| 26. |
- Joseph, Prajin, et al.
(author)
-
Polymer properties of softwood organosolv lignins produced in two different reactor systems
- 2023
-
In: Biopolymers. - : John Wiley and Sons Inc. - 0006-3525 .- 1097-0282. ; 114:12
-
Journal article (peer-reviewed)abstract
- Lignin, the second most abundant biopolymer on earth and with a predominantly aromatic structure, has the potential to be a raw material for valuable chemicals and other bio-based chemicals. In industry, lignin is underutilized by being used mostly as a fuel for producing thermal energy. Valorization of lignin requires knowledge of the structure and different linkages in the isolated lignin, making the study of structure of lignin important. In this article, lignin samples isolated from two types of reactors (autoclave reactor and displacement reactor) were analyzed by FT-IR, size exclusion chromatography, thermogravimetric analysis (TGA), and Py-GC-MS. The average molecular mass of the organosolv lignins isolated from the autoclave reactor decreased at higher severities, and FT-IR showed an increase in free phenolic content with increasing severity. Except for molecular mass and molecular mass dispersity, there were only minor differences between lignins isolated from the autoclave reactor and lignins isolated from the displacement reactor. Carbohydrate analysis, Py-GC–MS and TGA showed that the lignin isolated using either of the reactor systems is of high purity, suggesting that organosolv lignin is a good candidate for valorization.
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| 27. |
- Karlsson, J., et al.
(author)
-
Enzymatic degradation of carboxymethyl cellulose hydrolyzed by the endoglucanases Cel5A, Cel7B, and Cel45A from Humicola insolens and Cel7B, Cel12A and Cel45Acore from Trichoderma reesei
- 2002
-
In: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 63:1, s. 32-40
-
Journal article (peer-reviewed)abstract
- Enzymatic hydrolysis of carboxymethyl cellulose (CMC) has been studied with purified endoglucanases Hi Cel5A (EG II), Hi Cel7B (EG I), and Hi Cel45A (EG V)from Humicola insolens, and Tr Cel7B (EG I), Tr Cel12A (EG III), and Tr Cel45Acore (EG V)from Trichoderma reesei. The CMC, with a degree of substitution (DS) of 0.7, was hydrolyzed with a single enzyme until no further hydrolysis was observed. The hydrolysates were analyzed for production of substituted and non substituted oligosaccharides with size exclusion chromatographly (SEC) and with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF-MS). Production of reducing ends and of nonsubstituted oligosaccharides was determined as well. The two most effective endoglucanases for CMC hydrolysis were Hi Cel5.A and Tr Cel7B. These enzymes degraded CMC to lower molar mass fragments compared with the other endoglucanases. The products had the highest DS determined by MALDI-TOF-MS. Thus, Hi Cel5A and Tr Cel7B were less inhibited by the substituents than the other endoglucanases. The endoglucanase with clearly the lowest activity on CMC was Tr Cel45Acore. It produced less than half of the amount of reducing ends compared to Tr Cel7B; furthermore, the products had significantly lower DS. By MALDI-TOF-MS, oligosaccharide with different degree of polymerization (DP) and with different number of substituents could be separated and identified. The average oligosaccharide DS as function of DP could be measured for each enzyme after hydrolysis. The combination of techniques for analysis of product formation gave information on average length of unsubstituted blocks of CMC.
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| 28. |
- Kim, Seog K., et al.
(author)
-
Z- B TRANSITION IN POLY D(G-M5C)2 INDUCED BY INTERACTION WITH 4',6-DIAMIDINO-2-PHENYLINDOLE
- 1993
-
In: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 33:11, s. 1677-1686
-
Journal article (peer-reviewed)abstract
- The Z form of poly [d(G-m5C)2], in presence of Mg2+ ion, is found to be transformed into B form upon interaction with 4',6-diamidino-2-phenylindole (DAPI). The Z --> B transformation is complete at a mixing ratio of about 0.07 DAPI per DNA base pairs, i.e., each DAPI molecule may be related to the conversion of 6-7 base pairs. An interaction between DAPI and poly [d(G-m5C)2] in its Z form at low drug: DNA ratios is suggested from optical dichroism and time-resolved luminescence anisotropy results. The spectroscopic behaviour of DAPI indicates that the Z conformation of DNA does not provide normal binding sites for DAPI, such as groove or intercalation sites, but that the initial association may be of external nature. (C) 1993 John Wiley & Sons, Inc.
