Effects of ssDNA sequences on non-sequence-specific protein binding

Brush-Structured Chitosan/PolyHEMA with Thymine and Its Synergistic Effect on the Specific Interaction with ssDNA and Cellular Uptake

Cationic polymers are known to attach on an anionic cell surface and favor gene transportation/transfection into the cells. However, when the positive charges accumulate, they tend to cause cell damage and delivery failure. Chitosan (CS) is a potential cationic bio-derived polymer whose chemical structures can be modified to fine-tune the charges as well as the add-on functions. The present work demonstrates (i) the decoration of a nucleic acid sequence-like brush structure on CS to allow the specific interaction with DNA and (ii) delivery into the cell. By simply applying mercaptoacetic acid as the chain transfer agent, the grafting of poly(hydroxyethyl methacrylate) (PHEMA) containing Thy (P(HEMA-Thy)) on CS is possible. The brush-like P(HEMA-Thy) leads Thy moieties to be in sequences. The Thy sequences perform as poly[T] for the specific interaction with ssDNA. The synergistic effect of CS and Thy sequences, i.e., electrostatic and base pairing interactions, results in an effective and efficient binding with ssDNA as well as significant delivery, especially in cellular uptake and cell viability. The use of CS in combination with Thy sequences in brush-like structures on CS is a model for other polysaccharides to be conjugated with the as-designed nucleic acid sequences for potential gene delivery.

Recognition and Unfolding of c-MYC and Telomeric G-Quadruplex DNAs by the RecQ C-Terminal Domain of Human Bloom Syndrome Helicase

G-quadruplex (G4) is a noncanonical DNA secondary structure formed by Hoogsteen base pairing. It is recognized by various DNA helicases involved in DNA metabolism processes such as replication and transcription. Human Bloom syndrome protein (BLM), one of five human RecQ helicases, is a G4 helicase. While several studies revealed the mechanism of G4 binding and unfolding by the conserved RecQ C-terminal (RQC) domain of BLM, how RQC recognizes different G4 topologies is still unclear. Here, we investigated the interaction of Myc-22(14/23T) G4 from the c-Myc promoter and hTelo G4 from the telomeric sequence with RQC. Myc-22(14/23T) and hTelo form parallel and (3+1) hybrid topologies, respectively. Our circular dichroism (CD) spectroscopy data indicate that RQC can partially unfold the parallel G4, even with a short 3' overhang, while it can only partially unfold the (3+1) hybrid G4 with a 3' overhang of 6 nucleotides or longer. We found that the intrinsic thermal stability of G4 does not determine RQC-induced G4 unfolding by comparing T _m of G4s. We also showed that both parallel and (3+1) hybrid G4s bind to the β-wing region of RQC. Thermodynamic analysis using isothermal titration calorimetry (ITC) showed that all interactions were endothermic and entropically driven. We suggest that RQC partially unfolds the parallel G4 more efficiently than the (3+1) hybrid G4 and binds to various G4 structures using its β-wing region. By this information, our research provides new insights into the influence of G4 structure on DNA metabolic processes involving BLM.

Analysis of DNA binding by human factor xeroderma pigmentosum complementation group A (XPA) provides insight into its interactions with nucleotide excision repair substrates

Xeroderma pigmentosum (XP) complementation group A (XPA) is an essential scaffolding protein in the multiprotein nucleotide excision repair (NER) machinery. The interaction of XPA with DNA is a core function of this protein; a number of mutations in the DNA-binding domain (DBD) are associated with XP disease. Although structures of the central globular domain of human XPA and data on binding of DNA substrates have been reported, the structural basis for XPA's DNA-binding activity remains unknown. X-ray crystal structures of the central globular domain of yeast XPA (Rad14) with lesion-containing DNA duplexes have provided valuable insights, but the DNA substrates used for this study do not correspond to the substrates of XPA as it functions within the NER machinery. To better understand the DNA-binding activity of human XPA in NER, we used NMR to investigate the interaction of its DBD with a range of DNA substrates. We found that XPA binds different single-stranded/double-stranded junction DNA substrates with a common surface. Comparisons of our NMR-based mapping of binding residues with the previously reported Rad14-DNA crystal structures revealed similarities and differences in substrate binding between XPA and Rad14. This includes direct evidence for DNA contacts to the residues extending C-terminally from the globular core, which are lacking in the Rad14 construct. Moreover, mutation of the XPA residue corresponding to Phe-262 in Rad14, previously reported as being critical for DNA binding, had only a moderate effect on the DNA-binding activity of XPA. The DNA-binding properties of several disease-associated mutations in the DBD were investigated. These results suggest that for XPA mutants exhibiting altered DNA-binding properties, a correlation exists between the extent of reduction in DNA-binding affinity and the severity of symptoms in XP patients.

