A locked nucleic acid (LNA), also known as bridged nucleic acid (BNA), and often referred to as inaccessible RNA, is a modified RNA nucleotide in which the ribose moiety is modified with an extra bridge connecting the 2' oxygen and 4' carbon. The bridge "locks" the ribose in the 3'-endo (North) conformation, which is often found in the A-form duplexes. This structure provides for increased stability against enzymatic degradation. LNA also offers improved specificity and affinity in base-pairing as a monomer or a constituent of an oligonucleotide. LNA nucleotides can be mixed with DNA or RNA residues in a oligonucleotide.
A molecular logic gate is a molecule that performs a logical operation based on one or more physical or chemical inputs and a single output. The field has advanced from simple logic systems based on a single chemical or physical input to molecules capable of combinatorial and sequential operations such as arithmetic operations. Molecular logic gates work with input signals based on chemical processes and with output signals based on spectroscopic phenomena.
Nucleic acid design is the process of generating a set of nucleic acid base sequences that will associate into a desired conformation. Nucleic acid design is central to the fields of DNA nanotechnology and DNA computing. It is necessary because there are many possible sequences of nucleic acid strands that will fold into a given secondary structure, but many of these sequences will have undesired additional interactions which must be avoided. In addition, there are many tertiary structure considerations which affect the choice of a secondary structure for a given design.
Douglas "Doug" H. Turner is an American chemist and Professor of Chemistry at the University of Rochester.
This is a list of notable computer programs that are used for nucleic acids simulations.
DNA nanotechnology is the design and manufacture of artificial nucleic acid structures for technological uses. In this field, nucleic acids are used as non-biological engineering materials for nanotechnology rather than as the carriers of genetic information in living cells. Researchers in the field have created static structures such as two- and three-dimensional crystal lattices, nanotubes, polyhedra, and arbitrary shapes, and functional devices such as molecular machines and DNA computers. The field is beginning to be used as a tool to solve basic science problems in structural biology and biophysics, including applications in X-ray crystallography and nuclear magnetic resonance spectroscopy of proteins to determine structures. Potential applications in molecular scale electronics and nanomedicine are also being investigated.
Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule. The secondary structures of biological DNAs and RNAs tend to be different: biological DNA mostly exists as fully base paired double helices, while biological RNA is single stranded and often forms complex and intricate base-pairing interactions due to its increased ability to form hydrogen bonds stemming from the extra hydroxyl group in the ribose sugar.
Spherical nucleic acids (SNAs) are nanostructures that consist of a densely packed, highly oriented arrangement of linear nucleic acids in a three-dimensional, spherical geometry. This novel three-dimensional architecture is responsible for many of the SNA's novel chemical, biological, and physical properties that make it useful in biomedicine and materials synthesis. SNAs were first introduced in 1996 by Chad Mirkin’s group at Northwestern University.
A sequence-controlled polymer is a macromolecule, in which the sequence of monomers is controlled to some degree. This control can be absolute but not necessarily. In other words, a sequence-controlled polymer can be uniform or non-uniform (Ð>1). For example, an alternating copolymer synthesized by radical polymerization is a sequence-controlled polymer, even if it is also a non-uniform polymer, in which chains have different chain-lengths and slightly different compositions. A biopolymer with a perfectly-defined primary structure is also a sequence-controlled polymer. However, in the case of uniform macromolecules, the term sequence-defined polymer can also be used.
Robert Dirks was an American chemist known for his theoretical and experimental work in DNA nanotechnology. Born in Thailand to a Thai Chinese mother and American father, he moved to Spokane, Washington at a young age. Dirks was the first graduate student in Niles Pierce's research group at the California Institute of Technology, where his dissertation work was on algorithms and computational tools to analyze nucleic acid thermodynamics and predict their structure. He also performed experimental work developing a biochemical chain reaction to self-assemble nucleic acid devices. Dirks later worked at D. E. Shaw Research on algorithms for protein folding that could be used to design new pharmaceuticals.
