Abstract: A self-reconfiguring genome uses a cassette having operons or DNA sequences that code for guide RNA, reverse transcriptase, donor RNA, and a CRISPR cleavage enzyme. A self-reconfiguring genome may be based on lambda recombineering of in situ generated oligonucleotides. A method for programmable self-modification of a cellular genome includes transcribing guide RNA from a self-reconfiguring cassette, associating the transcribed guideRNA with the CRISPR enzyme, intercalating a region of complimentary sequence within an integration site of the genome, cutting upstream of a PAM site within the integration site; transcribing the donorRNA, translating donorRNA to double-stranded DNA, and recombining the double-stranded DNA via homologous recombination at the cut site of the integration site.

Abstract: In a method for generating an elongated nucleic acid molecule, a nucleic acid addition of a first nucleic acid molecule attached to a first 3? or 5? protecting group to a nucleic acid immobilized on a surface produces an intermediate-length immobilized nucleic acid. The first protecting group is dissociated from the first nucleic acid molecule. A second nucleic acid molecule that is attached to a second associated a 3? or 5? associated protecting group is added to the intermediate-length nucleic acid. The second associated protecting group is dissociated from the second nucleic acid molecule. A sequentially-extended elongated immobilized nucleic acid molecule having a desired sequence and length is produced by sequentially extending the intermediate-length immobilized nucleic acid by adding additional nucleic acid molecules with associated protecting groups to the intermediate-length nucleic acid and dissociating the associated protecting group after each addition.

Abstract: A self-reconfiguring genome uses a cassette having operons or DNA sequences that code for guide RNA, reverse transcriptase, donor RNA, and a CRISPR cleavage enzyme. A self-reconfiguring genome may be based on lambda recombineering of in situ generated oligonucleotides. A method for programmable self-modification of a cellular genome includes transcribing guide RNA from a self-reconfiguring cassette, associating the transcribed guideRNA with the CRISPR enzyme, intercalcating a region of complimentary sequence within an integration site of the genome, cutting upstream of a PAM site within the integration site; transcribing the donorRNA, translating donorRNA to double-stranded DNA, and recombining the double-stranded DNA via homologous recombination at the cut site of the integration site.

Abstract: Devices and methods integrate nanopore and microfluidic technologies for recording molecular characteristics of individual molecules such as, for example, biomolecules. Devices comprise a first substrate comprising a microchannel, a second substrate comprising a microchannel, the second substrate positioned below the first substrate, and a membrane having a thickness of about 0.3 nm to about 1 nm and comprising at least one nanopore, the membrane positioned between the first substrate and the second substrate, wherein a single nanopore of the membrane is constructed and arranged for electrical and fluid communication between the microchannel of the first substrate and the microchannel of the second substrate. To mitigate the effect of errors that occur during de novo DNA synthesis, longer DNA molecules are typically synthesized from shorter oligonucleotides by polymerase construction and amplification (PCA), or by other methods.

Abstract: A method for synthesizing long DNA constructs from oligonucleotide precursors directly within a microfluidic device uses several oligonucleotides at once. A precursor mix containing at least two oligonucleotide precursors with at least partial base complementarity is introduced into an input of a microfluidic chip and at least one cycle of at least one gene synthesis protocol is applied to fabricate a DNA construct containing the sequence of at least two oligonucleotide precursors. A method for the synthesis of a modified DNA construct includes electroporating at least one oligonucleotide encoding for at least one point mutation and having homology with at least one DNA region of a target cell into the target cell and incorporating the oligonucleotide into the target cell DNA through the action of recombination protein beta or a recombination protein beta functional homolog.

Abstract: In some aspects, the instant disclosure relates to the multiplexed encryption of information on nucleic acid molecules. In some aspects, the instant disclosure relates to a method of secure communication of information disseminated across at least one nucleic acid molecule, the method comprising (a) obtaining a modified keyboard comprising a personalized platform for translating text into a nucleic acid sequence; (b) translating a quantum of information into a nucleic acid message sequence using the modified keyboard of (a); and, (c) obtaining an at least one nucleic acid molecule, each molecule comprising: (i) the complete or a portion of the nucleic acid message sequence, and (ii) at least one contiguous stretch of randomized variable nucleic acid sequence flanking and/or inserted into the message sequence, thereby producing a nucleic acid molecule or a set of nucleic acid molecules containing the entire quantum of information.