Structure and assembly of filamentous bacteriophages

Filamentous bacteriophages are interesting paradigms in structural molecular biology, in part because of the unusual mechanism of filamentous phage assembly. During assembly, several thousand copies of an intracellular DNA-binding protein bind to each copy of the replicating phage DNA, and are then displaced by membrane-spanning phage coat proteins as the nascent phage is extruded through the bacterial plasma membrane. This complicated process takes place without killing the host bacterium. The bacteriophage is a semi-flexible worm-like nucleoprotein filament. The virion comprises a tube of several thousand identical major coat protein subunits around a core of single-stranded circular DNA. Each protein subunit is a polymer of about 50 amino-acid residues, largely arranged in an α-helix. The subunits assemble into a helical sheath, with each subunit oriented at a small angle to the virion axis and interdigitated with neighbouring subunits. A few copies of "minor" phage proteins necessary for infection and/or extrusion of the virion are located at each end of the completed virion. Here we review both the structure of the virion and aspects of its function, such as the way the virion enters the host, multiplies, and exits to prey on further hosts. In particular we focus on our understanding of the way the components of the virion come together during assembly at the membrane. We try to follow a basic rule of empirical science, that one should chose the simplest theoretical explanation for experiments, but be prepared to modify or even abandon this explanation as new experiments add more detail.

Ultrafast fluorescence decay profiles reveal differential unstacking of 2-aminopurine from neighboring bases in single-stranded DNA-binding protein subsites

Gene 5 protein (g5p) is a dimeric single-stranded DNA-binding protein encoded by Ff strains of Escherichia coli bacteriophages. The 2-fold rotationally symmetric binding sites of a g5p dimer each bind to four nucleotides, and the dimers bind with high cooperativity to saturate antiparallel single-stranded DNA (ssDNA) strands. Ultrafast time-resolved fluorescence spectroscopies were used to investigate the conformational heterogeneity and dynamics of fluorescent 2-aminopurine (2AP) labels sequestered by bound g5p. The 2AP labels were positioned within the noncomplementary antiparallel tail sequences of d(AC)(8) or d(AC)(9) of hairpin constructs so that each fluorescent label could probe a different subsite location within the DNA-binding site of g5p. Circular dichroism and isothermal calorimetric titrations yielded binding stoichiometries of approximately six dimers per oligomer hairpin when tails were of these lengths. Mobility shift assays demonstrated the formation of a single type of g5p-saturated complex. Femtosecond time-resolved fluorescence spectroscopy showed that the 2AP in the free (non-protein-bound) DNAs had similar heterogeneous distributions of conformations. However, there were significant changes, dominated by a large increase in the population of unstacked bases from ~22 to 59-68%, depending on their subsite locations, when the oligomers were saturated with g5p. Anisotropy data indicated that 2AP in the bound state was less flexible than in the free oligomer. A control oligomer was labeled with 2AP in the loop of the hairpin and showed no significant change in its base stacking upon g5p binding. A proposed model summarizes the data.

Circular dichroism spectra and electrophoretic mobility shift assays show that human replication protein A binds and melts intramolecular G-quadruplex structures

Noncanonical DNA structures such as G-quadruplexes might obstruct the binding of hRPA, compromising the accuracy of replication, and be a source of genomic instability. In this study, circular dichroism (CD) and electrophoretic mobility shift assay (EMSA) experiments were used to show that hRPA can bind and melt nontelomeric, intramolecular DNA G-quadruplexes under physiologically germane conditions. EMSA results show that hRPA binds to a 58-mer that includes an embedded quadruplex with an affinity equal to or greater than to nonquadruplex forming 58-mers. Moreover, hRPA binds to a 26-mer purine-rich quadruplex-forming sequence with an affinity indistinguishable from that for binding to the complementary pyrimidine-rich sequence. Under the same conditions, hRPA does not have significant affinity for binding to the duplex formed from the two sequences. Thus, DNA secondary structures can significantly modulate the binding affinity of hRPA over and above its known preference for pyrimidine-rich single-stranded sequences, so that at least some intramolecular G-quadruplex structures may not inhibit hRPA binding during DNA replication. CD spectral changes in combination with EMSA titrations suggest that one hRPA heterotrimer is sufficient to form a stable complex with an unfolded 26-mer G-quadruplex prior to the binding of a second hRPA molecule.

