Effects of guanine bases at the central loop on stabilization of the quadruplex DNAs and their interactions with Meso-tetrakis(N-methylpyridium-4-yl)porphyrin

Jeon, Seung Hyuck; Moon, Ji-Hye; Lee, Myung Won; Kim, Seog K.

doi:10.1016/j.bpc.2015.05.011

Cited by 4 publications

(2 citation statements)

References 40 publications

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“…The G-to-I substitution resulted in a slight decrease in the thermal stability; the G-to-A change triggered a larger destabilization. T m values were 50.8°C, 49.5°C, and 45.0°C for the wild-type, the I-modified, and the A-modified GQs, respectively [ 334 ]. Results of a recent study [ 335 ] have shown that incorporation of dI into selected positions of AS1411 GQ can elevate its biological activity.…”

Section: Natural Base Lesions and Epigenetic Modifications In Gq Dmentioning

confidence: 99%

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

Sági¹

2017

Journal of Nucleic Acids

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Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.

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Section: Natural Base Lesions and Epigenetic Modifications In Gq Dmentioning

confidence: 99%

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

Sági¹

2017

Journal of Nucleic Acids

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“…Several theoretical studies on these systems have been performed but, because of the large number of atoms, a lot of these papers investigate the structures of these systems with MD simulations including recent research. − Recently, MD study has been applied to two of the most powerful stabilizers RHPS4 and BRACO-19 of G-quadruplex systems and reveals that the central K + has little influence on the binding conformations of the bound stabilizers, but without the central K + , either RHPS4 or BRACO-19, cannot stabilize the structure of G-quadruplex. In contrast to MD, quantum mechanics (QM) approach can offer an inherently more accurate description of G-quadruplex structures, because it can consider the polarization − and, as known, it is more accurate in the treatment of hydrogen-bonding , and stacking interactions. , Only a few papers that use a QM method can be found in the literature.…”

Section: Introductionmentioning

confidence: 99%

Quantum Mechanical Investigation of the G-Quadruplex Systems of Human Telomere

Villani

2018

ACS Omega

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The three G-quadruplexes involved in the human telomere have been studied with an accurate quantum mechanical approach, and the possibility of reducing them to a simpler model has been tested. The similarities and the differences of these three systems are shown and discussed. Each system has been analyzed through different properties and compared to the others. In particular, we have considered: (1) the shape of the cavity and the atomic charges around it; (2) the electric field in and out of the cavity; (3) the stabilization energy due to the stacking of G-tetrads, to the H-bonds and to the ion interactions; and, finally, (4) to study the mechanism of the process of the ion inclusion in the cavity, the curves of potential energy due to the movement of the Na + and K + ions toward the cavity. The results suggest that a detailed study is essential in order to obtain the quantitative properties of these complex systems, but also that some qualitative behaviors can be schematized. Our study makes it clear that the entry of an ion in the cavity of these systems is a complex process, where it is possible to find stable structures with the ion out and in the cavity. Moreover, it is possible that more than one diabatic state is involved in this process.

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Behavior of the Guanine Base in G‐quadruplexes Probed by the Fluorescent Guanine Analog, 6‐Methyl Isoxanthopterin

Han

Chitrapriya

Lee

et al. 2017

Bulletin Korean Chem Soc

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In this study, circular dichroism (CD) spectrum and fluorescence techniques were used to examine the dynamic properties and microenvironment of the guanine base (G) at the central loop and at the middle of the G‐stem of the G‐quadruplex formed from the G3T2G3TGTG3T2G3 sequence (G‐quadruplex 1), in which the G base at the 10th and 13th position were replaced with a fluorescent G analog, 6‐methyl isoxanthopterin (6MI) (G‐quadruplex 2 and 3, respectively). For all G‐quadruplexes, the CD spectrum revealed a positive band at 263 nm and a shoulder at 298 nm, and the thermal melting profiles were the sum of at least two sigmoidal curves. These observations indicated the presence of two conformers in the G‐quadruplex. The fluorescence intensity of G‐quadruplex 2 was greater than 3, as expected from the extent of stacking interaction, which is larger in the G(6MI)G sequence than the T(6MI)T sequence. The efficiency of fluorescence quenching by the polar acrylamide quencher and negatively charged I− quencher were larger for G‐quadruplex 3, suggesting that 6MI in the G(6MI)G stem is exposed more to the aqueous environment compared to that in the T(6MI)T central loop. In the latter case, 6MI may direct to the center of the top G‐quartet layer. The possibility of hydrogen bond formation between the carbonyl group of 6MI and the acrylamide of the G‐quadruplex 3 was proposed.

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Effects of guanine bases at the central loop on stabilization of the quadruplex DNAs and their interactions with Meso-tetrakis(N-methylpyridium-4-yl)porphyrin

Cited by 4 publications

References 40 publications

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

Quantum Mechanical Investigation of the G-Quadruplex Systems of Human Telomere

Behavior of the Guanine Base in G‐quadruplexes Probed by the Fluorescent Guanine Analog, 6‐Methyl Isoxanthopterin

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