Abstract: The disclosure relates to the use of steganographic methods to camouflage information encoded on nucleic acids. Specifically, the method comprising preparing a pool of recombinant nucleic acid constructs, wherein at least one of the constnjcts comprises the nucleic acid sequence to be camouflaged and wherein the pool is heterogeneous with respect to the orientation of the nucleic acid sequence to be camouflaged, and the information is camouflaged using genetic recombination.

Abstract: In a method for generating an elongated nucleic acid molecule, a nucleic acid addition of a first nucleic acid molecule attached to a first 3? or 5? protecting group to a nucleic acid immobilized on a surface produces an intermediate-length immobilized nucleic acid. The first protecting group is dissociated from the first nucleic acid molecule. A second nucleic acid molecule that is attached to a second associated a 3? or 5? associated protecting group is added to the intermediate-length nucleic acid. The second associated protecting group is dissociated from the second nucleic acid molecule. A sequentially-extended elongated immobilized nucleic acid molecule having a desired sequence and length is produced by sequentially extending the intermediate-length immobilized nucleic acid by adding additional nucleic acid molecules with associated protecting groups to the intermediate-length nucleic acid and dissociating the associated protecting group after each addition.

Abstract: In a method for generating a long nucleic acid molecule, nucleic acids immobilized on a surface and having overlapping complementary sequences is released into solution. The overlapping complementary sequences are hybridized to form hybridized nucleic acids, followed by extension or ligation of the hybridized nucleic acids to synthesize the long nucleic acid molecule. The nucleic acids may comprise first and second series of nucleic acids having redundant overlapping sequences, wherein nucleic acids from the first and second series are complementary to each other. The complementary nucleic acids are hybridized to form the hybridized nucleic acids. The generated long nucleic acid molecule may have a predetermined sequence element, and it may be introduced into a system wherein the predetermined sequence element is required for replication, such that replication of the synthesized long nucleic acid molecule is indicative of the presence of the predetermined sequence element in the long nucleic acid molecule.

Abstract: Devices and methods integrate nanopore and microfluidic technologies for recording molecular characteristics of individual molecules such as, for example, biomolecules. Devices comprise a first substrate comprising a microchannel, a second substrate comprising a microchannel, the second substrate positioned below the first substrate, and a membrane having a thickness of about 0.3 nm to about 1 nm and comprising at least one nanopore, the membrane positioned between the first substrate and the second substrate, wherein a single nanopore of the membrane is constructed and arranged for electrical and fluid communication between the microchannel of the first substrate and the microchannel of the second substrate. To mitigate the effect of errors that occur during de novo DNA synthesis, longer DNA molecules are typically synthesized from shorter oligonucleotides by polymerase construction and amplification (PCA), or by other methods.

Abstract: A method for synthesizing long DNA constructs from oligonucleotide precursors directly within a microfluidic device uses several oligonucleotides at once. A precursor mix containing at least two oligonucleotide precursors with at least partial base complementarity is introduced into an input of a microfluidic chip and at least one cycle of at least one gene synthesis protocol is applied to fabricate a DNA construct containing the sequence of at least two oligonucleotide precursors. A method for the synthesis of a modified DNA construct includes electroporating at least one oligonucleotide encoding for at least one point mutation and having homology with at least one DNA region of a target cell into the target cell and incorporating the oligonucleotide into the target cell DNA through the action of recombination protein beta or a recombination protein beta functional homolog.

Abstract: A self-reconfiguring genome uses a cassette having operons or DNA sequences that code for guide RNA, reverse transcriptase, donor RNA, and a CRISPR cleavage enzyme. A self-reconfiguring genome may be based on lambda recombineering of in situ generated oligonucleotides. A method for programmable self-modification of a cellular genome includes transcribing guide RNA from a self-reconfiguring cassette, associating the transcribed guideRNA with the CRISPR enzyme, intercalcating a region of complimentary sequence within an integration site of the genome, cutting upstream of a PAM site within the integration site; transcribing the donorRNA, translating donorRNA to double-stranded DNA, and recombining the double-stranded DNA via homologous recombination at the cut site of the integration site.

Abstract: In a method for generating a long nucleic acid molecule, nucleic acids immobilized on a surface and having overlapping complementary sequences is released into solution. The overlapping complementary sequences are hybridized to form hybridized nucleic acids, followed by extension or ligation of the hybridized nucleic acids to synthesize the long nucleic acid molecule. The nucleic acids may comprise first and second series of nucleic acids having redundant overlapping sequences, wherein nucleic acids from the first and second series are complementary to each other. The complementary nucleic acids are hybridized to form the hybridized nucleic acids. The generated long nucleic acid molecule may have a predetermined sequence element, and it may be introduced into a system wherein the predetermined sequence element is required for replication, such that replication of the synthesized long nucleic acid molecule is indicative of the presence of the predetermined sequence element in the long nucleic acid molecule.

