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DNA Replication02:40

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DNA replication involves the separation of the two strands of the double helix, with each strand serving as a template from which the new complementary strand is copied.  After replication, each double-stranded DNA includes one parental or “old” strand and one “new” strand. This is known as semiconservative replication. The resulting DNA molecules have the same sequence and are divided equally into the two daughter cells.
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During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
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In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
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DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
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Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
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An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication...
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High-Density DNA and RNA microarrays - Photolithographic Synthesis, Hybridization and Preparation of Large Nucleic Acid Libraries
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Squaramide Formation for DNA-Encoded Library Synthesis.

Antoine Douchez1, Julien Poupart1, Gaoqiang Yang1

  • 1Drug Discovery Unit, Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec H3C 3J7, Canada.

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DNA-encoded libraries (DELs) enable small molecule discovery. A new, mild squaramide reaction is DNA-safe and compatible with DELs, expanding accessible chemical scaffolds for drug discovery.

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Area of Science:

  • Medicinal Chemistry
  • Chemical Biology
  • Organic Synthesis

Background:

  • DNA-encoded libraries (DELs) are powerful tools for discovering biologically active small molecules.
  • Key challenges in DELs include developing aqueous-phase reactions, minimizing DNA damage, and incorporating diverse chemical building blocks.
  • Accessing novel scaffolds for medicinal chemistry within DELs is often limited by DNA-supported chemistry constraints.

Purpose of the Study:

  • To develop a novel, DNA-compatible chemical transformation for use in DNA-encoded library synthesis.
  • To establish a robust squaramide formation reaction suitable for on-DNA chemistry.
  • To expand the range of accessible chemical scaffolds for drug discovery using DEL technology.

Main Methods:

  • A two-step squaramide formation reaction was designed and optimized.
  • The reaction's compatibility with aqueous conditions and DNA integrity was assessed.
  • The reaction's tolerance to various functional groups and its yield were evaluated.

Main Results:

  • A mild and high-yielding two-step squaramide formation reaction was successfully developed.
  • The reaction demonstrated excellent tolerance to a wide range of functional groups.
  • The methodology proved to be safe for DNA, causing minimal alterations.
  • The reaction is suitable for integration into DNA-encoded library workflows.

Conclusions:

  • The developed squaramide formation reaction is an ideal methodology for DNA-encoded libraries.
  • This advancement broadens the scope of chemical scaffolds accessible through DELs.
  • The reaction facilitates the discovery of novel small molecules with potential biological applications.