Nucleic acid conformation. Medical search. Frequent questions

The effect of DNA conformation on the dynamics of multidomain proteins. (jnu.ac.in)
Experimental methods of multi-dimensional NMR spectroscopy, dynamics and theoretical description of spin system evolution, multiple resonance NMR technique for structural studies of proteins and nucleic acids by NMR spectroscopy, contemporary methods of structural biology, studies of complex biomolecular systems. (muni.cz)
This concept is well exemplified by natural photosynthetic proteins, and can also be achieved in synthetic nucleic acid nanostructures. (uni-wuerzburg.de)
It can be used to measure the intramolecular stability of a broad spectrum of biomolecules, including proteins, nucleic acids, lipids and detergent micellar systems. (lu.se)

The purpose of this Notice of Funding Opportunity (NOFO) is to advance synthetic nucleic acid platforms for the rapid development and iterative testing of active and passive immunization strategies for HIV prevention, treatment, and cure. (nih.gov)
The utility and technical advantages of synthetic nucleic acid platforms (SNAP), including their efficacy, safety, speed of development, and ease of vaccine manufacture, were revealed during the COVID-19 pandemic, thus instilling hope that these technologies can be leveraged for the development of an effective HIV vaccine and broadly neutralizing antibody (bNAb) delivery. (nih.gov)

Furthermore, the 5.6 number designates this molecule as an isomerase that is capable of changing conformation in cellular molecules. (wikipedia.org)
many molecules have several possible three-dimensional structures, so predicting these structures remains out of reach unless obvious sequence and functional similarity to a known class of nucleic acid molecules, such as transfer RNA (tRNA) or microRNA (miRNA), is observed. (wikipedia.org)
M. Yevdokimov, "Magnetic properties of copper as a constituent of nanobridges formed between spatially fixed deoxyribonucleic acid molecules", JETP Letters, Vol. 81, 2005, pp. 327-329. (scirp.org)
Migration of nucleic acid molecules in an electric field is determined by size and conformation, allowing nucleic fragments of different sizes to be separated. (qiagen.com)

The replicative properties of prions stem from the capacity of PrP Sc to template its conformation on PrP C in a cyclical process resulting in exponential accumulation of prion infectivity ( 8 - 11 ). (cdc.gov)
Although they lack nucleic acids, prions exhibit heritable strain properties that influence disease outcomes, including the time between infection and disease onset (incubation period), clinical signs, patterns of neuronal degeneration and PrP Sc deposition in the central nervous system (CNS), and the ability to replicate in non-CNS tissues such as the lymphoreticular system and musculature ( 12 ). (cdc.gov)
The replication of prions involves the recruitment of the normally expressed prion protein, which has mainly an alpha-helical structure, into a disease-specific conformation that is rich in beta-sheet. (medscape.com)
Highly divergent hypotheses have been put forward regarding the makeup of the prions, including that they consist of nucleic acid only or protein only, are lacking both protein and nucleic acid, or are a polysaccharide. (medscape.com)
This hypothesis suggests that prions contain no nucleic acid and are referred to as PrP Sc . (medscape.com)

Incorporating Locked Nucleic Acid into oligonucleotides increases thermal duplex stability 2 and improves the specificity of oligonucleotide hybridization to target sequences. (sigmaaldrich.com)
In addition, the improved hybridization of the PCR primer or qPCR probe to its target may increase the melting temperature (T m ) by up to 8 °C per Locked Nucleic Acid monomer substitution in medium salt conditions compared to native-state DNA oligonucleotides 4 ( Table 1 ). (sigmaaldrich.com)
Due to Locked Nucleic Acid's improved hybridization characteristics with accompanied increase in T m , Locked Nucleic Acid oligonucleotides can be synthesized to be shorter, which overcomes certain design limitations that occur with native-state DNA oligonucleotides. (sigmaaldrich.com)

Guanidine-II aptamer conformations and ligand binding modes through the lens of molecular simulation. (mpg.de)
In this study, we use molecular dynamics simulation to investigate the chain conformations and dynamics of ring polymers under planar (1D) confinement as a function of film thickness. (aip.org)

The amino acid sequence of human rhodopsin, deduced from the nucleotide sequence of its gene, is 348 residues long and is 93.4% homologous to that of bovine rhodopsin. (nih.gov)

Secondary structure can be predicted from one or several nucleic acid sequences. (wikipedia.org)
The bold letters in the sequences denote Locked Nucleic Acid bases. (sigmaaldrich.com)
Specifically, Locked Nucleic Acid oligonucleotides can be designed to address traditionally problematic target sequences, such as AT- or GC-rich regions. (sigmaaldrich.com)
Cascade will release crRNAs that will bind with foreign nucleic acid sequences - via base pair matching to a "seed" sequence of nucleotides - and silence or otherwise inactivate them. (lbl.gov)

Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions. (muni.cz)
Chemical modifications are powerful tools to probe nucleic acid structure and protein-nucleic acid interactions. (caltech.edu)
Although the structure of RNA is highly flexible, the underlying dynamics of RNA are robust and are limited to transitions between the few conformations that preserve favourable base-pairing and stacking interactions. (duke.edu)