Evidence for direct contact between the RPA3 subunit of the human replication protein A and single-stranded DNA

Replication Protein A is a single-stranded (ss) DNA-binding protein that is highly conserved in eukaryotes and plays essential roles in many aspects of nucleic acid metabolism, including replication, recombination, DNA repair and telomere maintenance. It is a heterotrimeric complex consisting of three subunits: RPA1, RPA2 and RPA3. It possesses four DNA-binding domains (DBD), DBD-A, DBD-B and DBD-C in RPA1 and DBD-D in RPA2, and it binds ssDNA via a multistep pathway. Unlike the RPA1 and RPA2 subunits, no ssDNA-RPA3 interaction has as yet been observed although RPA3 contains a structural motif found in the other DBDs. We show here using 4-thiothymine residues as photoaffinity probe that RPA3 interacts directly with ssDNA on the 3'-side on a 31 nt ssDNA.

RPA repair recognition of DNA containing pyrimidines bearing bulky adducts

Recognition of new DNA nucleotide excision repair (NER) substrate analogs, 48-mer ddsDNA (damaged double-stranded DNA), by human replication protein A (hRPA) has been analyzed using fluorescence spectroscopy and photoaffinity modification. The aim of the present work was to find quantitative characteristics of RPA-ddsDNA interaction and RPA subunits role in this process. The designed DNA structures bear bulky substituted pyrimidine nitrogen bases at the inner positions of duplex forming DNA chains. The photoreactive 4-azido-2,5-difluoro-3- pyridin-6-yl (FAP) and fluorescent antracenyl, pyrenyl (Antr, Pyr) groups were introduced via different linker fragments into exo-4N of deoxycytidine or 5C of deoxyuridine. J-dU-containing DNA was used as a photoactive model of undamaged DNA strands. The reporter group was a fluorescein residue, introduced into the 5'-phosphate end of one duplex-forming DNA strand. RPA-dsDNA association constants and the molar RPA/dsDNA ratio have been calculated based on fluorescence anisotropy measurements under conditions of a 1:1 RPA/dsDNA molar ratio in complexes. The evident preference for RPA binding to ddsDNA over undamaged dsDNA distinctly depends on the adduct type and varies in the following way: undamaged dsDNA < Antr-dC-ddsDNA < mmdsDNA < FAPdU-, Pyr-dU-ddsDNA < FAP-dC-ddsDNA (K(D) = 68 +/- 1; 25 +/- 6; 13 +/- 1; 8 +/- 2, and 3.5 +/- 0.5 nM correspondingly) but weakly depends on the chain integrity. Interestingly the bulkier lesions not in all cases have a greater effect on RPA affinity to ddsDNA. The experiments on photoaffinity modification demonstrated only p70 of compactly arranged RPA directly interacting with dsDNA. The formation of RPA-ddsDNA covalent adducts was drastically reduced when both strands of DNA duplex contained virtually opposite located FAP-dC and Antr-dC. Thus RPA requires undamaged DNA strand presence for the effective interaction with dsDNA bearing bulky damages and demonstrates the early NER factors characteristic features underlying strand discrimination capacity and poor activity of the NER system toward double damaged DNA.

Complex formation between cationic beta-1,3-glucan and hetero-sequence oligodeoxynucleotide and its delivery into macrophage-like cells to induce cytokine secretion

A cationic polysaccharide bearing a beta-1,3-glucan main-chain structure (CUR-N(+)) forms a complex with a hetero-sequence oligonucleotide, that is, a CpG ODN, and facilitates the transportation of the resultant complex into a murine macrophage-like cell J774.A1, which induces an efficient secretion of a cytokine (IL-12) as compared with that induced by conventional carriers such as poly(ethyleneimine) (PEI) and poly(L-lysine) (PLL).

Human replication protein A unfolds telomeric G-quadruplexes

G-quadruplex structures inhibit telomerase activity and must be disrupted for telomere elongation during S phase. It has been suggested that the replication protein A (RPA) could unwind and maintain single-stranded DNA in a state amenable to the binding of telomeric components. We show here that under near-physiological in vitro conditions, human RPA is able to bind and unfold G-quadruplex structures formed from a 21mer human telomeric sequence. Analyses by native gel electrophoresis, cross-linking and fluorescence resonance energy transfer indicate the formation of both 1:1 and 2:1 complexes in which G-quadruplexes are unfolded. In addition, quadruplex opening by hRPA is much faster than observed with the complementary DNA, demonstrating that this protein efficiently unfolds G-quartets. A two-step mechanism accounting for the binding of hRPA to G-quadruplexes is proposed. These data point to the involvement of hRPA in regulation of telomere maintenance.