Synthesis and Evaluation of Oligonucleotide-Conjugated Pyrrole Polyamide-2′-Deoxyguanosine Hybrids as Novel Gene Expression Control Compounds

Abstract

DNA oligonucleotide-conjugated pyrrole polyamide-2'-deoxyguanosine hybrids were synthesized and examined as novel gene expression control compounds. The T(m) values and circular dichroism spectral analyses showed that the oligonucleotide-conjugated hybrids possess high DNA recognition and a very high binding affinity for DNA that includes the pyrrole polyamide binding sequence.

Synthesis and Evaluation of MGB Polyamide-Oligonucleotide Conjugates as Gene Expression Control Compounds

“…DNA oligonucleotides were purchased from Hokkaido System Science Co., Ltd. Compounds 2 , 3 , 4 , 5 , 7 , 9, and 12 were prepared as previously described [ 9 – 13 ]. The CPG support-bound 2′-deoxynucleoside 16 (B = C Bz ) and 2′-deoxynucleoside 3′-phosphoramidites 17 (B = T, C Bz , A Bz , and G iBu ) were purchased from Glen Research Corporation.…”

“…It was shown that Hybrid 1 possessed greater binding specificity compared with distamycin A [ 12 ]. Then, in an effort to examine the development of potential antisense drugs, we synthesized oligonucleotide ON 1 ( n = 3) conjugated to Hybrid 2 in lieu of Hybrid 1 containing the formyl group which is unstable under the basic conditions of deprotection during oligonucleotide solid-phase synthesis, and subsequently examined the binding ability of ON 1 ( n = 3) to complementary DNA ( Figure 2 ) [ 13 ]. Dervan et al [ 14 ], Zamecnik et al [ 15 ], Novopashina et al and Boutorine et al [ 16 – 21 ] have reported the synthesis and evaluation of oligonucleotides conjugated with one or two MGB polyamides to either the 5′- or 3′-ends.…”

“…It was expected that oligonucleotides conjugated with the MGB polyamide to the 2-exocyclic amino group of a guanine base, which is positioned above the floor of the minor groove of the DNA duplex, would possess high DNA binding ability. ON 1 ( n = 3), which includes a modified guanosine ( G ) in the 5′ direction in the oligonucleotide chain given the preferred orientation of the polyamide in the minor groove of dsDNA ( C -(pyrrole polyamide)- N /3′-(TTAAA)-5′ of the complementary target DNA) [ 22 – 24 ], was synthesized and evaluated as a model oligonucleotide [ 13 ]. From the T m and CD analyses, it was found that ON 1 ( n = 3) formed stable dsDNA with complementary DNA via action of the pyrrole amide moiety.…”

“…The binding ability of pyrrole polyamide-oligonucleotide conjugates to target DNA, and the inhibition of cell growth by pyrrole polyamide-2′-deoxyguanosine hybrids should be greatly influenced by the chain length of the pyrrole polyamide moiety and the length of the linker between the pyrrole polyamide moiety and the guanine base. Although we previously reported the synthesis of MGB polyamide-oligonucleotide conjugate ON 1 ( n = 3), with linked pyrrole amide tetramer (Py 4 -) at the 2-exocyclic amino group of a guanine base using 3-aminopropyl linker and evaluated the stability of modified dsDNA as described above [ 13 ], an examination of the length of the chain or linker connecting the pyrrole polyamide moiety to the guanine base and the DNA sequence recognition ability had not been investigated. In an effort to improve the activity of pyrrole polyamide-oligonucleotide conjugates, we performed the synthesis and evaluation of ON 1 and ON 2 with linked pyrrole polyamides (Py 4 - and Py 3 -) using various aminoalkyl linkers in terms of binding affinity for complementary DNA ( Figure 2 ).…”

Fast and efficient microwave synthetic methods for some new 2(1H)-pyridone arabinosides

“…Some nucleoside analogs have been used in preclinical studies for several therapeutic indications including anticancer activity (Shi and Schinazi, 2001;Kawashima et al, 2011;Chen et al, 2012;Van Poecke et al, 2012).…”