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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.
This article was published in the following journal.
Name: Journal of computational chemistry
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...
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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...
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.
To assess the safety and efficacy of a single fraction of radiotherapy using helical tomotherapy to treat bone metastases.
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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'
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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.
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...