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In solution, DAPK2 is in equilibrium between the cis-autoinhibited monomer or trans-autoinhibited dimer. Under physiological conditions, the equilibrium is shifted towards the monomeric form. In both cases, DAPK2 is locked in the autoinhibited conformation mediated by Ser318 autophosphorylation (represented as a red diamond). The phosphorylation of the C-terminal Thr369 (red circle), either by autophosphorylation or by PKB26 (or some other still unidentified kinase), creates a mode III 14-3-3-binding site. Because the 14-3-3 dimer contains two binding grooves, 14-3-3 can increase the local DAPK2 concentration and shift the equilibrium towards the DAPK2 dimer. Accordingly, the inactive form of DAPK2 is a trans-autoinhibited dimer with autophosphorylated Ser318 and Thr369 in a complex with the 14-3-3 dimer, which stabilizes the dimeric form of DAPK2, protects Ser318 against dephosphorylation, and prevents Ca2+/CaM binding to DAPK2. Alternatively, 14-3-3 proteins interact with only one molecule of DAPK2, which could allow a bidentate interaction in which the 14-3-3 dimer simultaneously interacts with both the C-terminal motif and the pSer318-containing motif within AID. This bidentate interaction would also protect pSer318 against dephosphorylation and destabilize Ca2+/CaM binding to DAPK2. In short, both Ca2+/CaM-dependent and -independent (based on Ser299 phosphorylation24, represented as a red triangle) DAPK2 activation require Thr369 and Ser318 dephosphorylation.
DNA binding proteins recognize the DNA base sequence (base readout) and the structural features of DNA (shape readout) as determinants of their target sites1. The structural features include parameters describing intra-base pair and inter-base pair2,3 spatial relationships as well as minor groove dimensions (width and depth). Although they are sequence-dependent, they can also be altered by factors such as DNA supercoiling and binding of drugs. For example, the binding of intercalating drugs such as doxorubicin (Dox), increases the inter-base pair distance and untwists the DNA, which in a closed DNA molecule results also in changes in writhe. Importantly, the structural features are interdependent, e.g. changes in DNA twist affect the groove widths4. This implies that topological changes, while partitioning into twist and writhe, would affect the shape read-out of a particular protein.
Histone H1 and HMGB1 both bind to the linker DNA where it enters/exits the nucleosomal core particle but exert opposing effects on chromatin structure5. Whereas histone H1 stabilizes nucleosome structure and facilitates higher order chromatin folding6, binding of HMGB1 enhances nucleosome sliding and decompacts chromatin7. Consequently, histone H1 represses transcription, contrasting with HMGB1, which promotes the interaction of transcription factors (TFs) with DNA. Although both proteins bind to DNA without sequence specificity, their binding is influenced by DNA structure. Histone H1 preferentially binds to superhelical plasmid DNA in vitro, a fact that may be explained by its increased potential to form multiple H1-DNA contacts on plectonemically wound DNA8. HMGB1 preferentially binds to pre-bent DNA, supercoiled DNA, damaged DNA, hemicatenanes and catenanes, four-way junctions and other non-B DNA structures in vitro9. Upon binding, HMGB1 further bends the DNA towards the major groove by an angle of about 77°. This bending results from the intercalation of three hydrophobic amino acids through the minor groove10,11.
Retinoic acid receptor (RAR) is a member of the nuclear receptor (NR) family of TFs, the activation of which is ligand-dependent. RAR requires heterodimerization with retinoid X receptor (RXR) for proper transactivation of its target genes. In chromatin, RAR-RXR heterodimeric complexes recognize a specific sequence called retinoic acid response element (RARE) composed of a direct repeat (DR) of AGGTCA sequences separated by a spacer of either 1, 2 or 5 bases, termed DR1, DR2 and DR5, respectively. Binding occurs through the major DNA groove15.
Drug intercalation to DNA increases the base pair rise while reducing the helix twist by an angle dependent on the intercalator molecule. This decrease in helix twist translates into an overall reduction in DNA twist, which is compensated by an increase in writhe within the chromatin loops23. To elucidate the possible contribution of superhelicity to the recovery profiles generated above (Fig. 1b and Fig. S1), we induced topological relaxation by nicking agents.