Cynthia J. Burrows is an American chemist, currently a distinguished professor in the department of chemistry at the University of Utah, where she is also the Thatcher Presidential Endowed Chair of Biological Chemistry. Burrows was the Senior Editor of the Journal of Organic Chemistry (2001-2013) and became Editor-in-Chief of Accounts of Chemical Research in 2014.,,
The Mukaiyama hydration is an organic reaction involving formal addition of an equivalent of water across an olefin by the action of catalytic bis(acetylacetonato)cobalt(II) complex, phenylsilane and atmospheric oxygen to produce an alcohol with Markovnikov selectivity.
Jeffrey I. Zink is an American molecular biologist and chemist currently a Distinguished Professor at University of California, Los Angeles whose interests are in materials, nanoscience, physical and inorganic chemistry. His current research is examining molecules containing metal and nanomaterials. He worked with Fraser Stoddart to help develop machines that could be applied to deliver drugs. According to Google Scholar, his highest citations are 2,503, 2,131, 1,968, 1,873, and 1,150.
Kenneth M. Merz Jr. is an American biochemist and molecular biologist currently the Joseph Zichis Chair and a distinguished university professor at Michigan State University and editor-in-chief of American Chemical Society's Journal of Chemical Information and Modeling. A highly cited expert in his field, his research interests are in computational chemistry and biology and computer-aided drug design (CADD). His group has been involved in developing the widely using AMBER suite of programs for simulating chemical and biological systems and the QUICK program for quantum chemical calculations.
Complex lasso proteins are proteins in which a covalent loop is pierced by another piece of the backbone. Subclass of complex lasso proteins are Lasso peptides in which the loop is formed by post-translational amide bridge.
Antibody-oligonucleotide conjugates or AOCs belong to a class of chimeric molecules combining in their structure two important families of biomolecules: monoclonal antibodies and oligonucleotides.
Mario Barbatti is a Brazilian physicist, computational theoretical chemist, and writer. He is specialized in the development and application of mixed quantum-classical dynamics for the study of molecular excited states. He is also the leading developer of the Newton-X software package for dynamics simulations. Mario Barbatti held an A*Midex Chair of Excellence at the Aix Marseille University between 2015 and 2019, where he is a professor since 2015.
In the context of chemistry and molecular modelling, the Interface force field (IFF) is a force field for classical molecular simulations of atoms, molecules, and assemblies up to the large nanometer scale, covering compounds from across the periodic table. It employs a consistent classical Hamiltonian energy function for metals, oxides, and organic compounds, linking biomolecular and materials simulation platforms into a single platform. The reliability is often higher than that of density functional theory calculations at more than a million times lower computational cost. IFF includes a physical-chemical interpretation for all parameters as well as a surface model database that covers different cleavage planes and surface chemistry of included compounds. The Interface Force Field is compatible with force fields for the simulation of primarily organic compounds and can be used with common molecular dynamics and Monte Carlo codes. Structures and energies of included chemical elements and compounds are rigorously validated and property predictions are up to a factor of 100 more accurate relative to earlier models.
Eric Meggers is a German chemist and professor of organic chemistry and chemical biology at the University of Marburg, Germany. His research currently focuses on the design of chiral catalysts for stereoselective synthesis.
In computational chemistry, natural resonance theory (NRT) is an iterative, variational functional embedded into the natural bond orbital (NBO) program, commonly run in Gaussian, GAMESS, ORCA, Ampac and other software packages. NRT was developed in 1997 by Frank A. Weinhold and Eric D. Glendening, chemistry professors at University of Wisconsin-Madison and Indiana State University, respectively. Given a list of NBOs for an idealized natural Lewis structure, the NRT functional creates a list of Lewis resonance structures and calculates the resonance weights of each contributing resonance structure. Structural and chemical properties, such as bond order, valency, and bond polarity, may be calculated from resonance weights. Specifically, bond orders may be divided into their covalent and ionic contributions, while valency is the sum of bond orders of a given atom. This aims to provide quantitative results that agree with qualitative notions of chemical resonance. In contrast to the "wavefunction resonance theory" (i.e., the superposition of wavefunctions), NRT uses the density matrix resonance theory, performing a superposition of density matrices to realize resonance. NRT has applications in ab initio calculations, including calculating the bond orders of intra- and intermolecular interactions and the resonance weights of radical isomers.
