Synthesis and Evaluation of Oligodeoxynucleotides Containing 3′-<i>C</i>-Aminomethyl-and 3′-<i>C</i>-Amethylthymidine

Wang, Guangyi; Middleton, Patrick J.; He, Liyan; Stoisavljevic, Vesna; Seifert, Wiliiied E.

doi:10.1080/07328319708001361

Cited by 15 publications

(15 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, this was not observed for ONs containing similar nucleotides with a C 1 3'-C-branch, e.g. 3'-C-(hydroxymethyl) [21], 3'-C-methyl [22] [23], and 3'-C-(aminomethyl) [23]. A 3'-Cbranch is expected to be oriented in a pseudoequatorial position, driving the sugar pucker towards a C(2')-endo conformation.…”

mentioning

confidence: 74%

“…The presence of the monomer Z with C(2')-endo conformation in the otherwise unmodified DNA strand might cause a rather significant distortion of the structure of the DNA´RNA duplex. For ONs containing 3'-C-(hydroxymethyl)- [21] [59], 3'-C-methyl- [22] [23], and 3'-C-(aminomethyl)thymidine [23] monomers, smaller decreases in DT m /mod. values were in general observed for duplexes towards complementary RNA.…”

Section: '-C-(aminoalkyl)-substituted Nucleosides and Onsmentioning

confidence: 99%

“…Compared with the few reports describing ONs containing 3'-C-branched monomers, ONs containing the 3'-C-(aminopropyl)-branched monomer Z show quite promising hybridization properties towards DNA. Thus, in general, ONs containing 3'-C-(hydroxymethyl)- [21], 3'-C-methyl- [22] [23], 3'-C-(aminomethyl)- [23], and 3'-C-allylnucleotide [20] monomers hybridize with complementary DNA with DT m /mod. values of approximately 0 to À 1.08 under medium salt conditions.…”

Section: '-C-(aminoalkyl)-substituted Nucleosides and Onsmentioning

confidence: 99%

“…It is thus evident that the combined exchange of the HOÀC(2') and the HOCH 2 ÀC(4') groups with a FÀC(2')/MeOÀC(2') group and a NH 2 CH 2 ÀC(4') group leads to increased thermal stability of duplexes with both DNA and RNA complements. The apparent sequence dependence on the influence of the different modifications on the thermal stability of the resulting duplexes stresses the importance of comparing only in identical sequence contexts and excludes direct comparison of the effect induced by, e.g., monomers X and U with effects reported in the literature for, e.g., 2'-O-alkyl-substituted ONs [5 ± 8] or 4'-C-(aminomethyl)-modified ONs [23].…”

mentioning

confidence: 98%

See 3 more Smart Citations

Oligonucleotides Containing Novel 4′-C- or 3′-C-(Aminoalkyl)-Branched Thymidines

Pfundheller¹,

Bryld²,

Olsen³

et al. 2000

HCA

View full text Add to dashboard Cite

The synthesis of four novel 3′‐C‐branched and 4′‐C‐branched nucleosides and their transformation into the corresponding 3′‐O‐phosphoramidite building blocks for automated oligonucleotide synthesis is reported. The 4′‐C‐branched key intermediate 11 was synthesized by a convergent strategy and converted to its 2′‐O‐methyl and 2′‐deoxy‐2′‐fluoro derivatives, leading to the preparation of novel oligonucleotide analogues containing 4′‐C‐(aminomethyl)‐2′‐O‐methyl monomer X and 4′‐C‐(aminomethyl)‐2′‐deoxy‐2′‐fluoro monomer Y (Schemes 2 and 3). In general, increased binding affinity towards complementary single‐stranded DNA and RNA was obtained with these analogues compared to the unmodified references (Table 1). The presence of monomer X or monomer Y in a 2′‐O‐methyl‐RNA oligonucleotide had a negative effect on the binding affinity of the 2′‐O‐methyl‐RNA oligonucleotide towards DNA and RNA. Starting from the 3′‐C‐allyl derivative 28, 3′‐C‐(3‐aminopropyl)‐protected nucleosides and 3′‐O‐phosphoramidite derivatives were synthesized, leading to novel oligonucleotide analogues containing 3′‐C‐(3‐aminopropyl)thymidine monomer Z or the corresponding 3′‐C‐(3‐aminopropyl)‐2′‐O,5‐dimethyluridine monomer W (Schemes 4 and 5). Incorporation of the 2′‐deoxy monomer Z induced no significant changes in the binding affinity towards DNA but decreased binding affinity towards RNA, while the 2′‐O‐methyl monomer Z induced decreased binding affinity towards DNA as well as RNA complements (Table 2).