This is partly because the extra oxygen in RNA increases the propensity for hydrogen bonding in the nucleic acid backbone. (wikipedia.org)
New approaches have been developed that take advantage of topological constraints in determining RNA backbone conformation based on secondary structure, and a limited set of other, easily accessible constraints. (duke.edu)
dblp: Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry. (uni-trier.de)

Roche Molecular Systems has been awarded US Patent No. 8,642,293 , "Disposable device for analyzing a liquid sample containing a nucleic acid with a nucleic acid amplification apparatus. (genomeweb.com)
Molecular genetic tests for detecting drug-resistance are, in general, just a variation of nucleic acid amplification (NAA) tests and can reliably provide information on the presence of mutations associated with drug resistance in 1 to 2 days. (cdc.gov)

Building on previous research, representative nucleic acid duplexes were split into logical monomer segments, and atomic coordinates were used to create solid models for 3D printing. (allenpress.com)

Interaction of Charged Amino-Acid Side Chains with Ions: An Optimization Strategy for Classical Force Fields. (mpg.de)
In DNA a sequence of three bases, which is called a codon, is responsible for the encoding of a single amino acid. (wikibooks.org)
The amino acid is added to a growing protein during the process of translation. (wikibooks.org)
Our previous studies using gene-targeted mouse models of chronic wasting disease (CWD) demonstrated that Norway and North America cervids are infected with distinct prion strains that respond differently to naturally occurring amino acid variation at residue 226 of the prion protein. (cdc.gov)

As more research labs and classrooms dive into the field of structural nucleic acid nanotechnology, students and researchers need access to interactive, dynamic, handheld models. (allenpress.com)

Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. (wikipedia.org)
A common problem for researchers working with RNA is to determine the three-dimensional structure of the molecule given only a nucleic acid sequence. (wikipedia.org)
Cornell Research Foundation has been awarded US Patent No. 8,642,269 , "Detection of nucleic acid sequence differences using coupled polymerase chain reactions. (genomeweb.com)
CRISPRs are transcribed and the long primary transcript is processed into a library of short CRISPR-derived RNAs (crRNAs), each of which contains a unique sequence that is complementary to a foreign nucleic acid challenger. (lbl.gov)

Changes to the conformation of coding and non-coding RNAs form the basis of elements of genetic regulation and provide an important source of complexity, which drives many of the fundamental processes of life. (duke.edu)

Scholars@Duke publication: Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation. (duke.edu)

For example, we have recently shown that Molecular Dynamics (MD) simulations, followed by quantum mechanics/molecular mechanics (QM/MM) calculation, provided detailed structural informations and binding energies of the complexes between nickel(II), copper(II), zinc(II) metallointercalators with nucleic acids in the canonical B conformation [1]. (unipa.it)

1-3 Ring polymers, unlike linear and branched polymers that have free chain ends, exhibit distinct physical properties in polymer melts due to their topology, which reduces the number of conformations available to the molecule. (aip.org)

These nucleic acid polymers encode for the all of the materials an organism needs to live in the form of genes. (wikibooks.org)
Today the most frequently used methods for prescreening disease genes for mutations are single strand conformation polymorphism analysis (SSCP) and denaturing high performance liquid chromatography (DHPLC). (bmj.com)

The VP-DSC provides fast, accurate transition midpoint (Tm) determination, as well as a thermodynamic profile that can provide insight into the factors that affect conformation and stability. (lu.se)
NMR spectroscopy or X-ray crystallography, but important width measurements at a single resonance frequency (or questions remain concerning the energetics, stability, and magnetic field strength), making it difficult to separate dynamics of this structurally diverse nucleic acid class. (lu.se)

Dynamic and flexible nucleic acid models can provide current and future scientists with physical intuition for the structure of DNA and the ways that DNA and its synthetic mimics can be used to build self-assembling structures and advanced nanomachines. (allenpress.com)
8-Br-dG should prove useful as a chemical probe for the conformation about glycosidic bonds in unusual nucleic acid structures. (caltech.edu)
Guanine quadruplexes are nucleic acid structures built ions in slow exchange with bulk ions. (lu.se)

DNA is a long chain of linear polymers containing deoxyribose sugars and their covalently bonded bases known as nucleic acids. (wikibooks.org)
Our results show that conformations of ring polymers are similar to the linear polymers under planar confinement, except that ring polymers are less compressed in the direction normal to the walls. (aip.org)
For branched polymers, due to the entropy barrier between different conformations, the longest relaxation time exhibits exponential growth with strand length, which is explained by the arm retraction model. (aip.org)

Table 1 Increasing the number of Locked Nucleic Acid bases in an oligonucleotide increases the T m . (sigmaaldrich.com)
The presence of a single base mismatch has a greater destabilizing effect on the duplex formation between an Locked Nucleic Acid oligonucleotide and its target than with a native-state DNA oligonucleotide. (sigmaaldrich.com)
Alloy Therapeutics announced the launch of its novel AntiClastic™ Antisense Oligonucleotide (AntiClastic ASO) platform, which employs optimally created spatial conformation nucleic acids that further enhance the drug-like properties of antisense. (biospace.com)

