20240035021. METHODS AND COMPOSITIONS FOR GENERATING A DELETION LIBRARY AND FOR IDENTIFYING A DEFECTIVE INTERFERING PARTICLE (DIP) simplified abstract (The J. David Gladstone Institutes)

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METHODS AND COMPOSITIONS FOR GENERATING A DELETION LIBRARY AND FOR IDENTIFYING A DEFECTIVE INTERFERING PARTICLE (DIP)

Organization Name

The J. David Gladstone Institutes

Inventor(s)

Leor S. Weinberger of Oakland CA (US)

Timothy J. Notton of San Francisco CA (US)

METHODS AND COMPOSITIONS FOR GENERATING A DELETION LIBRARY AND FOR IDENTIFYING A DEFECTIVE INTERFERING PARTICLE (DIP) - A simplified explanation of the abstract

This abstract first appeared for US patent application 20240035021 titled 'METHODS AND COMPOSITIONS FOR GENERATING A DELETION LIBRARY AND FOR IDENTIFYING A DEFECTIVE INTERFERING PARTICLE (DIP)

Simplified Explanation

The patent application describes methods and compositions for generating a deletion library and identifying a defective interfering particle (DIP). It also provides transposon cassettes. The subject method involves inserting a transposon cassette containing a target sequence for a sequence-specific DNA endonuclease into a population of circular target DNAs. This generates a population of transposon-inserted circular target DNAs. The population is then contacted with the sequence-specific DNA endonuclease, resulting in a population of cleaved linear target DNAs. The cleaved linear target DNAs are further contacted with one or more exonucleases to generate a population of deletion DNAs. Finally, the deletion DNAs are circularized to create a library of circularized deletion DNAs. The population of circular target DNAs can include viral genomic DNA, such as human immunodeficiency virus (HIV). The patent also provides HIV deletion mutants, including interfering and conditionally replicating mutants, along with related constructs.

  • Methods and compositions for generating a deletion library and identifying a defective interfering particle (DIP) are described.
  • Transposon cassettes are provided for use in the methods.
  • The method involves inserting a transposon cassette with a target sequence for a sequence-specific DNA endonuclease into circular target DNAs.
  • The transposon-inserted circular target DNAs are then cleaved into linear target DNAs using the sequence-specific DNA endonuclease.
  • The linear target DNAs are further processed with exonucleases to generate deletion DNAs.
  • The deletion DNAs are circularized to create a library of circularized deletion DNAs.
  • The population of circular target DNAs can include viral genomic DNA, such as HIV.
  • The patent also provides HIV deletion mutants, including interfering and conditionally replicating mutants, and related constructs.

Potential Applications

  • Development of deletion libraries for studying genetic elements and their functions.
  • Identification and characterization of defective interfering particles (DIPs) in viral populations.
  • Creation of HIV deletion mutants for studying viral replication and pathogenesis.
  • Investigation of the role of specific genetic sequences in various biological processes.

Problems Solved

  • Facilitates the generation of deletion libraries, which can aid in understanding the function of genetic elements.
  • Provides a method for identifying and studying defective interfering particles (DIPs) in viral populations.
  • Enables the creation of HIV deletion mutants, which can help elucidate viral replication mechanisms and develop targeted therapies.

Benefits

  • Allows for efficient and systematic generation of deletion libraries.
  • Provides a method for identifying and studying defective interfering particles (DIPs) in viral populations, which can contribute to understanding viral evolution and pathogenesis.
  • Facilitates the creation of HIV deletion mutants, which can aid in the development of novel antiviral strategies and vaccines.


Original Abstract Submitted

provided are methods and compositions for generating a deletion library, and methods and compositions for generating and identifying a defective interfering particle (dip). also provided are transposon cassettes. a subject method can include: inserting a transposon cassette comprising a target sequence for a sequence specific dna endonuclease into a population of circular target dnas to generate a population of transposon-inserted circular target dnas; contacting the population of transposon-inserted circular target dnas with the sequence specific dna endonuclease to generate a population of cleaved linear target dnas; contacting the population of cleaved linear target dnas with one or more exonucleases to generate a population of deletion dnas; and circularizing the deletion dnas to generate a library of circularized deletion dnas. the population of circular target dnas can include viral genomic dna. also provided ae human immunodeficiency virus (hiv) deletion mutants, e.g., interfering, conditionally replicating, hiv deletion mutants, and related constructs.

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