Neomycin sulfate

Neomycin sulfate belongs to a kind of aminoglycoside antibiotics, which is a potent inhibitor of hammerhead ribozyme cleavage reaction with a K₁ of 13.5 μM. 

Neomycin prefers to interact with the ribozyme-substrate complex, which reduces the cleavage rate by stabilizing the ground state of the complex thus destabilizing the transition state of the cleavage process [1]. Neomycin could inhibit the binding of Tat protein to the trans-activating region (TAR) element of HIV-1 RNA. It turns out that neomycin works as a noncompetitive inhibitor by binding to the Tat-TAR complex and increasing the K_off for dissociation of the peptide from the RNA [2].          

Neomycin is the most potent aminoglycoside in stabilizing a DNA triple helix, mainly direct to TAT, and mixed base DNA triplexes, better than known DNA minor groove binders and polyamines. TAT is the preference of triplets stabilized by neomycin, but CGC(+) triplets could be accommodated by it [3]. Neomycin induces a concentration- and voltage-dependent partial block of both the cytosolic and luminal faces of the channels, which shows more appetencies of the luminal area of interaction than the cytosolic area. Dissociation constant (K_b(0)) respectively are 210.20 ± 22.80 and 589.70 ± 184.00 nM for luminal and cytosolic area when zero-voltage. Neomycin also exhibits voltage-dependent relief of block when holding potentials >+ 60 mv [4].

Reference:

[1] Stage T K, Hertel K J, Uhlenbeck O C. Inhibition of the hammerhead ribozyme by neomycin [J]. RNA, 1995, 1(1): 95-101.

[2] Wang S, Huber P W, Cui M, et al. Binding of Neomycin to the TAR Element of HIV-1 RNA Induces Dissociation of Tat Protein by an Allosteric Mechanism [J]. Biochemistry, 1998, 37(16): 5549–5557.

[3] Arya D P, Micovic L, Charles I, et al. Neomycin binding to Watson-Hoogsteen (W-H) DNA triplex groove: a model [J]. Journal of the American Chemical Society, 2003, 125(13): 3733-3744.

[4] Mead F, Williams A J. Block of the ryanodine receptor channel by neomycin is relieved at high holding potentials [J]. Biophysical Journal, 2002, 82(4): 1953-1963.