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| 29. |
- Korolev, Nikolay, et al.
(author)
-
Molecular Dynamics Simulations Demonstrate the Regulation of DNA-DNA Attraction by H4 Histone Tail Acetylations and Mutations
- 2014
-
In: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 101:10, s. 1051-1064
-
Journal article (peer-reviewed)abstract
- The positively charged N-terminal histone tails play a crucial role in chromatin compaction and are important modulators of DNA transcription, recombination, and repair. The detailed mechanism of the interaction of histone tails with DNA remains elusive. To model the unspecific interaction of histone tails with DNA, all-atom molecular dynamics (MD) simulations were carried out for systems of four DNA 22-mers in the presence of 20 or 16 short fragments of the H4 histone tail (variations of the 16-23 a. a. KRHRKVLR sequence, as well as the unmodified fragment a. a. 13-20, GGAKRHRK). This setup with high DNA concentration, explicit presence of DNA-DNA contacts, presence of unstructured cationic peptides (histone tails) and K+ mimics the conditions of eukaryotic chromatin. A detailed account of the DNA interactions with the histone tail fragments, K+ and water is presented. Furthermore, DNA structure and dynamics and its interplay with the histone tail fragments binding are analysed. The charged side chains of the lysines and arginines play major roles in the tailmediated DNA-DNA attraction by forming bridges and by coordinating to the phosphate groups and to the electronegative sites in the minor groove. Binding of all species to DNA is dynamic. The structure of the unmodified fully-charged H4 16-23 a. a. fragment KRHRKVLR is dominated by a stretched conformation. The H4 tail a. a. fragment GGAKRHRK as well as the H4 Lys16 acetylated fragment are highly flexible. The present work allows capturing typical features of the histone tail-counterionDNA structure, interaction and dynamics.
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| 30. |
- Kwaambwa, Habauka M., et al.
(author)
-
Interactions of surfactants with a water treatment protein from Moringa oleifera seeds in solution studied by zeta-potential and light scattering measurements
- 2012
-
In: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 97:4, s. 209-218
-
Journal article (peer-reviewed)abstract
- Protein extracted from Moringa oleifera (MO) seeds has been advocated as a cheap and environmental friendly alternative to ionic flocculants for water purification. However, the nature and mechanism of its interaction with particles in water, as well as with dissolved surface-active molecules, are not well understood. In this article, we report studies of the protein and its interaction with four surfactants using dynamic light scattering (DLS), zeta-potential and turbidity measurements. Zeta-potential measurements identified points of charge reversal and the turbidity and DLS measurements were used to characterize the microstructure and size of protein-surfactant complexes. From the points of charge reversal, it was estimated that 7 anions are required to neutralize the positive charges of each protein molecule at pH 7. For protein mixtures with sodium dodecyl sulfate and dodecyl di-acid sodium salt, the peak in turbidity corresponds to concentrations with a large change in zeta-potential. No turbidity was observed for protein mixtures with either the nonionic surfactant Triton X-100 or the zwitterionic surfactant N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate. Changes of pH in the range 410 have little effect on the zeta-potential, turbidity, and the hydrodynamic radius reflecting the high isoelectric point of the protein. Addition of small amounts of salt has little effect on the size of protein in solution. These results are discussed in the context of the use of the MO protein in water treatment.
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| 31. |
- Lafitte, Géraldine, et al.
(author)
-
PFG-NMR diffusometry: A tool for investigating the structure and dynamics of noncommercial purified pig gastric mucin in a wide range of concentrations
- 2007
-
In: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 86:2, s. 165-175
-
Journal article (peer-reviewed)abstract
- For the first time, Pulsed Field Gradient-Nuclear Magnetic Resonance, a powerful noninvasive tool for studying the dynamics and structure of complex-gels, has been used to measure diffusion of probe molecules in aqueous solutions/gels of noncommercial purified pig gastric mucin (PGM), in a concentration range up to 5 wt%. Complementary data were obtained from rheology measurements. The combination of techniques revealed a strong pH dependency of the structure of the PGM samples while changes in concentration, ionic strength, and temperature appeared to induce less pronounced alterations. Viscosity was found to vary in a nonmonotonous way with pH, with the more viscous solutions found at intermediate pH. We propose that this finding is due to a reduced charge density at lower pH, which is expected to continuously increase the relative importance of hydrophobic associations. The results suggest a loose network of expanded fully charged PGM molecules woth considerable mobility at neutral pH (pH 7.4). At intermediate pH (pH 4), a three-dimensional expanded network is favored. At pH 1, the charge density is low and microphase seperation occurs since hydrophobic associations prevail. This leads to the formation of clusters concentrated in PGM molecules seperated by regions depleted in PGM. The results obtained increase our knowledge about the gastric mucosal layer, which in vivo contains mucin in the same concentration range as that of the samples investigated here. (c) 2007 Wiley Periodicals, Inc.
