Polyamine–Oligonucleotide Conjugates: A Promising Direction for Nucleic Acid Tools and Therapeutics

Abstract

Chemical modification and/or the conjugation of small functional molecules to oligonucleotides have significantly improved their biological and biophysical properties, addressing issues such as poor cell penetration, stability to nucleases and low affinity for their targets. Here, the authors review the literature reporting on the biophysical, biochemical and biological properties of one particular class of modification - polyamine-oligonucleotide conjugates. Naturally derived and synthetic polyamines have been grafted onto a variety of oligonucleotide formats, including antisense oligonucleotides and siRNAs. In many cases this has had beneficial effects on their properties such as target hybridization, nuclease resistance, cellular uptake and activity. Polyamine-oligonucleotide conjugation, therefore, represents a promising direction for the further development of oligonucleotide-based therapeutics and tools.

Towards Improved Oligonucleotide Therapeutics Through Faster Target Binding Kinetics

“…Conjugation of variousa mino groups to oligonucleotides has been described by af ew groups. [24,25] In most cases, the 2'-OH group of ribonucleosides has been used to conjugate fragments onto antisense oligonucleotides, which placest he fragment into the minor groove upon hybridization withatarget, but generally does not produce large increases in binding affinity.W ef ound that the modification of short 2'-OMe oligoribonucleotides by conjugation of polyamine groups to the C5- positiono fu ridineb ases endowst hem with greatly increased target-binding affinity,c omparing favorably with state of the art bicyclic [9,10,25] and tricyclic nucleic acids. [50] The pioneering work of Pçrschke and Eigen led to the "nucleation-zipping" modeli nw hich the initial formation of three base-pairs represents the rate-limiting step in the hybridization of two complementary oligonucleotides, that is, an oligonucleotide drug and its RNA target.…”

“…[1] The natural polyamines spermine and spermidine bind to and stabilizeR NAsi nc ells. [20][21][22][23][24] Recently,i tw as shown that polyamines conjugated to LNA oligonucleotidesh ad larger effects on target RNA binding. [16,17] In some cases polyamines (including oligospermines) [18,19] have been conjugated to oligonucleotides and have produced small increases in T M values (a few 8Cp er modification) with complementary RNA.…”

“…[16,17] In some cases polyamines (including oligospermines) [18,19] have been conjugated to oligonucleotides and have produced small increases in T M values (a few 8Cp er modification) with complementary RNA. [20][21][22][23][24] Recently,i tw as shown that polyamines conjugated to LNA oligonucleotidesh ad larger effects on target RNA binding. [25] During as earch for modifications that endow oligonucleotides with improved target-binding kinetics-increased k on and decreased k off -we discovered that conjugation of spermine via at riazole linker to C5o fp yrimidines in 2'-O-methyl (OMe) ribonucleotides produced very largei ncreases in target-RNA binding affinity.T he effects derived mostly from increases in rates of association.…”

“…Free polyamines also increase the T M values of oligonucleotides with complementary RNAs and DNAs under physiological conditions . In some cases polyamines (including oligospermines) have been conjugated to oligonucleotides and have produced small increases in T M values (a few °C per modification) with complementary RNA . Recently, it was shown that polyamines conjugated to LNA oligonucleotides had larger effects on target RNA binding …”

Self-neutralizing oligonucleotides with enhanced cellular uptake

“…18–21 The polyamines have been attached either to the 5′, or the 3′ end of the ONs, (known as ZIP-ONs) 22, 23 with few reports for attachment to the nucleobases. 24, 25 In most cases, polyamine conjugation had beneficial effects on target hybridization, 26 nuclease resistance, and cellular uptake.…”