scholarly journals Probing the Nucleic Acid Binding Properties of the Single-Stranded DNA Binding Protein of Bacteriophage T4 Replication Complex at Single Nucleotide Resolution

2017 ◽  
Vol 112 (3) ◽  
pp. 513a
Author(s):  
Benjamin R. Camel ◽  
Katherine Meze ◽  
Davis Jose ◽  
Peter H. von Hippel
Keyword(s):  
Nucleic Acid ◽  
Dna Binding ◽  
Bacteriophage T4 ◽  
Dna Binding Protein ◽  
Nucleic Acid Binding ◽  
Binding Properties ◽  
Single Nucleotide ◽  
Replication Complex ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

scholarly journals Genomic DNA preparation enabling multiple replicate reads for accurate nanopore sequencing

2015 ◽  
Author(s):  
Dimitra Tsavachidou
Keyword(s):  
Nucleic Acid ◽  
Error Rates ◽  
Nanopore Sequencing ◽  
Acid Molecule ◽  
Single Nucleotide ◽  
Nucleic Acid Molecule ◽  
Dna Strands ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution ◽  
Sequencing Procedure

Sequencing at single-nucleotide resolution using nanopore devices is performed with reported error rates 10.5-20.7% (Ip et al., 2015). Since errors occur randomly during sequencing, repeating the sequencing procedure for the same DNA strands several times can generate sequencing results based on consensus derived from replicate readings, thus reducing overall error rates. The method presented in this manuscript constructs copies of a nucleic acid molecule that are consecutively connected to the nucleic acid molecule. Such copies are useful because they can be sequenced by a nanopore device, enabling replicate reads, thus improving overall sequencing accuracy.

scholarly journals Mapping DNA conformations and interactions within the binding cleft of bacteriophage T4 single-stranded DNA binding protein (gp32) at single nucleotide resolution

2020 ◽  
Author(s):  
Benjamin R Camel ◽  
Davis Jose ◽  
Katarina Meze ◽  
Anson Dang ◽  
Peter H von Hippel
Keyword(s):  
Dna Binding ◽  
Bacteriophage T4 ◽  
Amino Acid Residues ◽  
Nucleic Acid Binding ◽  
Local Interactions ◽  
Single Stranded Dna ◽  
Exciton Coupling ◽  
Genome Expression ◽  
Binding Cleft ◽  
Nucleotide Resolution

Abstract In this study, we use single-stranded DNA (oligo-dT) lattices that have been position-specifically labeled with monomer or dimer 2-aminopurine (2-AP) probes to map the local interactions of the DNA bases with the nucleic acid binding cleft of gp32, the single-stranded binding (ssb) protein of bacteriophage T4. Three complementary spectroscopic approaches are used to characterize these local interactions of the probes with nearby nucleotide bases and amino acid residues at varying levels of effective protein binding cooperativity, as manipulated by changing lattice length. These include: (i) examining local quenching and enhancing effects on the fluorescence spectra of monomer 2-AP probes at each position within the cleft; (ii) using acrylamide as a dynamic-quenching additive to measure solvent access to monomer 2-AP probes at each ssDNA position; and (iii) employing circular dichroism spectra to characterize changes in exciton coupling within 2-AP dimer probes at specific ssDNA positions within the protein cleft. The results are interpreted in part by what we know about the topology of the binding cleft from crystallographic studies of the DNA binding domain of gp32 and provide additional insights into how gp32 can manipulate the ssDNA chain at various steps of DNA replication and other processes of genome expression.

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