Abstract: In a method for synthesizing a pool of nucleic acid molecules, a first nucleic acid has a first 5? region and a first 3? region and a second nucleic acid has a second 5? region and a second 3? region. The second 3? region and the first 5? region have identical nucleic acid sequences. The first 3? region is hybridized with an oligonucleotide, extending the hybridized oligonucleotide and producing a first extension product having a 3? region complementary to the first 5? region. The second nucleic acid is hybridized with the first extension product to hybridize the 3? region of the first extension product to the second 3? region, extending the 3? region of the first extension product and producing a second extension product having a 3? region complementary to the second 5? region. Error-containing molecules are separated from error-free molecules by a component that selects for a sequence error.

Abstract: A method for synthesizing a nucleic acid having a desired sequence and length comprises providing a solid support having an immobilized nucleic acid, performing a nucleic acid addition reaction to elongate the immobilized nucleic acid by adding a nucleotide or an oligonucleotide attached to a protecting group to the nucleic acid, determining whether the nucleotide or the oligonucleotide is added to the nucleic acid, removing the protecting group, and continuing until the immobilized nucleic acid has a desired sequence and length.

Abstract: In a method for synthesizing a pool of nucleic acid molecules, a first nucleic acid has a first 5? region and a first 3? region and a second nucleic acid has a second 5? region and a second 3? region. The second 3? region and the first 5? region have identical nucleic acid sequences. The first 3? region is hybridized with an oligonucleotide, extending the hybridized oligonucleotide and producing a first extension product having a 3? region complementary to the first 5? region. The second nucleic acid is hybridized with the first extension product to hybridize the 3? region of the first extension product to the second 3? region, extending the 3? region of the first extension product and producing a second extension product having a 3? region complementary to the second 5? region. Error-containing molecules are separated from error-free molecules by a component that selects for a sequence error.

Abstract: A method for synthesizing a nucleic acid having a desired sequence and length comprises providing a solid support having an immobilized nucleic acid, performing a nucleic acid addition reaction to elongate the immobilized nucleic acid by adding a nucleotide or an oligonucleotide to the nucleic acid, determining whether the nucleotide or the oligonucleotide is added to the nucleic acid by detecting whether there is an increase in electrophoretic force applied to the solid support when an electric field and a magnetic field gradient are applied to the support, wherein the increase in electrophoretic force applied to the support is caused by adding the nucleotide or the oligonucleotide to the nucleic acid, repeating the addition reaction and determination steps if the nucleotide or the oligonucleotide is not added to the nucleic acid, and continuing until the immobilized nucleic acid has a desired sequence and length.

Abstract: In a method for synthesizing a long nucleic acid molecule, a first immobilized nucleic acid has a first 5? region and a first 3? region and a second immobilized nucleic acid has a second 5? region and a second 3? region. The second 3? region and the first 5? region have identical nucleic acid sequences. An oligonucleotide is hybridized to the first 3? region, extending the hybridized oligonucleotide and producing a first extension product having a 3? region that is complementary to the first 5? region. The 3? region of the first extension product is hybridized to the second 3? region, extending the 3? region of the first extension product and producing a synthesized nucleic acid molecule having a 3? region that is complementary to the second 5? region, wherein the synthesized nucleic acid molecule has a sequence complementary to the first and second 3? and 5? regions.

Abstract: A method for synthesizing a nucleic acid having a desired sequence and length comprises providing a solid support having an immobilized nucleic acid, performing a nucleic acid addition reaction to elongate the immobilized nucleic acid by adding a nucleotide or an oligonucleotide to the nucleic acid, determining whether the nucleotide or the oligonucleotide is added to the nucleic acid by detecting whether there is an increase in electrophoretic force applied to the solid support when an electric field and a magnetic field gradient are applied to the support, wherein the increase in electrophoretic force applied to the support is caused by adding the nucleotide or the oligonucleotide to the nucleic acid, repeating the addition reaction and determination steps if the nucleotide or the oligonucleotide is not added to the nucleic acid, and continuing until the immobilized nucleic acid has a desired sequence and length.

Abstract: Inhibitors of HIV membrane fusion and a method of identifying drugs or agents which inhibit binding of the N-helix coiled-coil and the C helix of HIV gp41 envelope protein.