Compositions containing a nucleic acid nanostructure having a desired geometric shape and antigens bound to its surface are provided. The nanostructures can be, for example, in the form of a 6-helix bundle or icosahedron. The nanostructure design allows for control of the relative position and/or stoichiometry of the antigen bound to its surface. The antigens displayed on the nanostructure surface are arranged with the preferred number, spacing, and 3D organization to elicit a robust immune response. The displayed antigen can be an HIV immunogen such as eOD-GT6, eOD-GT8, or variants thereof. The compositions may thus be useful as immunogens, vaccines, immunostimulators, adjuvants, and the like. Methods of inducing immune responses, inducing protective immunity, inducing the production of neutralizing antibodies or inhibitory antibodies, inducing tolerance, and treating cancer, infectious or autoimmune diseases are also provided.

Methods for the top-down design of nucleic acid nanostructures of arbitrary geometry based on target shape of spherical or non-spherical topology are described. The methods facilitate 3D molecular programming of lipids, proteins, sugars, and RNAs based on a DNA scaffold of arbitrary 2D or 3D shape. Geometric objects are rendered as node-edge networks of parallel nucleic acid duplexes, and a nucleic acid scaffold routed throughout the network using a spanning tree formula. Nucleic acid nanostructures produced according to top-down design methods are also described. In some embodiments, the nanostructures include single-stranded nucleic acid scaffold, DX crossovers, and staple strands. In other embodiments, the nanostructures include single-stranded nucleic acid scaffold, PX crossovers and no staples. Modified nanostructures include chemically modified nucleotides and conjugated to other molecules are described.

Methods for the top-down design of nucleic acid nanostructures of arbitrary geometry based on target shape of spherical or non-spherical topology are described. The methods facilitate 3D molecular programming of lipids, proteins, sugars, and RNAs based on a DNA scaffold of arbitrary 2D or 3D shape. Geometric objects are rendered as node-edge networks of parallel nucleic acid duplexes, and a nucleic acid scaffold routed throughout the network using a spanning tree formula. Nucleic acid nanostructures produced according to top-down design methods are also described. In some embodiments, the nanostructures include single-stranded nucleic acid scaffold, DX crossovers, and staple strands. In other embodiments, the nanostructures include single-stranded nucleic acid scaffold, PX crossovers and no staples. Modified nanostructures include chemically modified nucleotides and conjugated to other molecules are described.

The present disclosure generally relates to finding genome rearrangements from sequencing data. DNA sequence analysis systems and methods directed to identifying all sequence variants in a genome are described herein. Such systems and methods demonstrate distinct and improved features relating to the accuracy and speed with which all sequence variants in a genome are identified.

The present disclosure generally relates to finding genome rearrangements from sequencing data. DNA sequence analysis systems and methods directed to identifying all sequence variants in a genome are described herein. Such systems and methods demonstrate distinct and improved features relating to the accuracy and speed with which all sequence variants in a genome are identified.

The present disclosure provides a method for identifying a nucleic acid, which may comprise incubating a cell that has been or is suspected of having been transfected or transduced with an exogenous ribonucleic acid (RNA) molecule or an exogenous deoxyribonucleic (DNA) molecule. Next, a morphological change of the cell may be identified. Next, contents of the cell may be processed to identify a nucleic acid sequence or a peptide, polypeptide, or protein or a sequence of the peptide, polypeptide, or protein. Next, the nucleic acid sequence or the peptide, polypeptide, or protein or the sequence of the peptide, polypeptide, or protein may be analyzed to determine an exogenous sequence of the exogenous RNA molecule or the exogenous DNA molecule. Next, the exogenous sequence of the exogenous RNA molecule or the exogenous DNA molecule may be identified as effecting the morphological change of the cell. The exogenous RNA molecule or the exogenous DNA molecule may encode genes or peptides, polypeptides, or proteins that inhibit, activate, or modulate a biochemical pathway within the cell, thereby causing the morphological change of the cell.

Attenuated viruses and methods of designing them are disclosed. In one embodiment, there is disclosed an attenuated form of a virulent virus comprising an RNA encoding a viral protein or a nucleic acid sequence transcribable to said RNA, wherein the folding energy or structure of the RNA is changed at positions of evolutionarily conserved RNA structures with respect to that of said RNA encoding said viral protein in the virulent virus so as to bring about attenuation of the virus.

The present subject matter relates to a voxel and methods of organizing an object into a three-dimensional (3D) array using the voxel. The voxel can include a plurality of frames including at least one single stranded (ss) DNA motif with at least one free base, wherein the at least one ssDNA motif hybridizes with a complementary strand fragment of other frames.

The present invention relates to a method for predicting the melting temperature (T.sub.m) of an oligonucleotide, in particular a primer or probe, in a PCR or hybridization assay. The method of present invention can accurately predict the T.sub.m of an oligonucleotide in various reaction environments using the equations for T.sub.m calculation, the equation including parameter values optimized for the reaction environment in which the oligonucleotide is to be used.

Processes to determine the effect of genetic sequence on gene expression levels are described. Generally, models are used to determine spatial chromatin profile from genetic sequence, which can be used in several downstream applications. The effect of the spatial chromatin profile on gene expression is also determined in some instances. Various methods further develop research tools, perform diagnostics, and treat individuals based on sequence effects on gene expression levels.