Book of Abstracts: Albany 2005
Cationic Phosphoramidate α-oligonucleotides Target Double Stranded DNA: Molecular Dynamics Study
Much effort has been invested in recent years in the development of novel approaches aimed at the specific suppression of unwanted gene expression leading to viral and malignant diseases. The sequencing of the human genome and the elucidation of many molecular pathways that are important in disease have provided unprecedented opportunities for the development of new therapeutics. So-called antisense/antigene oligonucleotides (ON), inhibiting gene expression by creation of a helical complex with target mRNA/DNA (carrying "sense" genetic information), represent a perspective approach in chemotherapy.
A potential means to improve the efficacy of steric-blocking antisense/antigene oligonucleotides is to increase their affinity for a target mRNA/DNA. The grafting of cationic amino/guanidino groups to the backbone of the ON is one way to achieve this. Cationic α-ON with phosphoramidate internucleoside linkages incorporated into ON with a non-natural α-anomeric configuration bound with high affinity to single-stranded DNA and RNA targets (1).
The present work deals with cationic α-ON targeting double stranded DNA. Various side-chain linkers enhancing ability of the α-ON strand to create a triple helical complex with the target DNA were tested. Linkers were based on either lysine (butyl-amino phosphoramidates) or arginine (butyl-guanidino phoshoroamidates) side chains (naturally occurring in proteins). Triple helical structure consisting of the natural dT12:dA12 duplex and cationic α-dT12 strand was used as a model system. Fully solvated molecular dynamics simulations revealed that both types of tethers are able to bridge the groove between nucleic acid strands and interact efficiently with phosphate groups in the dA12 strand. Direct hydrogen bonds between positively charged heads of linkers and negatively charged phosphate groups were established within the MD runs. Average values as well as time-development of distances between groups participating in the amino/guanidino-alkyl-phosphate hydrogen bonding were analyzed in details.
In acknowledgments, this work was supported by the Grant of the Ministry of Education, Youth and Sports of the Czech Republic (project No. MSM 0021620835) and the Grant Agency of Czech Republic (project No. 202/02/D114). Results have been partially obtained using computer facilities of the Metacentrum of the Czech Universities.
References and Footnotes
I. Barvik, Jr.