NMR structure of a parallel-stranded DNA duplex at atomic resolution

Nucleic Acids Research
V Rani ParvathyH T Miles

Abstract

DNA dodecamers have been designed with two cytosines on each end and intervening A and T stretches, such that the oligomers have fully complementary A:T base pairs when aligned in the parallel orientation. Spectroscopic (UV, CD and IR), NMR and molecular dynamics studies have shown that oligomers having the sequences d(CCATAATTTACC) and d(CCTATTAAATCC) form a parallel-stranded duplex when dissolved at 1:1 stoichiometry in aqueous solution. This is due to the C:C+ clamps on either end and extensive mismatches in the antiparallel orientation. The structure is stable at neutral and acidic pH. At higher temperatures, the duplex melts into single strands in a highly cooperative fashion. All adenine, cytosine and thymine nucleotides adopt the anti conformation with respect to the glycosidic bond. The A:T base pairs form reverse Watson-Crick base pairs. The duplex shows base stacking and NOEs between the base protons T(H6)/A(H8) and the sugar protons (H1'/H2'/H2") of the preceding nucleotide, as has been observed in antiparallel duplexes. However, no NOEs are observed between base protons H2/H6/H8 of sequential nucleotides, though such NOEs are observed between T(CH3) and A(H8). A three-dimensional structure of the parallel-stranded d...Continue Reading

References

Nov 6, 1989·FEBS Letters·N A TchurikovY D Nechipurenko
Aug 1, 1988·Journal of Biomolecular Structure & Dynamics·R Lavery, H Sklenar
Feb 1, 1989·Journal of Biomolecular Structure & Dynamics·R Lavery, H Sklenar
Apr 1, 1987·Journal of Biomolecular Structure & Dynamics·M CollJ A Subirana
Jul 29, 1988·Science·J H van de SandeT M Jovin
May 17, 1988·Biochemistry·K V CharyH T Miles
Sep 1, 1986·Biopolymers·N Pattabiraman
Oct 14, 1972·Journal of Molecular Biology·F IshikawaH T Miles
Apr 1, 1980·Proceedings of the National Academy of Sciences of the United States of America·E Westhof, M Sundaralingam
Sep 25, 1995·Nucleic Acids Research·T SudaR Kominami
Jan 1, 1994·Annual Review of Biophysics and Biomolecular Structure·S M Mirkin, M D Frank-Kamenetskii
Jun 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·H Robinson, A H Wang
Feb 1, 1996·Biopolymers·I FörtschC Zimmer
Nov 21, 1997·Journal of Molecular Biology·K PhillipsB Luisi
May 25, 1963·Nature·R LANGRIDGE, A RICH

❮ Previous
Next ❯

Citations

Oct 23, 2008·Annals of Biomedical Engineering·Raghvendra SinghStelios T Andreadis
Oct 14, 2011·Physical Chemistry Chemical Physics : PCCP·Gregory J O BeranThomas Hellman Morton
May 9, 2003·Nucleic Acids Research·Shan-Ho ChouAndrew H-J Wang
Oct 2, 2007·Nucleic Acids Research·Pradeep S PallanMartin Egli
Sep 30, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·William R Taylor
Jul 10, 2013·Molecular and Cellular Biology·Shivani MalikSukesh R Bhaumik
Jun 29, 2011·Organic & Biomolecular Chemistry·Mei-Ying PanYang He
Jan 24, 2012·Organic & Biomolecular Chemistry·Xin MingFrank Seela
Mar 28, 2013·The Journal of Physical Chemistry. B·Eline M Basílio Janke, Klaus Weisz
May 16, 2012·Chemical Communications : Chem Comm·Hang ZhaoQianming Chen
Oct 14, 2008·Gene·Pradip Bhattacharya, Ramesh K Bamezai
Sep 17, 2011·Chemistry & Biodiversity·Piotr Guga, Maria Koziołkiewicz
Aug 18, 2006·Journal of Theoretical Biology·William R Taylor
Aug 2, 2005·Computational Biology and Chemistry·William R Taylor
Nov 28, 2014·Dalton Transactions : an International Journal of Inorganic Chemistry·Benjamin J PagesJanice R Aldrich-Wright
Jun 5, 2013·Journal of Biomolecular Structure & Dynamics·Ol'ha O Brovarets'Dmytro M Hovorun
Nov 1, 2016·Langmuir : the ACS Journal of Surfaces and Colloids·Zhicheng HuangJuewen Liu
Jan 18, 2018·Chemistry : a European Journal·Takafumi MiyataKiyohiko Kawai
Aug 5, 2017·The FEBS Journal·Marta Szabat, Ryszard Kierzek
Dec 7, 2018·Rapid Communications in Mass Spectrometry : RCM·Jacob E PorterFrancisco Fernandez-Lima
Mar 15, 2018·Frontiers in Chemistry·Ol'ha O Brovarets'Dmytro M Hovorun
Nov 20, 2016·Angewandte Chemie·Soham MandalJens Müller
Jul 30, 2019·Biophysical Journal·Ofer KimchiLucy J Colwell
Oct 30, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Jim BachmannNikos L Doltsinis
Jun 1, 2010·Bioconjugate Chemistry·Akash K Jain, Santanu Bhattacharya
Jun 12, 2018·The Journal of Physical Chemistry. B·David ButcherFrancisco Fernandez-Lima
Oct 1, 2021·Chemical Reviews·Eric LargyValérie Gabelica

❮ 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.