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| 32. |
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| 33. |
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| 34. |
- Lindgren, Joel, 1982-, et al.
(author)
-
A GLP-1 receptor agonist conjugated to an albumin-binding domain for extended half-life
- 2014
-
In: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 102:3, s. 252-259
-
Journal article (peer-reviewed)abstract
- Glucagon-like peptide 1 (GLP-1) and related peptide agonists have been extensively investigated for glycaemic control in Type 2 diabetes, and may also have therapeutic applications for other diseases. Due to the short half-life (t1/2<2 min) of the endogenous peptide, caused by proteolytic degradation and renal clearance, different strategies for half-life extension and sustained release have been explored. In the present study, conjugates between a GLP-1 analogue and a 5 kDa albumin-binding domain (ABD) derived from streptococcal protein G have been chemically synthesized and evaluated. ABD binds with high affinity to human serum albumin, which is highly abundant in plasma and functions as a drug carrier in the circulation. Three different GLP-1-ABD conjugates, with the two peptides connected by linkers of two, four, and six PEG units, respectively, were synthesized and tested in mouse pancreatic islets at high (11 mM) and low (3 mM) glucose concentration. Insulin release upon stimulation was shown to be glucose-dependent, showing no significant difference between the three different GLP-1-ABD conjugates and unconjugated GLP-1 analogue. The biological activity, in combination with the high affinity binding to albumin, make the GLP-1-ABD conjugates promising GLP-1 receptor agonists expected to show extended in vivo half-life.
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| 35. |
- Lundqvist, Hans, et al.
(author)
-
Targeting peptides and positron emission tomography
- 2002
-
In: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 66:6, s. 381-92
-
Journal article (peer-reviewed)abstract
- Biologically active peptides have during the last decades made their way into conventional nuclear medicine diagnosis using single photon emission computed tomography (SPECT) and gamma-camera. Several clinical trails are also investigating the role of radiolabeled peptides for targeting radionuclide therapy. This has raised the question as to whether positron emission tomography (PET) can be used in order to obtain better quantitative information of the peptide distribution in tumor and healthy organs, i.e., to get a better dosimetry. Positron emitting analogs of the therapeutic radionuclides used have been produced and successfully applied in peptide pharmacokinetic measurements with PET. But the recent boom in (18)FDG-PET ((18)FDG = [(18)F]2-deoxy-2-fluoro-D-glucose), and with this a worldwide increasing number of PET systems, has also inspired several research groups to hunt for alternative labels to be used for peptide diagnostics and PET. The rapid kinetic of short peptides agrees well with the short half-lives of standard PET nuclides like (11)C and (18)F. Especially, (18)F appears to be excellent for labeling bioactive peptides due to its favorable physical and nuclear characteristics. However, with present techniques labeling peptides with (18)F is laborious and time-consuming, and is not yet a clinical alternative. Other halogens like (75, 76)Br and (124)I are, from the chemical point of view, easier to apply. But an even better labeling alternative may be positron emitting metal ions like (55)Co, (68)Ga, and (110m)In since they tend to give better intracellular retention and thus a better signal-to-background ratio than the halogen labels. The main drawback with these radionuclides is that they are not readily available. Some of these radionuclides also emit gamma in their decay that may affect the measuring properties of the PET equipment. This article reviews mainly the present situation of production and use of nonconventional positron emitters for peptide labeling.
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| 36. |
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| 37. |
- Lyng, Reidar, 1959, et al.
(author)
-
THE CD OF LIGAND-DNA SYSTEMS .1. POLY(DG-DC) B-DNA
- 1991
-
In: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 31:14, s. 1709-1720
-
Journal article (peer-reviewed)abstract
- A systematic theoretical study of the CD of double-stranded poly (dG-dC) and its complexes with small molecules is presented. The intrinsic CD of the polymer and the induced CD of a transition belonging to a molecule bound to DNA are calculated using the matrix method. The calculations show considerable differences between pyrimidine-purine and purine-pyrimidine binding sites, and we find that the induced CD of a groove bound molecule is one order of magnitude stronger than that of an intercalated molecule. The results form a sound basis for interpreting the CD of ligand-DNA systems in terms of molecular geometry, interactions, and spectroscopy.
