Conformational properties of dinucleoside monophosphates in solution: dipurines and dipyrimidines

Lee, Che-Hung; Ezra, F. S.; Kondo, Naoshi; Sarma, Ramaswamy H.; Danyluk, S.

doi:10.1021/bi00661a034

Cited by 185 publications

(149 citation statements)

References 67 publications

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“…5a and 5b show dimers; however, they also apply to n-mers where 5'-AMP molecules are added to both sides of the initial stack, leading to a perpetual headto-head or head-to-tail stacking pattern. Sarma and co-workers (54)(55)(56) have determined the molecular topology of 3',5'-, and 2',5'-pApAp dinucleotides in aqueous solution. In the first case the two adenine bases show a preference for a head-to-head stacking while the arrangement in the latter case is neither head-to-head nor head-to-tail.…”

Section: Resultsmentioning

confidence: 99%

The self-association of naturally occurring purine nucleoside 5′-monophosphates in aqueous solution

Neurohr¹,

Mantsch²

1979

Can. J. Chem.

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The parameters characterizing the base-stacking self-association of adenosine, inosine, and guanosine 5′-monophosphate have been obtained from 1H nmr dilution studies. The thermodynamic parameters for the formation of adenosine 5′-monophosphate stacks are ΔH0 = −14.5 kJ mol−1 and ΔS0 = −42.3 J K−1 mol−1, with an apparent equilibrium constant of Kc = 1.92 M−1 at 30 °C. The corresponding equilibrium constants for the self-association of inosine and guanosine 5′-monophosphate are 1.36 M−1 and 1.29 M−1, respectively. The negative enthalpy and entropy changes cannot be explained by the concept of classical hydrophobic interactions; however, they strongly support the conclusion that dipole induced dipole forces play a major role for base-stacking in aqueous solution. The sequence of the equilibrium constants for the purine nucleoside 5′-monophosphates can be well explained by the concept of mutual polarization. The stacking geometries for adenosine and inosine 5′-monophosphate are presented as obtained from fitting the experimental shift data to refined isoshielding contours. It is concluded that the stacking pattern is not restricted to a unique geometry.

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Section: Resultsmentioning

confidence: 99%

The self-association of naturally occurring purine nucleoside 5′-monophosphates in aqueous solution

Neurohr¹,

Mantsch²

1979

Can. J. Chem.

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“…Sugar pucker can influence the interphosphate distance between adjacent bases, with C′ 3 endo producing a more compressed backbone than C′2 endo (37). NMR studies have shown that the sugar pucker in poly(dT) is predominantly in the C′2 endo state (38) while poly(rU) is a 44∶56 mixture of C′2 endo and C′3 endo (39). Thus, we expect rU 40 to have a shorter contour length.…”

Section: Discussionmentioning

confidence: 99%

“…Thus, we expect rU 40 to have a shorter contour length. Also, while rU 40 is known to undergo the least stacking among the ribonucleotides, there is some evidence that rU 40 does in fact take part in some base stacking (39,40). We believe that base stacking in poly(rU) but not in poly(dT) may cause rU 40 to be more rigid than dT 40 .…”

Section: Discussionmentioning

confidence: 99%

Ionic strength-dependent persistence lengths of single-stranded RNA and DNA

Chen

Meisburger

Pabit

et al. 2011

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

347

434

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Dynamic RNA molecules carry out essential processes in the cell including translation and splicing. Base-pair interactions stabilize RNA into relatively rigid structures, while flexible non-base-paired regions allow RNA to undergo conformational changes required for function. To advance our understanding of RNA folding and dynamics it is critical to know the flexibility of these un-base-paired regions and how it depends on counterions. Yet, information about nucleic acid polymer properties is mainly derived from studies of ssDNA. Here we measure the persistence lengths (l p ) of ssRNA. We observe valence and ionic strength-dependent differences in l p in a direct comparison between 40-mers of deoxythymidylate (dT 40 ) and uridylate (rU 40 ) measured using the powerful combination of SAXS and smFRET. We also show that nucleic acid flexibility is influenced by local environment (an adjoining double helix). Our results illustrate the complex interplay between conformation and ion environment that modulates nucleic acid function in vivo.single molecule FRET | small angle X-ray scattering | worm-like chain | ion-nucleic acid interactions N ucleic acids in the cell are dynamic and undergo structural changes as they transmit and process genetic information. Dynamic processes related to biological function (e.g., transcription for DNA and recognition and folding for RNA) involve nonbase-paired regions that confer flexibility to the overall structure. For RNAs like riboswitches that exchange between multiple structures in equilibrium (1), conformational disorder is often an intrinsic property of the molecule and important for biological function. Even relatively stable molecules like catalytic introns and transfer RNA must pass through a disordered phase while folding. Thus, progress toward a mechanistic understanding of RNA folding and dynamics will require detailed knowledge of nucleic acid chain flexibility and its dependence on base content, solution conditions, and molecular context.In light of its importance to biology, it is surprising that RNA flexibility has not been studied in as much detail as DNA flexibility. Despite the chemical similarity of the RNA and DNA backbone, there is ample evidence from X-ray crystallography that the identity of the sugar (ribose vs. deoxy-ribose) affects backbone conformations (2). However, researchers have used the properties of DNA to understand RNA folding (3) because corresponding information for RNA was lacking. This difficulty motivates our present efforts to measure and directly compare the flexibilities of single-stranded nucleic acids (ssRNA and ssDNA).In the cell, RNA and DNA interact with cations that screen the negatively charged phosphate backbone. Both diffuse and specifically bound ions are important for RNA folding (4), and divalent ions are almost always required to stabilize RNA tertiary structures (5-8). A full mechanistic description of these ion effects is complicated by the fact that ions can interact with RNA differently during various stages of folding (9, ...

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“…monophosphates that are useful for chemical synthesis of short oligomers by diester chemistry or are used directly in enzymatic syntheses of various short oligomers [218][219][220][221] .…”

Section: Enzymatic Synthesis Of Deuterated Nucleosides or Nucleotidesmentioning

confidence: 99%

The Synthesis of Deuterionucleosides

Földesi

Trifonova

Kundu

et al. 2000

Nucleosides, Nucleotides and Nucleic Acids

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Conformational properties of dinucleoside monophosphates in solution: dipurines and dipyrimidines

Cited by 185 publications

References 67 publications

The self-association of naturally occurring purine nucleoside 5′-monophosphates in aqueous solution

The self-association of naturally occurring purine nucleoside 5′-monophosphates in aqueous solution

Ionic strength-dependent persistence lengths of single-stranded RNA and DNA

The Synthesis of Deuterionucleosides

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