Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

Conformational Dynamics and Mechanism of Interactions of Oligonucleotides with 3'-end of the East tRNAphe

A conformational dynamics and three dimensional atomic models of complexes between east tRNAphe and antisence 15-mer oligonucleotides (asON15) complementary to the 3'-end of tRNA, Figure 1, have been modeled.

Figure 1: Secondary structure of the tRNAphe with antisence oligonucleotides asON15 complementary to segment A62-A76, forming a major grove complex; in italic the position of the asON15 forming complex with T-loop.

A computational modeling has been done via the program package bison (1). It has been found that 15-mer oligonucleotide has three type of primary forming complexes with intact tRNAphe: (I) the major groove complex with the coaxial acceptor- and T-steams of the tRNAphe, Figure 2; (II) partially complementary complex with disordered T-loop, Figure 3; (III) double oligonucleotide complex consisted of T-loop and major groove complexes, Figure 4.

Figure 2: Major groove complex tRNAphe-asON15. Oligonucleotide asON15 5?-3? (up to down) in red, tRNAphe in blue, up to down are acceptor ACCA end, acceptor-, T-loop steam; right low corner, T-loop and D-loop; left low corner, anticodon loop.

Figure 3: T-loop complex of the tRNAphe-ON15. Complementary WC pairs C56-G7, G57-C6 ? low right corner.

Figure 4: Double asON15-tRNAphe complex. ON15 of the major grove complex, green; ON15 of the T-loop complex, red; tRNAphe, blue.

Oligonucleotide complex formation starts from initiation stage -- a formation of a complementary complex with free ACCA 3'-end of the tRNAphe and proceeds via major groove complex formation. Major grove complex is a triplex of the recombinant R-triplex type (2). The long acceptor steam allows to make a ?strong complex? with oligonucleotide, which delivers its 3?-end nucleotides to the vicinity of the T-loop, adjacent to the steam. These nucleotides destabilize the T-loop structure and initiate conformational rearrangement and a local destruction of the D- and T-loop junction. Disordered T-loop initiates a complementary pairing with asON15 and following formation of a complex with oligonucleotide. The T-loop complex has several complementary interactions with T-loop nucleotides and favorable H-bonds and stacking interactions with nucleotides in the vicinity of the D-, T-loop junction. A formation of the disordered complementary complex with T-loop is going through a minor conformational transition and destruction of the interaction between D- and T-loops. The final double oligonucleotide tRNAphe complex has the end-to-tail interactions between two asON15. The disordered T-loop allows a recombination between R-triplex oligonucleotide strands of the major groove complex and tRNAphe strand of 5?-end and formation of the full complementary complex between tRNAphe and antisence oligonucleotide. The major stages of the mechanism is follows from the calculation of the potential energy landscape of complexes along the conformational rearrangement pathway, i.e., the major groove R-triplex complexes versus the length N of the oligonucleotide, Figure 5, the T-loop complex, double asON15 complex and full complementary complex between asON15 and tRNAphe. The found mechanism of the conformational rearrangements of tRNAphe with asON15 is consistent with experimental data (3).

Figure 5: Potential energy of the tRNAphe complexes with oligonucleotides of N nucleotides of length docked on tRNA. Red filled circles, major groove complexes; diamond, T-loop complex; triangle down red, complex with asON18; star, average energy per asON15 for double ON15(MGR)+ON15(TL) complex; square, complementary complex tRNAphe-ON15.

The primary complex formation and following destruction of the tRNAphe native structure constitutes the mechanism of the ?molecular wedge?. The effective anticense oligonucleotide should consist of three segments: 1-complex initiator, 2-complex stabilizer, 3-loop destructor an have to be complementary to the tRNA structure element of [(fee end)/ loop-steam-loop].

The work is supported by RFFI projects No. 05-04-48322.

References and Footnotes
  1. Vorobjev, Y. N. Molecular Biology 39, 777?784 (2005). Translated from Molekulyarnaya Biologiya 39, 887?895 (2005).
  2. Zurkin, V. B., Raghunathan, G., Ulyanov, N. B., Jernigan, R. L. J Mol Biol 239, 181-200 (1994).
  3. Petyuk, V. A., Zenkova, M. A., Giedge, R., Vlasov, V. V. FEBS Lett 444, 217?222 (1999).

Y.N. Vorobjev

Institute of Chemical Biology and Fundamental Medicine of Siberian Brunch of the Russia Academy of Sciencies
8, Lavrentiev Ave.
Novosibirsk 630090

Email: ynvorob@niboch.nsc.ru