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| 38. |
- Lyng, Reidar, 1959, et al.
(author)
-
THE CD OF LIGAND-DNA SYSTEMS .2. POLY(DA-DT) B-DNA
- 1992
-
In: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 32:9, s. 1201-1214
-
Journal article (peer-reviewed)abstract
- A systematic theoretical study of the CD of [poly (dA-dT)]2 and its complexes with achiral small molecules is presented. The CD spectra of [poly (dA-dT)]2 and of poly (dA):poly(dT) are calculated for various DNA structures using the matrix method. The calculated and experimental spectra agree reasonably well for [poly(dA-dT)]2 but less well for poly(dA):poly(dT). The calculated CD spectrum of [poly(dA-dT)]2 fails to reproduce the wavelength region of 205-245 nm of the experimental spectrum. This discrepancy can be explained by a magnetic dipole allowed transition contributing significantly to the CD spectrum in this region. The induced CD of a transition moment of a molecule bound to [poly(dA-dT)]2 is also calculated. As was the case for [poly(dG-dC)]2, the induced CD of a groove bound molecule is one order of magnitude stronger than that of an intercalated molecule. The calculations also show considerable differences between pyrimidine-purine sites and purine-pyrimidine sites. Both signs and magnitudes of the CD induced into ligands bound in the minor groove agree with experimental observations.
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| 39. |
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| 40. |
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| 41. |
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| 42. |
- Melander, Erik, et al.
(author)
-
Improved method for quantitative analysis of the cyclotide kalata B1 in plasma and brain homogenate
- 2016
-
In: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 106:6, s. 910-916
-
Journal article (peer-reviewed)abstract
- This study provides a new method for quantifying the cyclotide kalata B1 in both plasma and brain homogenate. Cyclotides are ultra-stable peptides with three disulfide bonds that are interesting from a drug development perspective as they can be used as scaffolds. In this study we describe a new validated LC-MS/MS method with high sensitivity and specificity for kalata B1. The limit of quantification was 2 ng/mL in plasma and 5 ng/gmL in brain homogenate. The method was linear in the range 2-10,000 ng/mL for plasma and 5-2000 ng/g for brain. Liquid Chromatographic separation was performed on a HyPurity C18 column, 50 3 4.6 mm, 3 mm particle size. The method had inter-and intra-day precision and accuracy levels <15% and 12% respectively. Applying the method to in vivo plasma samples and brain homogenate samples from equilibrium dialysis yielded satisfying results and was able to describe the plasma pharmacokinetics and brain tissue binding of kalata B1. The described method is quick, reproducible and well suited to quantifying kalata B1 in biological matrices.
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| 43. |
- Mitsueda, Asako, et al.
(author)
-
Development of a Novel Nanoparticle by Dual Modification With the Pluripotential Cell-Penetrating Peptide PepFect6 for Cellular Uptake, Endosomal Escape, and Decondensation of an siRNA Core Complex
- 2013
-
In: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 100:6, s. 698-704
-
Journal article (peer-reviewed)abstract
- Development of novel devices for effective nucleotide release from nanoparticles is required to improve the functionality of nonviral delivery systems, because decondensation of nucleotide/polycation complexes is considered as a key step for cytoplasmic delivery of nucleotides. Previously, PepFect6 (PF6) comprised chloroquine analog moieties and a stearylated cell-penetrating peptide to facilitate endosomal escape and cellular uptake, respectively, was developed as a device for efficient siRNA delivery. As PF6 contains bulky chloroquine analog moieties, the polyplexes are expected to be loose structure, which facilitates decondensation. In the present study, siRNA was electrostatically condensed by PF6, and the PF6/siRNA complexes were coated with lipid membranes. The surface of the nanoparticles encapsulating the PF6/siRNA core (PF6-NP) was modified with PF6 for endosomal escape (PF6/PF6-NP). The RNAi effect of PF6/PF6-NP was compared with those of stearylated cell-penetrating peptide octaarginine (R8)-modified PF6-NP, R8-modified nanoparticles encapsulating the R8/siRNA core (R8-NP) and PF6-modified R8-NP. Nanoparticles encapsulating the PF6 polyplex, especially PF/PF-NP, showed a significant knockdown effect on luciferase activity of B16-F1 cells stably expressing luciferase. siRNA was widely distributed within the cytoplasm after transfection of the nanoparticles encapsulating the PF6 polyplex, while siRNA encapsulated in the R8-presenting nanoparticles was localized within the nuclei. Thus, the siRNA distribution was dependent on the manner of peptide-modification. In conclusion, we have successfully developed PF6/PF6-NP exhibiting a potent RNAi effect resulting from high cellular uptake, efficient endosomal escape and decondensation of the polyplexes based on the multifunctional cell penetrating peptide PF6. PF6 is therefore a useful pluripotential device for siRNA delivery. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 698-704, 2013.
