Flg. 4. Positional dcpcndcmr of arginine. l'hcbasic @on of Tat was qlaccd by eight lys'iand a sin& vginine located at the amino acidpositions indicated. Plasmids (25 ng) war uansfcctcdinm HeLa & and transactivation wasdctcsmhed as in Fig. 2.formation for this interaction, molecularmodeling (13) was used to locate the mostfavorable positions of two phosphates withhydrogen (H)-bonds to arginine. Thc bestarrangement (Fig. 6B) has a pair ofH-bonds between a phosphate and twoN,'s, and another pair of H-bonds betweenthe second phosphate and NY1 and N,. Eachphosphate is shared by a pau of nitrogem,with a dhance between phosphates of7.1 A(center to center dhance between phosphorusatoms). We define the atginine fork as aninteraction between a single arginine and apair of adjacent phosphates, which mediatesspecitic recognition of <strong>RNA</strong> strum. 0therarginine-ph&phate Fments are possible(for example, see legend to Fig. 6B),and arginine forks with additional H-bondsare possible (for example, with a specificbase or a 2' OH).To determine whether such phosphate~tsarefoundin<strong>RNA</strong>saucturrs,the modelad phosphate coordinates fiomFig.6B were superimposed on all phosphatepairs in t<strong>RNA</strong> crystal sauctures (14). Thcresults indicate that double-stranded A-form<strong>RNA</strong> cannot readily accommodate this arranguncnt;the P-P dismnce in the model(7.1 A) is longer than the P-P distance inA-form <strong>RNA</strong> (5.6 A), and the phosphateoxygcns in A-form <strong>RNA</strong> are not properlyoriented to form H-bonds between a slnglearginine and a pair of adjacent phosphates.Reasonable H-bonding arrangements aremuch mom likcly to be found at discontinuousregions of kNA, for example, at junctionsbetween double-stranded A-form<strong>RNA</strong> and a bulge or loop. <strong>The</strong> two criticalphosphates in are focated precisely atthe junction of the double-stranded stemand the 3-nudaotide bulge.<strong>The</strong> coaystll saucture of glutaminylt<strong>RNA</strong> syntheme-t<strong>RNA</strong> shows a similarinteradon of arginine with the acceptorstrand of t<strong>RNA</strong> (1). Arg133 forms H-bondswith two adjacent phosphates and an additionalH-bond with a ribose 2' OH. It isplausibkthatthearginineinTatahoimuactswith a 2' OH, thus discriminating between<strong>RNA</strong>andDNA(4).~wecannotrukout bascspecific comaas, fbr example, with anessentialuridiminthebulge(4,5, ll),itseensreasonablethatomtaasbetweenonearginineand a highly oriamd pair of pho@m&s canacaruntfin-themodestlo-to20-foldspccific-ity &Tat b i i to TAR (4, 5, 11). <strong>The</strong>~that~theovaallfbldingofTARandtheorientdtionoftheseparticularphcqhmxwnaintobedaamined.Inadditiontothe~cargininecontact,thechargeM t y ofthe basic region &Tat is importantfbrbii(5) andmayprovideanonspecific~c~ldtohelporientthe~.Tatisperhapsthesimplestarampkof<strong>RNA</strong>rewgdion in that a singk amino acid interactswith a single feature of the <strong>RNA</strong>; other p nteinsmayachievthighcrspecificirythmughmulliple algink<strong>RNA</strong>0rotherina;lctions.In the case of Tat, akhaugh <strong>RNA</strong> binding iscsaxial fbrthe modcst speciiicityfbrTARis~toaccountfbrthehigh spacificity &Tat function Other interactionsofTat,perhapswithcdtularpm&s,arelikely to be required.<strong>The</strong> recognition of TAR by Tat highlightsfundamental dXmnces between<strong>RNA</strong> recognition and DNA recognition. ItFlg. 5. Ethylation in- of R52, K, andwild-typc Tat pptidcs. Pcptides wac bound mahylated TAR <strong>RNA</strong> unda gel-shift conditiomthat gavc