Highlights•We describe the most recent methods to study DNA from electrons to
chromosomes.•Methods were classified as: electronic, atomistic, coarse grained, and …

DNA oligonucleotides are widely used in a diverse range of research fields from analytical
chemistry, molecular biology, nanotechnology to drug delivery. In these applications, DNA …

A robust understanding of the sequence-dependent thermodynamics of DNA hybridization
has enabled rapid advances in DNA nanotechnology. A fundamental understanding of the …

Recognition of single-stranded DNA (ssDNA) or single-stranded RNA (ssRNA) is important
for many fundamental cellular functions. A variety of single-stranded DNA-binding proteins …

During the last decade coarse-grained nucleotide models have emerged that allow us to
study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a …

We develop a robust coarse-grained model for single-and double-stranded DNA by
representing each nucleotide by three interaction sites (TIS) located at the centers of mass of …

As detailed structural characterizations of large complex DNA nanostructures are hard to
obtain experimentally, particularly if they have substantial flexibility, coarse-grained …

DNA carries the genetic information required for the synthesis of RNA and proteins and
plays an important role in many processes of biological development. Understanding the …

G-quadruplexes are the most important noncanonical DNA architectures. Many quadruplex-
forming sequences, including the human telomeric sequence d (GGGTTA) n, have been …

We present CGeNArate, a new model for molecular dynamics simulations of very long
segments of B-DNA in the context of biotechnological or chromatin studies. The developed …