Ab initio surface hopping dynamics calculations were performed to study the photophysical behavior of cytosine and guanine embedded in DNA using a quantum mechanical/molecular mechanics (QM/MM) approach. It was found that the decay rates of photo excited cytosine and guanine were affected in a completely different way by the hydrogen bonding to the DNA environment. In case of cytosine, the geom...

Background: Aberrant methylation of cytosine-guanine dinucleotide islands leads to inactivation of tumor suppressor genes in breast cancer. Tumor suppressor genes are unmethylated in normal tissue and often become hypermethylated during tumor formation, leading to gene silencing. We investigated the association between E-cadherin (CDH1) and estrogen receptor-α (ESRα) gene promoter methylation a...

A study of the characteristics of the guanine-cytosine bond is important to the understanding of its contributions to the secondary structure of nucleic acids. However, such a study is very difficult to carry out with synthetic homopolymers because of the occurrence of stable self-bonded guanine structures (1). It is almost impossible to obtain polyriboguanylic acid (poly Gl) in a single-strand...

In many prokaryotes, asymmetrical mutational or selective pressures have caused compositional skews between complementary strands of replication arms, especially sensitive in the distribution of guanine and cytosine. In Escherichia coli, most of the guanine/cytosine skew is caused by mutation rates differing on leading and lagging strands, but contribution of skewed functionally important guani...

The interaction of molecules with inorganic substrates is a crucial issue forapplications in molecular electronics. It influences important factors suchas the immobilization efficiency and charge injection through inter-face. Moreover, mechanical aspects connected to unfolding biologicalmolecules are important.We hereby present recent efforts our group tackle these problems,based on density fun...

The DNA double helix, one of the most amazing and important self-assembled structures found in nature is dependendent on the interaction between the DNA base molecules: Adenine (A) and Thymine (T); and Cytosine (C) and Guanine (G). Recently there have been a number of Scanning Tunneling Microscope (STM) experiments on the gold (111) surface in which the DNA base molecules (Adenine (A), Cytosine...

We present ab initio Hartree-Fock lattice calculations on adenine, guanine and hypoxanthine, and some pyrimidines, including cytosine and uracil derivatives. The electric field gradients at the nitrogen centres are related to NQR experimental determinations of nuclear quadrupole coupling constants. The calculations were performed as lattice calculations in the unit cell environment, with 6-31G ...

Coronaviruses are responsible for various diseases ranging from the common cold to severe infections like Middle East syndromes and acute respiratory syndrome. However, a new coronavirus strain known as COVID-19 developed into pandemic resulting in an ongoing global public health crisis. Therefore, there is need understand genomic transformations that occur within this family of viruses order l...

Metal ion interactions with DNA have far-reaching implications in biochemistry and DNA nanotechnology. Ag(+) is uniquely interesting because it binds exclusively to the bases rather than the backbone of DNA, without the toxicity of Hg(2+). In contrast to prior studies of Ag(+) incorporation into double-stranded DNA, we remove the constraints of Watson-Crick pairing by focusing on homo-base DNA ...