The structure of drug-deoxydinucleoside phosphate complex; generalized conformational behavior of intercalation complexes with RNA and DNA fragments

Shieh, Huey‐Sheng; Berman, Helen M.; Dabrow, Michael; Neidle, Stephen

doi:10.1093/nar/8.1.85

Cited by 137 publications

(70 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Thus far, our attempts to use intercalators to drive the polymerization of mononucleotides and dinucleotides in the absence of a preexisting template strand have proven unsuccessful. In the case of dinucleotides, we surmise that the nearest neighbor exclusion principle (46)(47)(48), which states that intercalators can bind at most between every other base pair, could potentially inhibit the coupling of dinucleotides, as dinucleotides are known to crystallize in the presence of intercalators with ligands bound both within and outside each minihelix (49), an arrangement that could block backbone coupling between dinucleotides. To find a possible means by which to circumvent this problem, we have initiated studies of intercalation of nucleic acids with alternative backbone linkages (50,51).…”

Section: Discussionmentioning

confidence: 99%

Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonucleotides in a prebiotic world

Horowitz

Engelhart

Chen

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The RNA world hypothesis proposes that nucleic acids were once responsible for both information storage and chemical catalysis, before the advent of coded protein synthesis. However, it is difficult to imagine how nucleic acid polymers first appeared, as the abiotic chemical formation of long nucleic acid polymers from mononucleotides or short oligonucleotides remains elusive, and barriers to achieving this goal are substantial. One specific obstacle to abiotic nucleic acid polymerization is strand cyclization. Chemically activated short oligonucleotides cyclize efficiently, which severely impairs polymer growth. We show that intercalation, which stabilizes and rigidifies nucleic acid duplexes, almost totally eliminates strand cyclization, allowing for chemical ligation of tetranucleotides into duplex polymers of up to 100 base pairs in length. In contrast, when these reactions are performed in the absence of intercalators, almost exclusively cyclic tetra-and octanucleotides are produced. Intercalator-free polymerization is not observed, even at tetranucleotide concentrations >10; 000-fold greater than those at which intercalators enable polymerization. We also demonstrate that intercalation-mediated polymerization is most favored if the size of the intercalator matches that of the base pair; intercalators that bind to Watson-Crick base pairs promote the polymerization of oligonucleotides that form these base pairs. Additionally, we demonstrate that intercalationmediated polymerization is possible with an alternative, nonWatson-Crick-paired duplex that selectively binds a complementary intercalator. These results support the hypothesis that intercalators (acting as 'molecular midwives') could have facilitated the polymerization of the first nucleic acids and possibly helped select the first base pairs, even if only trace amounts of suitable oligomers were available.base pair selection | origin of life | RNA world | polymerization | molecular evolution O ver the past two decades, significant evidence has been presented in support of the RNA world hypothesis, which proposes that RNA polymers predated coded proteins in early life (1, 2). Current support for this hypothesis includes the fact that contemporary life still uses RNA as an informational polymer and in chemical catalysis (3). The ability of RNA to catalyze reactions is exemplified by natural and artificial ribozymes that promote a wide variety of chemical reactions (4) as well as the observation that the catalytic core of the ribosome is comprised of RNA (5). Despite the attractiveness of the RNA world as a hypothetical stage of early life, it remains unclear how RNA [or a predecessor of RNA (6-11)] would initially have been synthesized without the aid of protein enzyme catalysis.Several distinct proposals have been presented for the abiotic origin of the first RNA polymers (10,(12)(13)(14)(15)(16)(17). Perhaps the most notable is that of Ferris and coworkers, in which mineral surfaces are used to locally concentrate and promote the polymerization of liga...

show abstract

Section: Discussionmentioning

confidence: 99%

Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonucleotides in a prebiotic world

Horowitz

Engelhart

Chen

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…From the crystal data about the Acridine Orange cation (Obendorf et al 1976;Reddy et al 1979;Mattia et al 1984Mattia et al , 1995Kuban et al 1985;Gordon et al 2003), the Proflavine cation (Jones and Neidle 1975;Shieh et al 1980Shieh et al , 1982Swaminathan et al 1982;Aggarwal et al 1984;Ara and El Bahij 2004;Varga et al 2007), Methylene Blue (Marr et al 1973;Kahn-Harari et al 1973;Endres et al 1977;Snaathorst et al 1981;Enescu et al 2000;Sours et al 2002;Kavitha et al 2004;Li et al 2005;Soneta and Miyamura 2006;Raj et al 2007), Eosin (Harrison et al 2007), Rhodamine B (Fujii et al 1995;Nishikiori and Fujii 1997;Soneta et al 2006), Ethyl Rhodamine G (Wang et al 1997;Fun et al 1997;Liu et al 1998;Adhikesavalu et al 2001;Zhang et al 2001), Para-rosaniline (Koh and Eriks 1971;Liu et al 2002;Xie 2008), and Crystal Violet (Spangler et al 1989;Lovell et al 1999;Lacour et al 2002;Soneta et al 2006), as well as the substituted 1-phenyl-azo-2-naph...…”