In view of the well-known winding effect of intercalators26,27 (and refs therein), we tested the possible role of internucleosomal superhelicity in determining HMGB1 binding in vivo. DNA supercoiling was relaxed by treating live U2OS2FP cells with hydrogen peroxide (H2O2), bleomycin or X-ray irradiation, and GFP-HMGB1 binding to DNA was evaluated by point FRAP. Given the short time interval between nicking and measurement, we expected that the breaks would still be unrepaired, or even if they were, the original levels of internucleosomal superhelicity would not have been re-established. Thus, if HMGB1 binding were sensitive to supercoiling, relaxation would affect its binding. Strikingly, none of these agents caused a change in FRAP recovery rate (Fig. 2), suggesting that intercalators influence HMGB1 binding directly rather than indirectly by changing twist-writhe partitioning.
The purpose of cleaning is to ensure naked contact between the stylus and the information encoded into the grooves, and nothing between the two, hence the use of alcohol to dissolve any surface contaminants (cigarette smoke, skin oils, mould-release, airborne matter) which are then vacuumed away.
The solution is wetting agent, an additive used in the photographic industry where the same issue was encountered in washing photographic films and papers. Wetting agent reduces the surface tension of water, and was developed to ensure even washing of photographic film and papers, promote even drying without water marks or residues, and imparting anti-static qualities.
As an alternative to Ilfotol, I did quite a bit of research and found that wetting agents are added to insecticides. These can be brought seperate to the insecticide, thus in this case it is almost 100% Tridecanol. The advantage being that it is available in much smaller quantities. I will test the mixture in my Spinclean and report back if it doesent work.
I have mail ordered one set of vinyl records clamp and small motorized rotary device and stainless steel Ultrasonic Cleaner Bath, (inside measrmnt: 30×15×10cm made in China costing approx. $250). Now that I got your receipe it will soon be operational when it arrives. My problem is how to vacuum clean the cleaned records. Many vinyl lovers (incld. Michael Fremer) advocate ultrasonic cleaning as a good and safe way to clean vinyl records thoroughly. There are also some advertisements about one complete set of ultrasonic cleaner kit, ready to use. As I live in Indonesia far away on the other side of the globe from America ordering such ready set from USA would be costly and cumbersome (because of the impossibly complicated official custom procedures in Indonesia). So I ordered only the small clamping and rotating parts from USA (still had to pay $70 custom tax) and buy the 6 litres china made ultrasonic cleaner bath from one domestic online company, costing ca. $250. And now is the problem with drying the clean but wet vinyl records. I can let them dry by just put them vertically in array on dish stander like in the kitchen. Or I can blow them dry with the help of ordinary elevtric fan, or with an air compressor and a fine air filter to prevent oil or dirt particles get through and destroy the grooves on the vinyl disk. Of course there are commercial vinyl record vacuum dryers on the market but it would cost you some more dear money. Maybe you could suck the wetness on the vinyl disk with an ordinary vacuum cleaner but you should use a very clean sucking head with fine and flexible brush to prevent damage on the delicate vinyl surface.
I found that the mix with ethanol works better than using IPA alcohol. In my experience I noticed that ethanol gets the dirt and grease better out of the grooves. Plus, bio ethanol is much cheaper than IPA. But 100% ethanol uses Bitrex to denatured the alcohol for consumption. Bitrex is a acid as we all know. So how much damage can it do even in very small amount (1 liter Bitrex is used for 100.000 liter ethanol).
Have replaced your recommendation of Ilford Ilfotol with Tetanal Mirasol 2000 Antistatic (a German wetting agent). I made up a solution of 200ml using slightly less than 1ml of the wetting agent. The results are just superb.
I have been using the formula for a year now and have seen no issues. If you are using tap water with a high mineral content that could explain the residue. The best is to use lab grade reagent water category I or II
I have no idea what all these different products do, but I do recognise what ends up on my stylus (when I have to clean it due to residue). I council against anything with detergent function that could leave residue in the groove. It simply replaces historical detritus with syrupy gunk, which deadens the stylus response to (clean) groove walls.
I think the two different cleaners are complementary, with IPA better at shifting 50 years of muck, while the Knosti is more effective on mould-release and antistatic properties. In any event, a second clean does help further reduce clicks and pops from any more stubborn detritus in the grooves.
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