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| 44. |
- Moon, J. H., et al.
(author)
-
DNA structural features responsible for sequence-dependent binding geometries of Hoechst 33258
- 1996
-
In: Biopolymers. - 0006-3525 .- 1097-0282. ; 38:5, s. 593-606
-
Journal article (peer-reviewed)abstract
- The complexes of Hoechst 33258 with poly[d(A-T)(2)], poly[d(I-C)(2)], poly[d(G-C)(2)], and poly[d(G-m(5)C)(2)] were studied using linear dichroism, CD, and fluorescence spectroscopies. The Hoechst-poly[d(I-C)(2)] complex, in which there is no quanine amino group protruding in the minor groove, exhibit spectroscopic properties that are very similar to those of the Hoechst-poly[d(A-T)(2)] complex. When bound to both of these polynucleotides, Hoechst exhibits an average orientation angle of near 45 degrees relative to the DNA helix axis for the long-axis polarized low-energy transition, a relatively strong positive induced CD, and a strong increase in fluorescence intensity-leading us to conclude that this molecule also binds in the minor groove of poly[d(I-C)(2)]. By contrast, when bound to poly[d(G-C)(2)], Hoechst shows a distinctively different behavior. The strongly negative reduced linear dichroism in the ligand absorption region is consistent with a model in which part of the Hoechst chromophore is intercalculated between DNA bases. From the low drug:base ratio onset of excitonic effects in the CD and fluorescence emission spectra, it is inferred that another part of the Hoechst molecule may sit in the major groove of poly[d(G-C)(2)] and poly[d(G-m(5)C)(2)] and preferentially stacks into dimers, though this tendency is strongly reduced for the latter polynucleotide. Based on these results, the importance of the interactions of Hoechst with the exocyclic amino group of guanine and the methyl group of cytosine in determining the binding modes are discussed.
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| 45. |
- Muthusamy, Karen, et al.
(author)
-
Microwave Assisted SPPS of Amylin and Its Toxicity of the Pure Product to RIN-5F Cells
- 2010
-
In: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 94:3, s. 323-330
-
Journal article (peer-reviewed)abstract
- The 37-amino acid polypeptide islet amyloid polypeptide (IAPP), or amylin, is found as amyloid aggregates in the islets of Langerhans in patients with type II diabetes. Herein, we report an efficient microwave assisted solid phase peptide synthesis of amylin (IAPP). The most efficient synthesis used double and triple couplings and 10 equiv. of amino acids. Double couplings were used for most amino acids, whereas triple couplings were utilized for amino acids in selected regions. The most effective method for formation of the disulfide bond in amylin was found to be iodine oxidation. The highest purity amylin was obtained when the crude peptide was purified with HPLC before formation of the disulfide bond. The cytotoxicity of the synthesized amylin product to RIN-5F cells was determined. The synthesized amylin exhibits an exponential increase of cytotoxicity at concentrations >35 mu M. Transmission electron microscope studies of a sample of amylin shows that insoluble amyloid fibrils spontaneously formed when 45 mu M solution of synthesized amylin was incubated in a suitable buffer for 6 h.
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| 46. |
- Niebling, Stephan, et al.
(author)
-
The Impact of Interchain Hydrogen Bonding on b-Hairpin Stability is Readily Predicted by Molecular Dynamics Simulation
- 2015
-
In: Peptide Science. - : Wiley. - 1097-0282 .- 0006-3525. ; 104:6, s. 703-706
-
Journal article (peer-reviewed)abstract
- Peptides are frequently used model systems for protein folding. They are also gaining increased importance as therapeutics. Here, the ability of molecular dynamics (MD) simulation for describing the structure and dynamics of β-hairpin peptides was investigated, with special attention given to the impact of a single interstrand sidechain to sidechain interaction. The MD trajectories were compared to structural information gained from solution NMR. By assigning frames from restraint-free MD simulations to an intuitive hydrogen bond on/off pattern, folding ratios and folding pathways were predicted. The computed molecular model successfully reproduces the folding ratios determined by NMR, indicating that MD simulation may be straightforwardly used as a screening tool in β-hairpin design.