Section: Dye Aggregatesmentioning

confidence: 99%

Lignin selective dyes: quantum-mechanical study of their characteristics

Perdih

2011

Cellulose

View full text Add to dashboard Cite

The mechanism of dye-bonding to the lignin component of the fibre was checked using the quantum-mechanical and crystallographic approach. The calculated data support the conclusion that for the selectivity of cationic dyes for lignin, a high partial negative charge on accessible substituents on the periphery of the molecule is the most important, but not an exclusive factor. Besides the delocalized positive charge, what is also important for the interaction of a dye with hemicellulose, is the dye's ability to be involved in hydrogen bonds, whereas for the interaction with lignin also its ability of stacking to it.

show abstract

“…So far the P2,2,2 space group has only been observed for one form of tetranucleotide d(B'CCGG) (Conner et al, 1984) which structure has not yet been reported, and for dinucleotides. Most of them are complexed with intercalating drugs, d(GpG)-cisplatin (Sherman et al, 1988), d(CpG)-dimethylproflavine (Sakore et al, 1984), d(CpG)-proflavine (Shieh et al, 1980), d(pTpT)-Na' salt (Camerman et al, 1976), r(ApA)-proflavine (Neidle et al, 1978) and r(ApA)-Ca' salt (Einspahr et al, 1981). However, the length of a dinucleotide hardly reflects a helical structure close to the natural DNA-type double helices.…”

mentioning

confidence: 99%

Orthorhombic crystal structure of the A‐DNA octamer d(GTACGTAC)

d’Estaintot

Dautant

Courseille

et al. 1993

European Journal of Biochemistry

View full text Add to dashboard Cite

The X-ray crystal structure of the double-helical A-DNA octanucleotide d(GTACGTAC) has been solved by molecular replacement and refined to a resolution of 0.219 nm. The final R-factor is equal to 16.1% for 1516 observed reflections with F > 4 @ ) . The sequence crystallizes as an A-DNA-type double helix in the orthorhombic space group P21212, with one duplex molecule solvated by 66 water molecules in the asymmetric unit. Cell parameters are a = 3.860 nm, b = 5.082 nm, c = 2.174 nm. It is the first time that such a crystal form has been observed. This orthorhombic structure has been compared with the tetragonal structure of the same oligonucleotide. It adopts a bent structure with an unusual packing between symmetry-related molecules.In the last decade, a significant number of single-crystal X-ray structure determinations of oligonucleotides have been performed. This aspect of research seems now of crucial importance to an understanding of the role of DNA and RNA structures in biological systems, all the more so since some of the available structures in the data banks are used as starting material in modeling studies for the design of drugs and inhibitors of pathogenic organisms.For a long time, the global conformations observed for DNA in solution were not consistent with the solid-state conformations. From these X-ray diffraction studies, DNA polymorphism is now an established fact. The coexistence of A and B conformations has also been detected for the same oligonucleotide within a crystal (Doucet et al., 1989;Bingman et al., 1992), displaying a possible adaptation of the DNA toward the recognition site of a protein. The relationship between base sequence length or base composition and the influence of crystal-lattice forces in determining the type of global conformation adopted, are some of the many fundamental questions starting to be investigated. Jain et al. (1989Jain et al. ( , 1991 grew crystals of the DNA octamer d(GTGTA-CAC) in two crystal forms, tetragonal P4,2,2 and hexagonal P6,22. Compared to the tetragonal form, the hexagonal double helix more closely resembles the fibre-diffraction A-DNA and displays a higher tilt angle, correlated with a larger displacement from the helix axis, a lower rise for each residue and a smaller major-groove width. Most of the disparity in some nucleotides between the two crystal forms is due to distortions that seem to arise from differences in the intermolecular contacts. The authors explained these alterations by packing differences, responsible for distortions at several locations on the duplexes.

show abstract

The structure of drug-deoxydinucleoside phosphate complex; generalized conformational behavior of intercalation complexes with RNA and DNA fragments

Cited by 137 publications

References 17 publications

Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonucleotides in a prebiotic world

Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonucleotides in a prebiotic world

Lignin selective dyes: quantum-mechanical study of their characteristics

Orthorhombic crystal structure of the A‐DNA octamer d(GTACGTAC)

Contact Info

Product

Resources

About