Nucleic acid stain-dependent single strand conformation polymorphisms [PDF]
BioTechniques, 2004 Single strand conformational poly-morphism (SSCP) is a mobility shift analysis of single-stranded DNA (ss-DNA) by nondenaturing polyacryl-amide gel electrophoresis to detect DNA sequence polymorphisms (1). Typical SSCP protocols detect single strands by autoradiography (2–4) or by treatment with a DNA stain after electrophoresis (5–12).
David R. McKee, M. Scott Thomson
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Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking
PLoS ONE, 2022 Aptamers are single-stranded oligonucleotides, formerly evolved by Systematic Evolution of Ligands by EXponential enrichment (SELEX), that fold into functional three-dimensional structures.
Ricardo Oliveira +5 more
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Developing Community Resources for Nucleic Acid Structures
Life, 2022 In this review, we describe the creation of the Nucleic Acid Database (NDB) at Rutgers University and how it became a testbed for the current infrastructure of the RCSB Protein Data Bank. We describe some of the special features of the NDB and how it has
Helen M. Berman +2 more
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Solvent interactions stabilising nucleic acid conformers [PDF]
Nucleic Acids Research, 1989 The transition of oligonucleotides from the B to the A conformation has been studied by the use of simple geometric calculations aimed at finding possible hydration sites which could stabilize these conformations. The method involves the classification of equally spaced grid points, surrounding the oligonucleotide, into groups depending on whether a ...
R J, Elliott, J M, Goodfellow
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Effects of 2'-O-methyl nucleotide substitution on EcoRI endonuclease cleavage activities. [PDF]
PLoS ONE, 2013 To investigate the effect of sugar pucker conformation on DNA-protein interactions, we used 2'-O-methyl nucleotide (2'-OMeN) to modify the EcoRI recognition sequence -TGAATTCT-, and monitored the enzymatic cleavage process using FRET method.
Guojie Zhao +4 more
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Optimizing scoring function of protein-nucleic acid interactions with both affinity and specificity. [PDF]
PLoS ONE, 2013 Protein-nucleic acid (protein-DNA and protein-RNA) recognition is fundamental to the regulation of gene expression. Determination of the structures of the protein-nucleic acid recognition and insight into their interactions at molecular level are vital ...
Zhiqiang Yan, Jin Wang
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Structural basis of R-loop recognition by the S9.6 monoclonal antibody
Nature Communications, 2022 The S9.6 monoclonal antibody is widely used to map R-loops genome wide. Here, Bou-Nader et al., define the nucleic acid-binding specificity of S9.6 and report its crystal structures free and bound to a hybrid, which reveal the asymmetric recognition of ...
Charles Bou-Nader +4 more
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Metal-Binding Antimicrobial Peptide SIF4 Kills Escherichia coli by Targeting Cytoplasmic Biomacromolecules without Cytoplasmic Membrane Damage: A Mechanistic Study [PDF]
Shipin Kexue, 2023 To explore how metal-binding antimicrobial peptide SIF4 kills foodborne Escherichia coli by targeting nucleic acid and protein in the cytoplasmic membrane without cytoplasmic membrane damage, the effect of SIF4 on intracellular nucleic acid biosynthesis ...
LI Yuzhen, XIAO Huaiqiu, LIU Miao, WANG Lin, ZENG Mengqi, ZHAO Mouming
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High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors [PDF]
, 2020 The vast majority of organisms possess transcription elongation factors, the functionally similar bacterial Gre and eukaryotic/archaeal TFIIS/TFS. Their main cellular functions are to proofread errors of transcription and to restart elongation via ...
James, Katherine +2 more
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Conformational analysis of nucleic acids revisited: Curves+ [PDF]
Nucleic Acids Research, 2009 We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it ...
Lavery, R. +4 more
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