The helix-inversion mechanism in double-stranded helical oligomers bridged by rotary cyclic boronate esters.

08:00 EDT 16th May 2019 | BioPortfolio

Summary of "The helix-inversion mechanism in double-stranded helical oligomers bridged by rotary cyclic boronate esters."

Attracted by the numerous regulatory functions of double-helical biopolymers such as DNA, many researchers have synthesized various double-helical systems. A recently synthesized double-stranded helical oligomer covalently bridged by rotary boronate esters (BBDD) was shown to undergo helix-inversion that might serve as platform to design rotor systems. However, the detailed helix-inversion mechanism could not be investigated experimentally. Direct molecular dynamics simulations based on density-functional tight-binding energies and gradients computed on-the-fly reveal that disentanglement to the unraveled form and following exchange of the twisted terminal trimethylsilyl (TMS) groups are prerequisites for the observed helix-inversion. The potential of mean force confirms that the originally assumed "concurrent" rotation of the boronate esters and the helix-inversion involves shorter time scale "step-wise" processes, triggered by the disentanglement and exchange of the TMS groups. These results indicate that inversion dynamics of double-helical molecules such as BBDD may be controllable by chemical fine-tuning of the terminal groups. © 2019 Wiley Periodicals, Inc.


Journal Details

This article was published in the following journal.

Name: Journal of computational chemistry
ISSN: 1096-987X


DeepDyve research library

PubMed Articles [9206 Associated PubMed Articles listed on BioPortfolio]

Sequence-controlled Stimuli-responsive Single-Double Helix Conversion between 1:1 and 2:2 Chloride-Foldamer Complexes.

The primary sequence in biopolymers carries the information to direct folded secondary structures, modulate their stabilities, and control the resultant functions. Our ability to encode such informati...

Amyloid Self-Assembly of hIAPP8-20 via the Accumulation of Helical Oligomers, α-Helix to β-Sheet Transition, and Formation of β-Barrel Intermediates.

The self-assembly of human islet amyloid polypeptide (hIAPP) into β-sheet-rich nanofibrils is associated with the pathogeny of type 2 diabetes. Soluble hIAPP is intrinsically disordered with N-termin...

Genome-wide mapping of nucleotide excision repair with XR-seq.

Nucleotide excision repair is a versatile mechanism to repair a variety of bulky DNA adducts. We developed excision repair sequencing (XR-seq) to study nucleotide excision repair of DNA adducts in hum...

Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study.

One of the fundamental events in protein folding is α-helix formation, which involves sequential development of a series of helical hydrogen-bonds between the backbone C=O group of residues i and the...

Probing the role of dispersion energy on structural transformation of double-stranded xylo- and ribo-nucleic acids.

The structural transformation of double-stranded octameric xyloNA and RNA were probed by modulating the dispersion energy. For the RNA, the increase and the decrease in dispersion energy lead to over-...

Clinical Trials [3172 Associated Clinical Trials listed on BioPortfolio]

Role of Antibodies Against Glutamate Receptors and Double Stranded DNA in Epilepsy Patients

The investigators will check the serum of epilepsy patients for antibodies against glutamate receptors and double stranded DNA. They will characterise the patients (by the kind of epilepsy...

Negative Pressure Vs. Compression in Venous Ulcers

This study randomises patients with venous leg ulcers, to be managed either using conventional compression bandages or a bridged vacuum assisted closure system under compression.

Helical Tomotherapy as a Radiotherapy Technique for Treating Bone Metastases

To assess the safety and efficacy of a single fraction of radiotherapy using helical tomotherapy to treat bone metastases.

Nelfinavir in Systemic Lupus Erythematosus

Systemic Lupus Erythematosus (SLE) is a chronic autoimmune disease in which the body's immune system attacks different parts of the body. SLE is characterized by inflammation that leads t...

Study on 'The Use of Non-Contrast Helical Computerized Tomogram in Predicting Treatment Outcomes of Upper Ureteric Stone by Extracorporeal Shock Wave Lithotripsy Using the Sonolith 4000+ Lithotripter'

The purpose of this research is to assess the role of non-contrast helical computerized tomogram in predicting the treatment outcome of upper ureteric stone by extracorporeal shock wave li...

Medical and Biotech [MESH] Definitions

RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.

A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).

An endoribonuclease that is specific for double-stranded RNA. It plays a role in POST-TRANSCRIPTIONAL RNA PROCESSING of pre-RIBOSOMAL RNA and a variety of other RNA structures that contain double-stranded regions.

Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)

An APOBEC deaminase that functions as an inhibitor of RETROVIRIDAE replication and inhibits the mobility of RETROTRANSPOSONS via deaminase-dependent and independent mechanisms. It is selective for SINGLE-STRANDED DNA and does not deaminate double-stranded DNA or single or DOUBLE-STRANDED RNA. It exhibits potent antiviral activity against VIF PROTEIN deficient HIV-1 through the creation of hypermutations in the VIRAL DNA. It also has anti-viral activity against SIMIAN IMMUNODEFICIENCY VIRUSES and HEPATITIS B VIRUS.

Quick Search


DeepDyve research library

Relevant Topic

Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...

Searches Linking to this Article