show abstract

mentioning

confidence: 74%

Section: '-C-(aminoalkyl)-substituted Nucleosides and Onsmentioning

confidence: 99%

Section: '-C-(aminoalkyl)-substituted Nucleosides and Onsmentioning

confidence: 99%

mentioning

confidence: 98%

See 2 more Smart Citations

Oligonucleotides Containing Novel 4′-C- or 3′-C-(Aminoalkyl)-Branched Thymidines

Pfundheller¹,

Bryld²,

Olsen³

et al. 2000

HCA

View full text Add to dashboard Cite

show abstract

“…An example of a building block is the 3Ј-C-hydroxymethyl-branched nucleoside monomer 2 (Figure 1), which have been incorporated into ODNs and found to improve the enzymatic stability of the ODN and to be more or less neutral concerning the binding affinity for complementary nucleic acid sequences. [6,7] Also other 3Ј-C-modifications have been prepared, and in general neutral or slightly decreased binding affinities were found. [7,8] A 3Ј-C-alkyl substituent is expected to be oriented in a pseudoequatorial position, driving the nucleoside monomer towards an S-type conformation.…”

Section: Introductionmentioning

confidence: 99%

Synthesis of the 3′‐C‐Hydroxymethyl‐Branched Locked Nucleic Acid Thymidine Monomer

et al. 2008

View full text Add to dashboard Cite

A 3′‐C‐hydroxymethyl‐branched Locked Nucleic Acid (LNA) monomer 3 was synthesized from diacetone‐α‐D‐glucose taking advantage of a stereoselective Grignard reaction for the introduction of a vinyl group, an aldol/Cannizzarro sequence for introducing the 4′‐substituent, oxidative cleavage of the vinyl group using a RuO4‐based protocol, Vorbrüggen‐type nucleobase coupling and finally the ring closure by ether formation giving the bicyclic skeleton. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)

show abstract

Aromatization and ring cyclization: A better understanding on the ring cyclization mechanism of 3‐amino‐6‐hydrazino‐1,2,4‐triazin‐5(2H)‐one reacted with acetic acid in N,N‐dimethylformamide

Hwang

2005

Journal of Heterocyclic Chem

View full text Add to dashboard Cite

In this paper we report that the title compound (3) reacts with excess N,N‐dimethylformamide (DMF) containing two equivalents of acetic acid to afford 6‐amino‐1,2,4‐triazolo[3,4‐f][1,2,4]triazin‐8(7H)‐one (1). When 3‐amino‐2‐benzyl‐6‐hydrazino‐1,2,4‐triazin‐5(2H)‐one (6), the N‐2 benzylated derivative of 3, is treated under the same conditions, ring cyclization does not occur; instead, 3‐amino‐2‐benzyl‐6‐(2‐formyl‐hydrazino)‐1,2,4‐triazin‐5(2H)‐one (7) is formed. Single‐crystal X‐ray analysis of a 3‐ethyl derivative of compound 1 reveals the predominant tautomeric structure to be the 7H‐tautomer (7H‐1). From these results, we propose a reasonable cyclization mechanism that incorporates two important points: (1) the tautomerism of the N‐2 hydrogen with the C‐5 oxo group aromatizes the 1,2,4‐triazine ring, and (2) the DMF is proto‐nated by acetic acid on the nitrogen atom, then deamination occurs where DMF is attacked by the 6‐hydrazino group of 3 or 6.

show abstract

Synthesis and Evaluation of Oligodeoxynucleotides Containing 3′-C-Aminomethyl-and 3′-C-Amethylthymidine

Cited by 15 publications

References 16 publications

Oligonucleotides Containing Novel 4′-C- or 3′-C-(Aminoalkyl)-Branched Thymidines

Oligonucleotides Containing Novel 4′-C- or 3′-C-(Aminoalkyl)-Branched Thymidines

Synthesis of the 3′‐C‐Hydroxymethyl‐Branched Locked Nucleic Acid Thymidine Monomer

Aromatization and ring cyclization: A better understanding on the ring cyclization mechanism of 3‐amino‐6‐hydrazino‐1,2,4‐triazin‐5(2H)‐one reacted with acetic acid in N,N‐dimethylformamide

Contact Info

Product

Resources

About