A New Way to Investigate the Hydrogen Bonds of DNA

A New Way to Investigate the Hydrogen Bonds of DNA

by John Emsley

WHAT'S HOT IN CHEMISTRY...

Rank	Paper	Citations This Period May-Jun 00	Rank Last Period Mar-Apr 00
1	A.T. Brünger, et al., *"Crystallography & NMR System: a new software suite for macromolecular structure determination,"* Acta Cryst. D, 54:905-21, 1 September 1998. [10 institutions worldwide] *120JA	80	1
2	T.C. Terwilliger, J. Berendzen, "Automated MAD and MIR structure solution," Acta Crystallograph. D - Biol. Crystallograph., 55:849-61, April 1999. [Los Alamos Natl. Lab., NM] *188NW	19	9
3	D.W. Old, J.P. Wolfe, S.L. Buchwald, "A highly active catalyst for palladium-catalyzed cross-coupling reactions: Room-temperature Suzuki coupling and amination of unactivated aryl chlorides," J. Amer. Chem. Soc., 120(37):9722-3, 23 September 1998. [MIT, Cambridge, MA]	14	†
4	A. Altomare, et al., *"SIR97: a new tool for crystal structure determination and refinement,"* J. Appl. Cryst., 32:115-9, 1 February 1999. [U. Bari, Italy; Piazza U., Perugia, Italy; CNR, Inst. Struct. Chem. G. Giacomello, Rome, Italy] *173NK	14	†
5	A. Dingley, S. Grzesiek, "Direct observation of hydrogen bonds in nucleic acid base pairs by internucleotide ²JNN couplings," J. Amer. Chem. Soc., 120(33):8293-7, 26 August 1998. [Heinrich Heine U. Dusseldorf, Germany; Inst. Struct. Biol., Julich, Germany] *114PX	13	+
6	L.A. Curtiss, et al., "Gaussian-3 (G3) theory for molecules containing first and second-row atoms," J. Chem. Phys., 109(18):7764-76, 8 November 1998. [Argonne Natl. Lab., IL; Lucent Technol., Murray Hill, NJ; Northwestern U., Evanston, IL] *132ZZ	12	7
7	E. Meggers, M.E. Michel-Beyerle, B. Giese, "Sequence dependent long range hole transport in DNA," J. Amer. Chem. Soc., 120(49):12950-5, 16 December 1998. [U. Basel, Switzerland; Tech. U. Munich, Garching, Germany] *149MW	12	6
8	F. Cordier, S. Grzesiek, "Direct observation of hydrogen bonds in proteins by interresidue ^3hJ_NC' scalar couplings," J. Amer. Chem. Soc., 121(7):1601-2, 24 February 1999. [Inst. Struct. Biol., Julich, Germany; Heinrich Heine U. Dusseldorf, Germany] *173HE	12	†
9	G. Cornilescu, J.-S. Hu, A Bax, "Identification of the hydrogen bonding network in a protein by scalar couplings," J. Amer. Chem. Soc., 121(12): 2949-50, 31 March 1999. [NIDDKD, NIH, Bethesda, MD] *182QR	11	†
10	A.J. Dingley, et al., "Internucleotide scalar couplings across hydrogen bonds in Watson-Crick and Hoogsteen base pairs of a DNA triplex," J. Amer. Chem. Soc., 121(25):6019-27, 30 June 1999. [Univ. Calif., Los Angeles; U. Arizona, Tucson; Inst. Struct. Biol., Julich, Germany; U. Dusseldorf, Germany] *212KX	11	†
SOURCE: ISI’s Hot Papers Database. the Legend.

f all chemical bonds, hydrogen bonds are the weakest, the most important, the least understood, and the hardest to measure. This litany of extremes makes them all the more fascinating, and in the current Hot Ten they are the subject of papers #5, #8, #9, and #10. Three of the papers are coauthored by Stephan Grzesiek, formerly of the Institute of Structural Biology, at the Research Center of Jülich, Germany now at the University of Basel, Switzerland and his skill is in bringing sophisticated nuclear magnetic resonance (NMR) techniques to bear on the problem.

Without hydrogen bonds there could be no life because they hold the double helix of DNA together, and this they do by charge attractions. A hydrogen bonded to oxygen, or nitrogen, becomes slightly positively charged which enables it to attract a center of negative charge on another molecule, such as another oxygen or nitrogen atom. The hydrogen bond is then written, e.g., O-H…N, with the dotted line signifying the hydrogen bond. There are also O-H…O, N-H…O and N-H…N bonds, the last being among the weakest.

The secondary effects they have on structures, molecular vibrations, etc., can be used to infer hydrogen bonding, but there is no primary way of observing them because of their inherent weakness. NMR appears to be the least useful technique because neither of the common isotopes, oxygen-16 or nitrogen-14, has a magnetic nucleus. However, nitrogen-15 has a magnetic moment, and by replacing ¹⁴N by N, Grzesiek has opened up a new area of investigating these enigmatic bonds.

Paper #5 reports for the first time the direct observation by NMR of an N-H…N hydrogen bond between nucleic acids enriched with ¹⁵N, by measuring the coupling of the nitrogen atoms. Grzesiek, working with Andrew Dingley of the Heinrich-Heine University in Düsseldorf, has been able to do this and show that the coupling is surprisingly large. Normally atomic nuclei only couple with each other if they are linked by normal chemical bonds, and in theory hydrogen bonds have neither the strength nor stability for this to occur.

The German researchers studied an ¹⁵N enriched sample of the T1 domain of the potato spindle tuber viroid and were able to prove that N-H...N hydrogen bonding was present between the base pairs, uridine…adenosine and guanosine…cytidine, with couplings of approximately 7 Hz. How could they be certain that the signals they were observing are due to N-H…N hydrogen bonds? The answer was to use triple resonance techniques to examine base pairs that hydrogen bond only via O-H…N hydrogen bonds, and show that the signal they had previously observed was absent.

Grzesiek’s second paper on hydrogen bonds, #8, coauthored by Florence Cordier, Heinrich-Heine University, extends the work in an even more remarkable way by measuring the NMR coupling between nitrogens and carbons in the backbone hydrogen bonds of the human protein ubiquitin. The carbons are part of a carbonyl (C=O) group, so are one removed from the hydrogen bond, i.e., N-H…O=C.

This time they used material enriched with ¹⁵N and ¹³C (normal ¹²C has no nuclear magnet), and there too was the evidence for these hydrogen bonds, albeit with an interaction an order of magnitude weaker (at -0.25 to -0.9 Hz) than the N-H…N coupling. Nevertheless, the couplings correlate with the strength of the hydrogen bond, being stronger in the stronger bonds. These findings were confirmed by paper #9, which is from the researchers of Ad Bax’s group based at NIH, Bethesda, Maryland.

Grzesiek’s third paper, #10, was done in conjunction with Dingley and researchers at UCLA (James Masse, Robert Peterson, and Juli Feigon) and the University of Arizona (Michael Barfield). Together they studied not only the hydrogen bonding of Watson-Crick base pairs but also of Hoogsten base pairs within a DNA triplex consisting of one purine and two pyrimidine strands. Four different base pairs were identified, their various couplings distinguished–including those of the weaker interactions at the "frayed ends" of the DNA chains–and relationships with other hydrogen bonding parameters, such as bond length, were established. In addition they were able to show that density functional computer simulations by computer could reproduce these findings exactly.

Dr. John Emsley is Science Writer in Residence
at the Department of Chemistry, University of Cambridge, U.K.