进行了几何构型全自由度优化,获得它们在气相和水相中的几何结构和电子结构,将PCM(极化连续介质模型)反应场溶剂模型用于水相计算.结果显示,在气相和水相中,烯醇式的稳定性大于酮式.Path A的过渡态结构为平面四元环,而Path B的过渡态结构为平面六元环;Path B所需活化能较低,约为Path A所需活化能的1/2.     

Stabilization of G‐Quadruplex DNA with Platinum(II) Schiff Base Complexes: Luminescent Probe and Down‐Regulation of c‐myc Oncogene Expression

The interactions of a series of platinum(II) Schiff base complexes with c‐myc G‐quadruplex DNA were studied. Complex [PtL ^1a ] ( 1 a ; H₂L ^1a =N,N′‐bis(salicylidene)‐4,5‐methoxy‐1,2‐phenylenediamine) can moderately inhibit c‐myc gene promoter activity in a cell‐free system through stabilizing the G‐quadruplex structure and can inhibit c‐myc oncogene expression in cultured cells. The interaction between 1 a and G‐quadruplex DNA has been examined by ¹H NMR spectroscopy. By using computer‐aided structure‐based drug design for hit‐to‐lead optimization, an in silico G‐quadruplex DNA model has been constructed for docking‐based virtual screening to develop new platinum(II) Schiff base complexes with improved inhibitory activities. Complex [PtL ³ ] ( 3 ; H₂L ³ = N,N′‐bis{4‐[1‐(2‐propylpiperidine)oxy]salicylidene}‐4,5‐methoxy‐1,2‐phenylenediamine) has been identified with a top score in the virtual screening. This complex was subsequently prepared and experimentally tested in vitro for its ability to stabilize or induce the formation of the c‐myc G‐quadruplex. The inhibitory activity of 3 (IC₅₀=4.4 μM ) is tenfold more than that of 1 a . The interaction between 1 a or 3 with c‐myc G‐quadruplex DNA has been examined by absorption titration, emission titration, molecular modeling, and NMR titration experiments, thus revealing that both 1 a and 3 bind c‐myc G‐quadruplex DNA through an external end‐stacking mode at the 3’ terminal face of the G‐quadruplex. Such binding of G‐quadruplex DNA with 3 is accompanied by up to an eightfold increase in the intensity of photoluminescence at λ_max=652 nm. Complex 3 also effectively down‐regulated the expression of c‐myc in human hepatocarcinoma cells.     

Discrimination of single‐stranded DNA homopolymers by sieving out G‐quadruplex using tiny solid‐state nanopores

Nanopore sensor has been developed as a promising technology for DNA sequencing at the single‐base resolution. However, the discrimination of homopolymers composed of guanines from other nucleotides has not been clearly revealed due to the easily formed G‐quadruplex in aqueous buffers. In this work, we report that a tiny silicon nitride nanopore was used to sieve out G tetramers to make sure only homopolymers composed of guanines could translocate through the nanopore, then the 20‐nucleotide long ssDNA homopolymers could be identified and differentiated. It is found that the size of the nucleotide plays a major role in affecting the current blockade as well as the dwell time while DNA is translocating through the nanopore. By the comparison of translocation behavior of ssDNA homopolymers composed of nucleotides with different volumes, it is found that smaller nucleotides can lead to higher translocation speed and lower current blockage, which is also found and validated for the 105‐nucleotide long homopolymers. The studies performed in this work will improve our understanding of nanopore‐based DNA sequencing at single‐base level.     

Calculation and analysis of vibrational spectra of adenine–thymine,guanine–cytosine,and adenine–uracil complementary pairs in the condensed state

We have calculated the frequencies of the normal vibrations of the complementary nucleic acid base pairs adenine–thymine, guanine–cytosine, adenine–uracil, corresponding to the Watson–Crick structure, and the adenine–uracil pair, corresponding to the Hoogsteen structure, in condensed states and we interpret the spectra. We determine the contributions of hydrogen bonds to the vibrational modes of the complementary pairs. We have analyzed the nature of the relative displacements of the nucleic acid bases as integral molecular units along the hydrogen bonds. We show the role of hydrogen bonds in tautomeric interconversions of complementary nucleic acid base pairs. Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 76, No. 1, pp. 84–92, January–February, 2009.     

Iso-guanine quintet complexes coordinated by mono valent cations (Na+, K+, Rb+, and Cs+)

The geometric structures, the interaction energies, the vibrational characteristics, and the electronic structures of the complexes of the isoguanine (isoG) quintet coordinated with mono valent cations (Na(+), K(+), Rb(+), and Cs(+)) have been studied based on the nonplanar models. The geometry of the local minimum structure of the Na(+)-isoG quintet complex deviates significantly from the planar structure. The geometric characteristics of the Na(+)-isoG quintet complex support the experimental findings that Na(+) is unlikely to induce the formation of the isoG quintet-based pentaplexes. Similar to the guanine tetraplexes, the ionic selectivity of the isoG quintet-based pentaplexes is largely dominated by the hydration energy of the cations. After hydration correction, the positive value of the free energy difference for the formation of the Na(+)-isoG quintet complex (DeltaG(f)) suggests that the isoG quintet is unable to capture the hydrated Na(+). The negative values of DeltaG(f) for the K(+) and Rb(+) complexes implies that both ions have the tendency to be inserted into the isoG pentaplexes. This study suggests that, to elucidate the high Cs(+) selectivity of isoG pentaplexes, it is necessary to extend the model from the isoG quintet to the isoG decamer.     

Caught in the Loop: Binding of the [Ru(phen)2(dppz)]2+ Light-Switch Compound to Quadruplex DNA in Solution Informed by Time-Resolved Infrared Spectroscopy

Ultrafast time-resolved infrared (TRIR) is used to report on the binding site of the [Ru(phen)₂(dppz)]²⁺ “light-switch” complex with both bimolecular (Oxytricha nova telomere) and intramolecular (human telomere) guanine-quadruplex structures in both K⁺ and Na⁺ containing solutions. TRIR permits the simultaneous monitoring both of the “dark” and “bright” states of the complex and of the quadruplex nucleobase bases, the latter via a Stark effect induced by the excited state of the complex. These data are used to establish the contribution of guanine base stacking and loop interactions to the binding site of this biologically relevant DNA structure in solution. A particularly striking observation is the strong thymine signal observed for the Na⁺ form of the human telomere sequence, which is expected to be in the anti-parallel conformation.