Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study

Physical Chemistry Chemical Physics : PCCP
M KabeláčM Šíp

Abstract

Molecular dynamics (MD) simulations of single-stranded (ss) and double-stranded (ds) oligonucleotides anchored via an aliphatic linker to a graphene surface were performed in order to investigate the role of the surface charge density in the structure and orientation of attached DNA. Two types of interactions of DNA with the surface are crucial for the stabilisation of the DNA-surface system. Whereas for a surface with a zero or low positive charge density the dispersion forces between the base(s) and the surface dominate, the higher charge densities applied on the surface lead to a strong electrostatic interaction between the phosphate groups of DNA, the surface and the ions. At high-charge densities, the interaction of the DNA with the surface is strongly affected by the formation of a low-mobility layer of counterions compensating for the charge of the surface. A considerable difference in the behaviour of the ds-DNA and ss-DNA anchored to the layer was observed. The ds-DNA interacts with the surface at low- and zero-charge densities exclusively by the nearest base pair. It keeps its geometry close to the canonical B-DNA form, even at surfaces with high-charge densities. The ss-DNA, owing to its much higher flexibility, has ...Continue Reading

References

Sep 1, 1996·Analytical Chemistry·A P AbelH M Widmer
Mar 15, 1997·Nucleic Acids Research·M S ShchepinovE M Southern
Feb 28, 1998·Nucleic Acids Research·C F EdmanM J Heller
Mar 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·J SantaLucia
Dec 1, 1996·Nature Biotechnology·J A FergusonD R Walt
Jan 29, 2002·Nucleic Acids Research·A W PetersonR M Georgiadis
May 7, 2002·Analytical Sciences : the International Journal of the Japan Society for Analytical Chemistry·J LiZ Tang
Nov 22, 2002·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Arnold Vainrub, B Montgomery Pettitt
Apr 15, 2003·Nature Materials·Ming ZhengNancy G Tassi
Jun 26, 2003·Journal of the American Chemical Society·Arnold Vainrub, B Montgomery Pettitt
Aug 9, 2003·Nucleic Acids Research·Scott TaylorAnthony Guiseppi-Elie
Jan 14, 2004·Nucleic Acids Research·F FixeC B V Christensen
Mar 30, 2004·Biopolymers·Arnold Vainrub, B Montgomery Pettitt
Nov 20, 2004·The Journal of Chemical Physics·Daniel J Price, Charles L Brooks
May 12, 2005·Nano Letters·Gang LuEfthimios Kaxiras
Jun 28, 2005·Nucleic Acids Research·Rasmus Wernersson, Henrik Bjørn Nielsen
Jul 22, 2005·Langmuir : the ACS Journal of Surfaces and Colloids·Bong Jin HongJoon Won Park
Oct 4, 2005·Journal of Computational Chemistry·David A CaseRobert J Woods
Jul 11, 2006·Nucleic Acids Research·Yang GaoRosina M Georgiadis
Aug 23, 2006·Applied Bioinformatics·Wuju Li, Xiaomin Ying
Dec 15, 2006·Analytical Chemistry·Sarah J HurstChad A Mirkin
Dec 26, 2006·Journal of Microbiological Methods·Jean-Christophe AvarreGilles Béna
Aug 7, 2007·Journal of the American Chemical Society·Xiongce Zhao, J Karl Johnson
Dec 12, 2007·Nano Letters·Robert R JohnsonMichael L Klein
Dec 22, 2007·Chemical Reviews·Audrey SassolasLoïc J Blum
Jul 3, 2008·The Journal of Physical Chemistry. B·In Suk Joung, Thomas E Cheatham
Sep 11, 2008·Journal of the American Chemical Society·Shoma KugaHiroshi Kawarada
Jan 27, 2010·Journal of Virological Methods·Miroslav SipPetr Dedic
Mar 1, 2008·Journal of Chemical Theory and Computation·Berk HessErik Lindahl

❮ Previous
Next ❯

Citations

Sep 2, 2015·Physical Chemistry Chemical Physics : PCCP·Martin PykalMichal Otyepka
May 16, 2020·Physical Chemistry Chemical Physics : PCCP·Huishu MaXiaoling Lei
May 28, 2013·Journal of Materials Chemistry. B, Materials for Biology and Medicine·Huacheng ZhangYanli Zhao
Jul 18, 2017·Chemistry : a European Journal·Zhen XuHaiping Fang
Sep 26, 2017·The Journal of Physical Chemistry. B·J G VilhenaRubén Pérez
Aug 14, 2019·The Journal of Physical Chemistry. B·Timothy C MooreClare McCabe

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.