5 research outputs found
1H and 13C resonance assignments of a guanine sensing riboswitchās terminator hairpin
Here we report the nearly complete base assignments and partial sugar assignments of the 35-residue terminator hairpin of the Bacillus subtilisxpt-pbuX-mRNA guanine sensing riboswitch
Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals
Hepatitis B virus (HBV) replication is initiated by binding of its reverse transcriptase (P) to the apical stem-loop (AL) and primer loop (PL) of epsilon, a highly conserved RNA element at the 5ā²-end of the RNA pregenome. Mutation studies on duck/heron and human in vitro systems have shown similarities but also differences between their Pāepsilon interaction. Here, NMR and UV thermodynamic data on AL (and PL) from these three species are presented. The stabilities of the duck and heron ALs were found to be similar, and much lower than that of human. NMR data show that this low stability stems from an 11-nt internal bulge destabilizing the stem of heron AL. In duck, although structured at low temperature, this region also forms a weak point as its imino resonances broaden to disappearance between 30 and 35Ā°C well below the overall AL melting temperature. Surprisingly, the duck- and heron ALs were both found to be capped by a stable well-structured UGUU tetraloop. All avian ALs are expected to adhere to this because of their conserved sequence. Duck PL is stable and structured and, in view of sequence similarities, the same is expected for heron - and human PL
Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predeterminedāinduced fit mechanism
All known guanine-sensing riboswitches regulate gene expression by specifically binding to guanine (G) or related analogs with high affinity to switch off transcription. The aptamers of this class of riboswitches are characterized by three helices (P1āP3), surrounding a central core of phylogenetically conserved nucleotides and a long-range loopāloop interaction. To gain more insight into the switching mechanism, we present here a comparison between the solution-state structures of the G-free and G-bound forms of the guanine aptamer from the xpt-pbuX operon of Bacillus subtilis, as derived from NMR chemical shifts and magnetic-field-induced residual dipolar couplings. The high-resolution NMR analysis shows the G-free aptamer is highly structured with parallel P2 and P3 helices and the long-range loopāloop interaction already present, implying that the structure is largely preformed to bind the ligand. Structural changes upon guanine binding are found to be localized to the central core. In the free state, the G-quadruple interaction and two base pairs of the P1 stem flanking the central core appear to be largely disordered. The ligand thus binds via a combined predeterminedāinduced fit mechanism, involving a previously unstructured five-residue loop of the J2ā3 junction that folds over the ligand. These limited additional interactions within a preorganized setting possibly explain how the aptamer rapidly responds to ligand binding, which is necessary to switch the structural state of the expression platform within a narrow time frame before the RNA polymerase escapes the 5ā²-UTR
Thermodynamics and NMR studies on Duck,
Hepatitis B virus (HBV) replication is initiated by binding of its reverse transcriptase (P) to the apical stem-loop (AL) and primer loop (PL) of epsilon, a highly conserved RNA element at the 50-end of the RNA pregenome. Mutation studies on duck/heron and human in vitro systems have shown similarities but also differences between their Pāepsilon interaction. Here, NMR and UV thermodynamic data on AL (and PL) from these three species are presented. The stabilities of the duck and heron ALs were found to be similar, and much lower than that of human. NMR data show that this low stability stems from an 11-nt internal bulge destabilizing the stem of heron AL. In duck, although structured at low temperature, this region also forms a weak point as its imino resonances broaden to disappearance between 30 and 358C well below the overall AL melting temperature. Surprisingly, the duck- and heron ALs were both found to be capped by a stable well-structured UGUU tetraloop. All avian ALs are expected to adhere to this because of their conserved sequence. Duck PL is stable and structured and, in view of sequence similarities, the same is expected for heron- and human PL
Comparison of the H-imino NMR spectra (5Ā°C, HO) of (top) and (bottom) apical stem-loop
<p><b>Copyright information:</b></p><p>Taken from "Thermodynamics and NMR studies on and HBV encapsidation signals"</p><p></p><p>Nucleic Acids Research 2007;35(8):2800-2811.</p><p>Published online 11 Apr 2007</p><p>PMCID:PMC1885660.</p><p>Ā© 2007 The Author(s)</p> Assigned peaks are labeled by residue numbers and unassigned peaks by asterisks. Residue numbers in the upper part of are superscripted with an asterisk for clarity