The structure of the enzyme includes both a helicase domain, which is responsible for separating nucleic acids, and a topoisomerase domain, which is responsible for the actual introduction of coils into DNA. (wikipedia.org)
5.6.2 designates the enzyme further as being capable of altering nucleic acid, or DNA, conformations. (wikipedia.org)
DNA is a nucleic acid which is capable of duplicating itself via the enzyme known as DNA polymerase. (wikibooks.org)

This article is about the computational prediction of nucleic acid structure. (wikipedia.org)

Nucleic Acid Research. (jnu.ac.in)
H. Tokumitsu, H. Ichikawa, Y. Fukumori, "Chitosan-gadopentetic acid complex nanoparticles for gadolinium neutron-capture therapy of cancer: preparation of novel emulsion-droplet coalescence technique and characterization", Pharmaceutical Research, Vol. 16, 1999, pp. 1830-1835. (scirp.org)
Nucleic Acids Research , 17 (8), 3229-3245. (tmu.edu.tw)

Pink) mutant DNA analysis with Locked Nucleic Acid mutant probe (16mer with 3 Locked Nucleic Acid bases). (sigmaaldrich.com)
Purple) wild-type DNA with Locked Nucleic Acid mutant Probe (16mer with 3 Locked Nucleic Acid bases). (sigmaaldrich.com)

Locked Nucleic Acid PCR primers and qPCR probes are compatible with all real-time thermocyclers and end-point analytical detection instruments. (sigmaaldrich.com)

The ability of oligonucleotides to discriminate between alleles via SNPs is greatly enhanced by the incorporation of Locked Nucleic Acid bases 6-8 ( Figure 2 ). (sigmaaldrich.com)
Shorter oligonucleotides incorporating Locked Nucleic Acid bases can be used at the same temperatures as longer native-state DNA oligonucleotides. (sigmaaldrich.com)
With Locked Nucleic Acid oligonucleotides, the selective placement of Locked Nucleic Acid bases facilitates the optimal design of highly-specific, shorter oligonucleotides that perform well, even at lengths of only 13 to 20 bases. (sigmaaldrich.com)

The infectious agent in the prion disease is composed mainly or entirely of an abnormal conformation of a host-encoded glycoprotein called the prion protein. (medscape.com)

For experimental methods, see Nucleic acid structure determination . (wikipedia.org)
H. Tokumitsu, J. Hiratsuka, Y. Sakurai, T. Kobayashi, H. Ichikawa, Y. Fukumori, "Gadolinium neutron-capture therapy using novel gadopentetic acid-chitosan complex nanoparticles: in vivo growth suppression of experimental melanoma solid tumor", Cancer Letters, Vol. 150, pp. 177-182. (scirp.org)

DNA stands for deoxyribonucleic Acid . (wikibooks.org)

A new inhibited conformation of the KD is observed in a DFG-out conformation and with the glycine-rich loop adopting a structure that blocks ATP binding to the active site. (rcsb.org)
This bridge-locked in the 3'-endo conformation-restricts the flexibility of the ribofuranose ring and locks the structure into a rigid bicyclic formation. (sigmaaldrich.com)
Structure of Locked Nucleic Acid and native-state DNA monomers. (sigmaaldrich.com)
Through a combination of cryo-electron microscopy and three-dimensional image reconstruction, they have determined the structure of a protein complex called "Cascade," that acts as a surveillance system for detecting and inactivating the nucleic acid of invading pathogens. (lbl.gov)
Identified phosphosites were mapped on the Pol II structure which provided indications that they might play a role in regulating the conformation of the clamp region and, as a consequence, interaction of Pol II with nucleic acids. (cipsm.de)

New analogs of the commercial asymmetric monomethine cyanine dyes thiazole orange (TO) and thiazole orange homodimer (TOTO) with hydroxypropyl functionality were synthesized and their properties in the presence of different nucleic acids were studied. (mdpi.com)

The US Army has been awarded US Patent No. 8,642,746 , "Unique calibrator polynucleotides and methods of using in quantitative nucleic acid assays. (genomeweb.com)

For instance, acid base balance in an organism depends on a series of events that are cooperating in a way that if a single procedure was not there, then the whole system would be malfufunctiong. (sciforums.com)
The tecnique of SSCP analysis is based on the principle that changes in nucleic acid composition affect the conformation of single stranded DNA and thereby the mobility of the fragment when it is subjected to electrophoresis under non-denaturing conditions. (bmj.com)

However, when present, both ions are found near the binding site for nucleic acids. (wikipedia.org)

Nucleic acids can be modified either randomly by a variety of chemical reagents or site-specifically with synthetic base analog substitutions. (caltech.edu)
Locked Nucleic Acid in PCR primers, qPCR probes, and other types of oligonucleotides is soluble in water and standard buffers as well as follows Watson-Crick base-pairing rules. (sigmaaldrich.com)

The effect of DNA conformation on protein sliding. (jnu.ac.in)

Anatomy4

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Phenomena and Processes89

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