Solution structure of 2',5' d(G4C4). Relevance to topological restrictions and nature's choice of phosphodiester links

European Journal of Biochemistry
B J PremrajN Yathindra

Abstract

The NMR structure of 2',5' d(GGGGCCCC) was determined to gain insights into the structural differences between 2',5'- and 3',5'-linked DNA duplexes that may be relevant in elucidating nature's choice of sugar-phosphate links to encode genetic information. The oligomer assumes a duplex with extended nucleotide repeats formed out of mostly N-type sugar puckers. With the exception of the 5'-terminal guanine that assumes the syn glycosyl conformation, all other bases prefer the anti glycosyl conformation. Base pairs in the duplex exhibit slide (-1.96 A) and intermediate values for X-displacement (-3.23 A), as in ADNA, while their inclination to the helical axis is not prominent. Major and minor grooves display features intermediate to A and BDNA. The duplex structure of iso d(GGGGCCCC) may therefore be best characterized as a hybrid of A and BDNA. Importantly, the results confirm that even 3' deoxy 2',5' DNA supports duplex formation only in the presence of distinct slide (>or=-1.6 A) and X-displacement (>or=-2.5 A) for base pairs, and hence does not favor an ideal BDNA topology characterized by their near-zero values. Such restrictions on base pair movements in 2',5' DNA, which are clearly absent in 3',5' DNA, are expected to impo...Continue Reading

References

Apr 11, 1992·Nucleic Acids Research·R KierzekD H Turner
Oct 1, 1986·Journal of Biomolecular Structure & Dynamics·M CollA Rich
Dec 16, 1983·Biochemical and Biophysical Research Communications·M RanceK Wüthrich
Jun 1, 1996·Journal of Biomolecular Structure & Dynamics·H SawaiH Ozaki
Jun 6, 1998·Nucleic Acids Research·R E Dickerson
Nov 13, 1998·Nucleic Acids Research·M J Damha, A Noronha
Dec 2, 1998·Journal of Biomolecular Structure & Dynamics·B J Premraj, N Yathindra
Jun 26, 1999·Science·A Eschenmoser
May 9, 2001·Biochemical and Biophysical Research Communications·B J PremrajN Yathindra
Dec 6, 2001·Journal of the American Chemical Society·R N Hannoush, M J Damha
Jan 11, 2003·Journal of Biomolecular NMR·Olivier MauffretSerge Fermandjian

❮ Previous
Next ❯

Citations

Feb 23, 2011·Chemical Communications : Chem Comm·Namrata ErandeVaijayanti A Kumar
Feb 12, 2014·Proceedings of the National Academy of Sciences of the United States of America·Jia ShengJack W Szostak
Dec 31, 2016·Nucleic Acids Research·Fusheng ShenJia Sheng
Oct 20, 2015·Organic & Biomolecular Chemistry·Manisha N AherVaijayanti A Kumar
Jan 21, 2010·Journal of Biomolecular Structure & Dynamics·Aditi BorkarDhananjay Bhattacharyya
Nov 28, 2013·Chemical Communications : Chem Comm·Anita D GunjalVaijayanti A Kumar
Nov 27, 2019·Marine Pollution Bulletin·Ganesh Kumar ADharani G
Mar 25, 2009·Journal of the American Chemical Society·Eric D HorowitzNicholas V Hud

❮ 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.