The present invention relates to fusion proteins comprising (i) a fusion moiety based on SEQ ID NO:1 and (ii) a protein. Also provided are nucleic acids encoding such fusion proteins and compositions comprising such fusion proteins. The invention also provides a method for increasing the expression level of a protein in a host cell or increasing the level of secretion of a protein from a host cell, said methods employing a fusion moiety in accordance with the invention. The invention further provides a method of producing a protein, said method comprising culturing an Aliivibrio wodanis host cell comprising a heterologous nucleic acid molecule encoding a protein under conditions suitable for the expression of the encoded protein. Certain deposited strains of Aliivibrio wodanis are also provided.

The invention provides an exonuclease or an enzymatically active fragment thereof, said exonuclease having the amino acid sequence of SEQ ID No. 1 or an amino acid sequence which is at least about 50% identical thereto, wherein said exonuclease or enzymatically active fragment thereof (i) is substantially irreversibly inactivated by heating at a temperature of about 55° C. for 10 minutes in a buffer consisting of 10 mM Tris-HCl, pH 8.5 at 25° C., 50 mM KCl and 5 mM MgCl.sub.2; (ii) is substantially specific for single stranded DNA; and (iii) has a 3′-5′ exonuclease activity. The invention further provides a method of removing single stranded DNA from a sample, a method of nucleic acid amplification, a method of reverse transcription and a method of nucleic acid sequence analysis in which the exonuclease or enzymatically active fragment thereof is used. The invention still further provides nucleic acids encoding said exonuclease or an enzymatically active fragment thereof and kits or compositions comprising the same.

Various embodiments are directed to using nuclease expression in tissues that influences cell-free DNA end signatures/motifs and size of overhang between DNA strands. Embodiments can identify a nuclease that is being differentially regulated in abnormal cells relative to normal cells. Embodiments can determine that the nuclease preferentially cuts DNA into DNA molecules having: (i) a particular sequence end signature; or (ii) a specified length of overhang between a first strand and a second strand. A parameter can be determined for a biological sample based on an amount of DNA molecules that include an end sequence corresponding to the particular sequence end signature and/or a measured property correlating to the specified length of overhang. The parameter can be used to determine a characteristic of a tissue type, a fractional concentration of clinically-relevant DNA molecules, or a level of abnormality of a tissue type in the biological sample.

The present invention relates to fusion proteins comprising (i) a fusion moiety based on SEQ ID NO:1 and (ii) a protein. Also provided are nucleic acids encoding such fusion proteins and compositions comprising such fusion proteins. The invention also provides a method for increasing the expression level of a protein in a host cell or increasing the level of secretion of a protein from a host cell, said methods employing a fusion moiety in accordance with the invention. The invention further provides a method of producing a protein, said method comprising culturing an Aliivibrio wodanis host cell comprising a heterologous nucleic acid molecule encoding a protein under conditions suitable for the expression of the encoded protein. Certain deposited strains of Aliivibrio wodanis are also provided.

The invention provides an exonuclease or an enzymatically active fragment thereof, said exonuclease having the amino acid sequence of SEQ ID NO:1 or an amino acid sequence which is at least about 50% identical thereto, wherein said exonuclease or enzymatically active fragment thereof (i) is substantially irreversibly inactivated by heating at a temperature of about 55 C. for 10 minutes in a buffer consisting of 10 mM Tris-HCl, pH 8.5 at 25 C., 50 mM KCl and 5 mM MgCl.sub.2; (ii) is substantially specific for single stranded DNA; and (iii) has a 3-5 exonuclease activity. The invention further provides a method of removing single stranded DNA from a sample, a method of nucleic acid amplification, a method of reverse transcription and a method of nucleic acid sequence analysis in which the exonuclease or enzymatically active fragment thereof is used. The invention still further provides nucleic acids encoding said exonuclease or an enzymatically active fragment thereof and kits or compositions comprising the same.

The invention provides an exonuclease or an enzymatically active fragment thereof, said exonuclease having the amino acid sequence of SEQ ID NO:1 or an amino acid sequence which is at least about 50% identical thereto, wherein said exonuclease or enzymatically active fragment thereof (i) is substantially irreversibly inactivated by heating at a temperature of about 55 C. for 10 minutes in a buffer consisting of 10 mM Tris-HCl, pH 8.5 at 25 C., 50 mM KCl and 5 mM MgCl.sub.2; (ii) is substantially specific for single stranded DNA; and (iii) has a 3-5 exonuclease activity. The invention further provides a method of removing single stranded DNA from a sample, a method of nucleic acid amplification, a method of reverse transcription and a method of nucleic acid sequence analysis in which the exonuclease or enzymatically active fragment thereof is used. The invention still further provides nucleic acids encoding said exonuclease or an enzymatically active fragment thereof and kits or compositions comprising the same.

Provided in some aspects are methods for light-controlled in situ surface patterning of a substrate comprising a step of blocking or ablating oligonucleotide molecules in a boundary region separating a plurality of spot regions, and attaching oligonucleotides to oligonucleotide molecules in a first one or more of the spot regions.

The invention provides an exonuclease or an enzymatically active fragment thereof, said exonuclease having the amino acid sequence of SEQ ID NO:1 or an amino acid sequence which is at least about 50% identical thereto, wherein said exonuclease or enzymatically active fragment thereof (i) is substantially irreversibly inactivated by heating at a temperature of about 55 C. for 10 minutes in a buffer consisting of 10 mM Tris-HCl, pH 8.5 at 25 C., 50 mM KCl and 5 mM MgCl.sub.2; (ii) is substantially specific for single stranded DNA; and (iii) has a 3-5 exonuclease activity. The invention further provides a method of removing single stranded DNA from a sample, a method of nucleic acid amplification, a method of reverse transcription and a method of nucleic acid sequence analysis in which the exonuclease or enzymatically active fragment thereof is used. The invention still further provides nucleic acids encoding said exonuclease or an enzymatically active fragment thereof and kits or compositions comprising the same.

The present disclosure provides improved genome editing compositions and methods for editing a double-strand DNA target site. The disclosure further provides genome edited cells produced by the compositions and methods described.

Methods for producing a linear deoxyribonucleic acid (DNA) product with enhanced resistance to nuclease digestion are provided. The methods comprise, (a) digesting a double-stranded DNA molecule with an endonuclease that cleaves an endonuclease target sequence to generate a digested double-stranded DNA molecule, wherein the digested double-stranded DNA molecule comprises a linear double-stranded region, and a truncated protelomerase sequence at a first end, wherein the truncated protelomerase target sequence is non-functional; (b) appending a first adaptor molecule to the first end of the digested double-stranded DNA molecule and appending a second adaptor molecule to the second end of the digested double-stranded DNA molecule to generate a precursor double-stranded DNA molecule, wherein the first adaptor molecule comprises a truncated protelomerase target sequence that forms a first functional protelomerase target sequence with the truncated protelomerase sequence at the first end of the digested double-stranded DNA molecule; and (c) incubating the precursor double-stranded DNA molecule with a protelomerase to generate the linear DNA product, wherein the protelomerase closes the first end of the precursor double-stranded DNA molecule at the first functional protelomerase target sequence.