Homology in Trivaline Complex Formation with dsDNA and ssRNA

Abstract

It has been shown by the equilibrium dialysis that at a polyU concentration above the "critical" one, the complete polymer saturation with trivaline reaches approximately 0.7 trivaline molecules per one phosphate group. i.e. at these conditions peptide dimer occupies on polyU a site of three bases (phosphates) in length. The trivaline complex with polyU at a concentration lower than the "critical" one does not reveal any noticeable fluorescence, but has rather significant positive linear dichroism at 265 and 330 nm. The trivaline-nucleic acids complex has a significant fluorescence at any dsDNA concentration while with polyU it is only so at a concentration above the "critical" one. Electron microscopy has shown that at a rather high concentration of dsDNA molecules in solution a "biduplex" structure undergoes an additional stage of compaction, during which the extended particles more than 30 nm in diameter are formed.

Trivaline Molecular Complexes with Trinucleotides Form in Solution the Extended, about 1000 Å in Length Structures

“…To a first approximation, there is no difference whether the latter is incorporated in a duplex or exists isolated in solution (15). Some positions of this model were confirmed in (16,17,(24)(25)(26).…”

“…As it has been supposed ( 16,17,(24)(25)(26) for complexes with long polynucleotides, such "stacking" structures are also able to associate with each other "side by side", and this can explain the presence in solution of extended structures of various thickness.…”

“…We think that like DHTV complexes with polymers (16,17,(24)(25)(26), molecules of two such tetrameric complexes oftrinucleotides with trivaline are able to join each other by nucleic-nucleic contacts-Hoogsteen's hydrogen bonds. An octameric structure is formed (Figure 7).1t is similar with the "quadruplex" structure which may be formed by two duplexes of free DNA In fact, ds and ss polymers as well as trinucleotides in diameter (10,15,16) This is approximately twice more than in the earlier described tetrameric structure (10,15,16).…”

Concatemerization of tRNA molecules in the presence of trivaline derivative

“…The DHTV dimer binding on nucleic acids was highly cooperative [19, 20]. DHTV formed monomeric and β‐dimeric complexes on single‐stranded polymers [21], and, in addition to these types, β‐sandwich peptide structures [19]were observed on double‐stranded polymers. Profound similarity was found between DHTV binding to single‐ and double‐stranded polymers.…”

“…This made possible the improvement of the above‐mentioned model [22]and the development of a universal model explaining the formation of the following nucleopeptide structures: (1) a pseudoduplex structure made by two single‐stranded nucleic acid molecules positioned side by side and saturated with DHTV forming β‐dimers [21]; (2) quadruplex structures consisting of two nucleic acid duplexes or pseudoduplexes with DHTV bound in the form of β‐sandwiches [21, 22]. Such quadruplex structures could result from peptide‐peptide or nucleo‐nucleic interaction [22]; they were both later confirmed in experiments [23]. The quadruplex structures could give rise to ‘higher order compact' structures [21, 22]containing several quadruplex units arranged side by side and concatemeric structures in which numerous quadruplex units could be aligned one after another.…”