Abstract: Methods and systems are provided to induce hypermutation, produce phage libraries displaying mutagenized immunoglobulin variable regions, and conduct affinity maturation based on the use of activation-induced deoxycytidine deaminase (AID) and a low fidelity DNA polymerase eta (pol ?). High affinity monoclonal antibodies or antigen-binding fragments thereof produced by these methods are also demonstrated.

Abstract: The structure, function and methods associated with proteins from the APOBEC family, which are involved in diverse biological functions, is disclosed. In one embodiment, the structure of APOBEC-3G (Apo3G) is disclosed. In another embodiment, a method of using APOBEC-3G (Apo3G) and/or Apo3G-CD2 to restrict the replication of Human Immunodeficiency Virus (HIV) and Hepatitis B virus (HBV) via cytidine deamination on ssDNA or RNA binding is disclosed. In yet another embodiment, the high-resolution crystal structure of an enzymatically active APOBEC protein, the C-terminal deaminase domain of Apo3G (Apo3G-CD2) is disclosed.

Abstract: Sequencing methods and methods for synthesizing DNA probes using mutant bacteriophage T4 DNA polymerases which have increased ability to incorporate modified nucleotides for the synthesis of long or short chains of complementary, modified, e.g., fluorophore-labeled DNA. In general, the mutant T4 DNA polymerases retain 3'.fwdarw.5' exonuclease activity; hence, reduction or elimination of 3'.fwdarw.5' exonuclease activity is not a prerequisite for efficient synthesis of a complementary fluorophore-labeled or other modified DNA. In fact, retention of 3'.fwdarw.5' exonuclease activity increases accuracy of DNA replication, because these exonucleases proofread or edit the product of DNA replication.

Abstract: Variant family B DNA polymerases, examples of which have reduced or no 3'.fwdarw.5' exonuclease activity. These variant polymerases have utility as DNA sequencing polymerases.

Abstract: Method for identifying and isolating variant T4 DNA polymerase by isolating and selecting for T4 strains having variant DNA polymerase defective in DNA replication, and at least one additional mutation which corrects or compensates for said defect in DNA replication; identifying the additional mutation(s) and introducing the mutation(s) into T4 phage or T4 DNA polymerase expression vectors.

Abstract: There are provided variant family B DNA polymerases having no 3'.fwdarw.5' exonuclease activity. These variant polymerases have utility as DNA sequencing polymerases. Methods for DNA sequencing with family B DNA polymerases and chain-terminating nucleotides not previously used for sequencing have been developed. The methods disclosed involve the use of family B DNA polymerases not known heretofore to have utility in DNA sequencing, such as variant or wild type forms of phage T4 DNA polymerase or Escherichia coli DNA polymerase II, with novel combinations of deoxynucleotides and chain-terminating nucleotides.