Jul 13, 2007

Dinucleotide TpT and its 2'-O-Me analogue possess different backbone conformations and flexibilities but similar stacked geometries

The Journal of Physical Chemistry. B
Guillaume P H SantiniJean A H Cognet


UV irradiation at 254 nm of 2'-O,5-dimethyluridylyl(3'-5')-2'-O,5-dimethyluridine (1a) and of natural thymidylyl(3'-5')thymidine (1b) generates the same photoproducts (CPD and (6-4)PP; responsible for cell death and skin cancer). The ratios of quantum yields of photoproducts obtained from 1a (determined herein) to that from 1b are in a proportion close to the approximately threefold increase of stacked dinucleotides for 1a compared with those of 1b (from previous circular dichroism results). 1a and 1b however are endowed with different predominant sugar conformations, C3'-endo (1a) and C2'-endo (1b). The present investigation of the stacked conformation of these molecules, by unrestrained state-of-the-art molecular simulation in explicit solvent and salt, resolves this apparent paradox and suggests the following main conclusions. Stacked dinucleotides 1a and 1b adopt the main characteristic features of a single-stranded A and B form, respectively, where the relative positions of the backbone and the bases are very different. Unexpectedly, the geometry of the stacking of two thymine bases, within each dinucleotide, is very similar and is in excellent agreement with photochemical and circular dichroism results. Analyses of molecu...Continue Reading

  • References
  • Citations5


  • We're still populating references for this paper, please check back later.

Mentioned in this Paper

Malignant Neoplasm of Skin
Molecular Dynamics
In Silico
In Vivo NMR Spectroscopy
High Pressure Liquid Chromatography Procedure
Dinucleoside Polyphosphates

Trending Feeds


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.

Coronavirus Protein Structures

Deciphering and comparing the proteins of different coronaviruses forms a basis for understanding SARS-CoV-2 evolution and virus-receptor interactions. This feed follows studies analyzing the structures of coronavirus proteins, thereby revealing potential drug target sites.

DDX3X Syndrome

DDX3X syndrome is caused by a spontaneous mutation at conception that primarily affects girls due to its location on the X-chromosome. DDX3X syndrome has been linked to intellectual disabilities, seizures, autism, low muscle tone, brain abnormalities, and slower physical developments. Here is the latest research.

ALS: Stress Granules

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease characterized by cytoplasmic protein aggregates within motor neurons. TDP-43 is an ALS-linked protein that is known to regulate splicing and storage of specific mRNAs into stress granules, which have been implicated in formation of ALS protein aggregates. Here is the latest research.

Fusion Oncoproteins in Childhood Cancers

This feed explores the function of fusion oncoproteins in specific childhood cancers, including those from racial/ethnic minority and underserved groups, and to provide preclinical assessment of potential therapeutics and how fusion oncoproteins influence gene expression to perturb normal cellular programs to block lineage differentiation and development

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.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.

Mitotic-exit networks with cytokinesis

Cytokinesis is the highly regulated process that physically separates daughter and mother cells in late mitosis. The mitotic-exit network (MEN), the signalling pathway that drives mitotic exit, directly regulates cytokinesis. Discover the latest research on mitotic-exit networks with cytokinesis here.

DNA Replication Origin

DNA replication is initiated as specific gene sequences, called origins, that function to start DNA replication. Pre-replication complexes are assembled at these origins during the G1 phase of the cell cycle. These sequences allow for targeted activation or deactivation of replication. Discover the latest research on DNA replication origins here.