Recent progress in non-native nucleic acid modifications
While Nature harnesses RNA and DNA to store, read and write genetic information, the
inherent programmability, synthetic accessibility and wide functionality of these nucleic acids …
inherent programmability, synthetic accessibility and wide functionality of these nucleic acids …
Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes
O Doluca, JM Withers, VV Filichev - Chemical reviews, 2013 - ACS Publications
Guanine's array of hydrogen bond donors and acceptors lead it to take part in structures as
diverse as B-DNA, Z-DNA, hairpins, cruciforms, triplexes, and G-quadruplexes; these …
diverse as B-DNA, Z-DNA, hairpins, cruciforms, triplexes, and G-quadruplexes; these …
[HTML][HTML] Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers
We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field,
where emphasis has been made on the correct representation of the α/γ concerted rotation …
where emphasis has been made on the correct representation of the α/γ concerted rotation …
Triplex forming oligonucleotides: sequence-specific tools for gene targeting
MP Knauert, PM Glazer - Human molecular genetics, 2001 - academic.oup.com
Sequence-specificity is the key to effective genetic targeting. With specificity, targeted genes
can be manipulated in multiple ways; without it, gene therapy agents become loose canons …
can be manipulated in multiple ways; without it, gene therapy agents become loose canons …
New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey
Hoogsteen (HG) base pairs (bps) provide an alternative pairing geometry to Watson–Crick
(WC) bps and can play unique functional roles in duplex DNA. Here, we use structural …
(WC) bps and can play unique functional roles in duplex DNA. Here, we use structural …
Insights into Watson–Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A
In the canonical DNA double helix, Watson–Crick (WC) base pairs (bps) exist in dynamic
equilibrium with sparsely populated (∼ 0.02–0.4%) and short-lived (lifetimes∼ 0.2–2.5 ms) …
equilibrium with sparsely populated (∼ 0.02–0.4%) and short-lived (lifetimes∼ 0.2–2.5 ms) …
Simulations of nucleic acids and their complexes
Recent years have seen considerable progress in simulations of nucleic acids.
Improvements in force fields, simulation techniques and protocols, and increasing computer …
Improvements in force fields, simulation techniques and protocols, and increasing computer …
Label-free DNA-methylation detection by direct ds-DNA fragment screening using poly-purine hairpins
CS Huertas, A Aviñó, C Kurachi, A Piqué… - Biosensors and …, 2018 - Elsevier
Cancer diagnosis continuously evolves due to the better understanding of tumorigenic
processes. DNA-methylation is consolidated as an effective biomarker for cancer prognosis …
processes. DNA-methylation is consolidated as an effective biomarker for cancer prognosis …
Nucleic acid triple helices: stability effects of nucleobase modifications
J Robles, A Grandas, E Pedroso… - Current Organic …, 2002 - ingentaconnect.com
In the last years DNA triplexes have been the subject of a very intense research effort, which
has been summarized in a vast number of books and reviews (see for example refs.[1-16]) …
has been summarized in a vast number of books and reviews (see for example refs.[1-16]) …
Computational chemistry and molecular modelling basics
The use of computers for predicting the structures and properties of biomolecules has
closely paralleled computer development since the 1950s, and has been one of the core …
closely paralleled computer development since the 1950s, and has been one of the core …