Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplex
نویسندگان
چکیده
We systematically investigated effects of molecular crowding with trimethylamine N-oxide (TMAO) as a zwitterionic and protective osmolyte and urea as a nonionic denaturing osmolyte on conformation and thermodynamics of the canonical DNA duplex and the non-canonical DNA G-quadruplex. It was found that TMAO and urea stabilized and destabilized, respectively, the G-quadruplex. On the other hand, these osmolytes generally destabilize the duplex; however, it was observed that osmolytes having the trimethylamine group stabilized the duplex at the lower concentrations because of a direct binding to a groove of the duplex. These results are useful not only to predict DNA structures and their thermodynamics under physiological environments in living cells, but also design of polymers and materials to regulate structure and stability of DNA sequences.
منابع مشابه
Is There any Possible Association Between Trimethylamine N-Oxide (TMAO) and Cancer? A Review Study
Background: During the transit of digested animal source foods, gut microbiota synthesize metabolites that can affect the body cells. One of these metabolites, i.e. Trimethylamine (TMA) that is an intermediary metabolite, ultimately leads to the production of Trimethylamine N-oxide (TMAO). Several studies have been conducted to show the association between TMAO and different diseases. This arti...
متن کاملNatural isoflavones regulate the quadruplex–duplex competition in human telomeric DNA
Effects of natural isoflavones on the structural competition of human telomeric G-quadruplex d[AG(3)(T(2)AG(3))(3)] and its related Watson-Crick duplex d[AG(3)(T(2)AG(3))(3)-(C(3)TA(2))(3)C(3)T] are investigated by using circular dichroism (CD), ESI-MS, fluorescence quenching measurement, CD stopped-flow kinetic experiment, UV spectroscopy and molecular modeling methods. It is intriguing to fin...
متن کاملThe effects of DNA supercoiling on G-quadruplex formation
Guanine-rich DNAs can fold into four-stranded structures that contain stacks of G-quartets. Bioinformatics studies have revealed that G-rich sequences with the potential to adopt these structures are unevenly distributed throughout genomes, and are especially found in gene promoter regions. With the exception of the single-stranded telomeric DNA, all genomic G-rich sequences will always be pres...
متن کاملG-quadruplex formation in human telomeric (TTAGGG)4 sequence with complementary strand in close vicinity under molecularly crowded condition
Chromosomes in vertebrates are protected at both ends by telomere DNA composed of tandem (TTAGGG)n repeats. DNA replication produces a blunt-ended leading strand telomere and a lagging strand telomere carrying a single-stranded G-rich overhang at its end. The G-rich strand can form G-quadruplex structure in the presence of K+ or Na+. At present, it is not clear whether quadruplex can form in th...
متن کاملA New Cationic Porphyrin Derivative (TMPipEOPP) with Large Side Arm Substituents: A Highly Selective G-Quadruplex Optical Probe
The discovery of uncommon DNA structures and speculation about their potential functions in genes has brought attention to specific DNA structure recognition. G-quadruplexes are four-stranded nucleic acid structures formed by G-rich DNA (or RNA) sequences. G-rich sequences with a high potential to form G-quadruplexes have been found in many important genomic regions. Porphyrin derivatives with ...
متن کامل