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| 47. |
- Nilsson, K Peter R, et al.
(author)
-
Solution structure of chi-conopeptide MrIA, a modulator of the human norepinephrine transporter.
- 2005
-
In: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 80:6, s. 815-823
-
Journal article (peer-reviewed)abstract
- The chi-conopeptides MrIA and MrIB are 13-residue peptides with two disulfide bonds that inhibit human and rat norepinephrine transporter systems and are of significant interest for the design of novel drugs involved in pain treatment. In the current study we have determined the solution structure of MrIA using NMR spectroscopy. The major element of secondary structure is a beta-hairpin with the two strands connected by an inverse gamma-turn. The residues primarily involved in activity have previously been shown to be located in the turn region (Sharpe, I. A.; Palant, E.; Schroder, C. I.; Kaye, D. M.; Adams, D. J.; Alewood, P. F.; Lewis, R. J. J Biol Chem 2003, 278, 40317-40323), which appears to be more flexible than the beta-strands based on disorder in the ensemble of calculated structures. Analogues of MrIA with N-terminal truncations indicate that the N-terminal residues play a role in defining a stable conformation and the native disulfide connectivity. In particular, noncovalent interactions between Val3 and Hyp12 are likely to be involved in maintaining a stable conformation. The N-terminus also affects activity, as a single N-terminal deletion introduced additional pharmacology at rat vas deferens, while deleting the first two amino acids reduced chi-conopeptide potency.
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| 48. |
- Nordén, Bengt, 1945, et al.
(author)
-
Mismatch detection in homologous strand exchange amplified by hydrophobic effects
- 2021
-
In: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 112:4
-
Journal article (peer-reviewed)abstract
- In contrast to DNA replication and transcription where nucleotides are added and matched one by one, homologous recombination by DNA strand exchange tests whole sequences for complementarity, which requires elimination of mismatched yet thermodynamically stable intermediates. To understand the remarkable sequence specificity of homologous recombination, we have studied strand exchange between a 20-mer duplex containing one single mismatch (placed at varied positions) with the matching single strand in presence of poly(ethylene glycol) representing a semi-hydrophobic environment. A FRET-based assay shows that rates and yields of strand exchange from mismatched to matched strands rapidly increase with semi-hydrophobic co-solute concentration, contrasting previously observed general strand exchange accelerating effect of ethyl glycol ethers. We argue that this effect is not caused simply by DNA melting or solvent-induced changes of DNA conformation but is more complex involving several mechanisms. The catalytic effects, we propose, involve strand invasion facilitated by reduced duplex stability due to weakened base stacking (“longitudinal breathing”). Secondly, decreased water activity makes base-pair hydrogen bonds stronger, increasing the relative energy penalty per mismatch. Finally, unstacked mismatched bases (gaps) are stabilized through partly intercalated hydrophobic co-solvent molecules, assisting nucleation of strand invasion at the point of mismatch. We speculate that nature long ago discovered, and now exploits in various enzymes, that sequence recognition power of nucleic acids may be modulated in a hydrophobic environment.
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| 49. |
- Nordén, Bengt, 1945, et al.
(author)
-
Nucleic acid–metal interactions: V. The effect of silver(I) on the structures of A- and B-DNA forms
- 1986
-
In: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 25:8, s. 1531-1545
-
Journal article (peer-reviewed)abstract
- The interaction of silver(I) with DNA has been studied with uv LD in aqueous solution and in a humid anisotropic poly(vinyl alcohol) host (B-DNA) and also in 80% ethanolic solution (A-DNA). Addition of silver ions has a pronounced effect on the dichroic spectra of DNA, indicating that the DNA structure is significantly altered. By correlation with calculated reduced LD spectra, using intensities and moments of the corresponding electronic transitions of the DNA bases, the experimental spectra of DNA at high silver content may be interpreted in terms of tilt and roll angles of the bases in the double helix. In ethanolic A-DNA solution there is a pronounced decrease in the orientation by flow of DNA, suggesting that the complexation of DNA to silver may be accompanied by the formation of compact tertiary structures.
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| 50. |
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